Molecular cloning studies have revealed the existence of two additional genes that encode phosphoribosyl pyrophosphate synthetase-like proteins, one widely expressed (phosphoribosyl pyrophosphate synthetase 2) and one whose expression appears to be confined to the testis (phosphoribosyl pyrophosphate synthetase 1-like 1) (Taira et al. 1989; 1991). Neither of these proteins has been purified and characterized enzymatically, nor have variations in the abundance or sequence of either protein been associated with alterations in human nucleotide metabolism (Roessler et al. 1993; Becker et al. 1996), so their dimerization and ability to catalyze the synthesis of PRPP from D-ribose 5-phosphate are inferred here on the basis of their predicted amino acid sequence similarity to phosphoribosyl pyrophosphate synthetase 1.
R-HSA-1971475 A tetrasaccharide linker sequence is required for GAG synthesis The biosynthesis of dermatan sulfate/chondroitin sulfate and heparin/heparan sulfate glycosaminoglycans (GAGs) starts with the formation of a tetrasaccharide linker sequence to the core protein. The first step is the addition of xylose to the hydroxy group of specific serine residues on the core protein. Subsequent additions of two galactoses and a glucuronide moiety completes the linker sequence. From here, the next hexosamine addition is critical as it determines which GAG is formed (Lamberg & Stoolmiller 1974, Pavao et al. 2006).
R-HSA-5619084 ABC transporter disorders The ATP-binding cassette (ABC) transporters form a large family of transmembrane proteins that utilise the energy from the hydrolysis of ATP to facilitate the movement of a wide variety of substrates against a concentration gradient across membrane bilayers. Substrates include amino acids, lipids, inorganic ions, peptides, saccharides, peptides for antigen presentation, metals, drugs, and proteins. Of the 48 known ABC transporters in humans, 15 are associated with a defined human disease (Tarling et al. 2013, Woodward et al. 2011, Dean 2005, Kemp et al. 2011, Ueda 2011, Chen & Tiwari 2011).
R-HSA-1369062 ABC transporters in lipid homeostasis A defined subset of the ABC transporter superfamily, the ABCA transporters, are highly expressed in monocytes and macrophages and are regulated by cholesterol flux which may indicate their role in in chronic inflammatory diseases (Schmitz and Kaminski 2001, Schmitz et al. 2000). Some D and G members of the ABC transporter family are also important in lipid transport (Voloshyna & Reiss 2011, Morita & Imanaka 2012, Morita et al. 2011).
R-HSA-382556 ABC-family proteins mediated transport The ATP-binding cassette (ABC) superfamily of active transporters involves a large number of functionally diverse transmembrane proteins. They transport a variety of compounds through membranes against steep concentration gradients at the cost of ATP hydrolysis. These substrates include amino acids, lipids, inorganic ions, peptides, saccharides, peptides for antigen presentation, metals, drugs, and proteins. The ABC transporters not only move a variety of substrates into and out of the cell, but are also involved in intracellular compartmental transport. Energy derived from the hydrolysis of ATP is used to transport the substrate across the membrane against a concentration gradient. Human genome contains 48 ABC genes; 16 of these have a known function and 14 are associated with a defined human disease (Dean et al. 2001, Borst and Elferink 2002, Rees et al. 2009).
R-HSA-9033807 ABO blood group biosynthesis Perhaps the most important and widely studied blood group is the ABO blood group. It consists of antigens found on the outer surface of red cells and corresponding antibodies in plasma. The majority of the world's population (~80%) are 'secretors' which means that the antigens present in their blood will also be found in other body fluids such as saliva. An individual can be a Secretor (Se) or a non-secretor (se) and this is completely independent of whether the individual is of blood type A, B, AB, or O. From a very early age, the immune system develops antibodies against whichever ABO blood group antigens are not found on the individual's RBCs. Thus, a blood group A individual will have anti-B antibodies and a blood group B individual will have anti-A antibodies. Individuals with the most common blood group, O, will have both anti-A and anti-B in their plasma. Blood group AB is the least common, and these individuals will have neither anti-A nor anti-B in their plasma.
The primary structure of these antigens is an oligosaccharide precursor sequence on to which one or more sugars are attached at specific locations. The blood group oligosaccharide antigens A, B and H are produced by enzymes expressed by these genes and form the basis of the ABO 'blood type' phenotypes. A and B antigens were originally identified on red blood cells (RBCs) but later identified on other cell types and in bodily secretions. The ABO blood group system is important in blood transfusion, cell/tissue/organ transplantation and forensic evidence at crime scenes.
The H antigen is formed with the addition of a fucose sugar onto one of two precursor oligosaccharide sequences (Type 1 chains are Gal β1,3 GlcNAc β1,3 Gal R and Type 2 chains are Gal β1,4 GlcNAc β1,3 Gal R; where R is a glycoprotein (Type 1) or glycosphingolipid (Type 2). Type 2 chains are only found on RBCs, epithelial cells and endothelial cells. The H gene expressed in hematopoietic cells produces α-1,2-fucosyltransferase 1 (FUT1) which adds a fucose to Type 2 chains to form the H antigen in non-secretors. Type 1 chains are found in secretors. The Se gene expressed in secretory glands produces α-1,2-fucosyltransferase 2 (FUT2) which adds a fucose to Type 1 chains to form the H antigen in secretors.
The H antigen is abundant in individuals with blood group O and is the essential precursor for the production of A and B antigens. A and B antigens are formed by the action of glycosyltransferases encoded by functional alleles at the ABO genetic locus. The co dominant A allele encodes A transferase, which transfers an N acetylgalactosamine (GalNAc) sugar to the H antigen forming the A antigen. Similarly, the co dominant B allele encodes B transferase, which transfers a galactose (Gal) sugar to the H antigen forming the B antigen. Individuals who have both A and B alleles form the AB antigen. Individuals who are homozygous for the recessive O allele express the H antigen but do not form A or B antigens as they lack both the glycosyltransferase enzymes for their formation. Mutant alleles of the corresponding FUT1 or FUT2 genes result in either a H– phenotype (Bombay phenotype, Oh) or a weak H phenotype (para Bombay) where the affected individual cannot form H, A or B antigens (Kaneko et al. 1997, Koda et al. 1997). The biosyntheses of the A, B and H antigens are described in this section (Ewald & Sumner 2016, Scharberg et al. 2016).
R-HSA-9660821 ADORA2B mediated anti-inflammatory cytokines production The natural ligand for adenosine receptor A2B (ADORA2B) is extracellular adenosine (Ad-Rib), formed from the reduction of ATP by ENTDPases. ATP enters the extracellular space in response to parasite infection, tissue injury, apoptosis amongst other stress factors and has chemotactic and excitatory effects (Cekic et al.2016).
The reduction of ATP to Ade Rib is thought to be a regulatory mechanism by which the synthesis of anti inflammatory cytokines is induced. In addition, killing mechanisms are switched off (Figueiredo et al. 2016). Accordingly, increased expression of ADORA2B in monocytes correlates with higher Leishmania donovani parasites loads alongside increment of IL10 production (Vijayamahantesh et al. 2016). Exacerbation of lesion development in L. amazonensis infected mice also correlated with high amounts of Ade Rib (Figueiredo et al. 2016).
R-HSA-418592 ADP signalling through P2Y purinoceptor 1 Co-activation of P2Y1 and P2Y12 is necessary for complete platelet activation. P2Y1 is coupled to Gq and helps trigger the release of calcium from internal stores, leading to weak and reversible platelet aggregation. P2Y12 is Gi coupled, inhibiting adenylate cyclase, leading to decreased cAMP, a consequent decrease in cAMP-dependent protein kinase activity which increases cytoplasmic [Ca2+], necessary for activation (Woulfe et al. 2001).
In activated platelets, P2Y12 signaling is required for the amplification of aggregation induced by all platelet agonists including collagen, thrombin, thromboxane, adrenaline and serotonin. P2Y12 activation causes potentiation of thromboxane generation, secretion leading to irreversible platelet aggregation and thrombus stabilization.
R-HSA-392170 ADP signalling through P2Y purinoceptor 12 Co-activation of P2Y1 and P2Y12 is necessary for complete platelet activation. P2Y1 is coupled to Gq and helps trigger the release of calcium from internal stores, leading to weak and reversible platelet aggregation. P2Y12 is Gi coupled, inhibiting adenylate cyclase, leading to decreased cAMP, a consequent decrease in cAMP-dependent protein kinase activity which increases cytoplasmic [Ca2+], necessary for activation (Woulfe et al. 2001).
In activated platelets, P2Y12 signaling is required for the amplification of aggregation induced by all platelet agonists including collagen, thrombin, thromboxane, adrenaline and serotonin. P2Y12 activation causes potentiation of thromboxane generation, secretion leading to irreversible platelet aggregation and thrombus stabilization.
R-HSA-198323 AKT phosphorylates targets in the cytosol Following activation, AKT can phosphorylate an array of target proteins in the cytoplasm, many of which are involved in cell survival control. Phosphorylation of TSC2 feeds positively to the TOR kinase, which, in turn, contributes to AKT activation (positive feedback loop).
R-HSA-198693 AKT phosphorylates targets in the nucleus After translocation into the nucleus, AKT can phosphorylate a number of targets there such as CREB, forkhead transcription factors, SRK and NUR77.
R-HSA-211163 AKT-mediated inactivation of FOXO1A The unphosphorylated form of FOXO1A shuttles between the nucleus and cytoplasm, maintaining a substantial concentration of this protein in the nucleoplasm, where it functions as a transcription factor. Phosphorylation of the protein, catalyzed by activated AKT, causes its exclusion from the nucleus (Zhang et al. 2002).
R-HSA-9700645 ALK mutants bind TKIs Aberrant signaling by activated forms of ALK can be inhibited by tyrosine kinase inhibitors (TKIs). ALK, like other tyrosine kinase receptors, is activated through a series of phosphorylation and conformational changes that move the receptor from the inactive form to the fully activated form. Type II TKIs bind to the inactive form of the receptor at a site adjacent to the ATP-binding cleft, while type I TKIs bind to the active form (reviewed in Roskoski, 2013). Type I inhibitors crizotinib, brigatinib, alectinib, ceritinib and lorlatinib are all approved for treatment of ALK-dependent cancer. Development of resistance to TKIs is not uncommon, however, either through acquisition of secondary mutations or through activation of bypass pathways that remove the dependence on ALK signaling (reviewed in Lovly and Pao, 2012; Lin et al, 2017; Della Corte et al, 2018).
R-HSA-112122 ALKBH2 mediated reversal of alkylation damage AlkB is an E.coli alpha-ketoglutarate- and Fe(II)-dependent dioxygenase that oxidizes the relevant methyl groups and releases them as formaldehyde. Two human homologs of AlkB, ALKBH2 and ALKBH3, both remove 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) from methylated polynucleotides in an alpha-ketoglutarate-dependent reaction. They act by direct damage reversal with the regeneration of the unsubstituted bases. E.coli AlkB and human ALKBH2 and ALKBH3 can also repair 1-ethyladenine (1-etA) residues in DNA with the release of acetaldehyde (Duncan et al., 2002, Lee et al. 2005).
R-HSA-112126 ALKBH3 mediated reversal of alkylation damage ALKBH3, like ALKBH2, is a homolog of E.coli alpha-ketoglutarate- and Fe(II)-dependent dioxygenase AlkB that oxidizes methyl groups on alkylated DNA bases and releases them as formaldehyde. Like ALKBH2, ALKBH3 removes 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) from methylated polynucleotides in an alpha-ketoglutarate-dependent reaction and regenerates unsubstituted bases. Like ALKBH2, ALKBH3 can also repair 1-ethyladenine (1-etA) residues in DNA with the release of acetaldehyde (Duncan et al., 2002, Lee et al. 2005). While ALKBH2 has a preference for double strand DNA (dsDNA), ALKBH3 has a preference for single strand DNA (ssDNA). ALKBH3 efficiently repairs dsDNA in the presence of ASCC3 DNA helicase, which unwinds dsDNA, thus providing the single strand substrate for ALKBH3 (Dango et al. 2011).
R-HSA-163680 AMPK inhibits chREBP transcriptional activation activity AMP-activated protein kinase (AMPK) is a sensor of cellular energy levels. A high cellular ratio of AMP:ATP triggers the phosphorylation and activation of AMPK. Activated AMPK in turn phosphorylates a wide array of target proteins, as shown in the figure below (reproduced from (Hardie et al. 2003), with the permission of D.G. Hardie). These targets include ChREBP (Carbohydrate Response Element Binding Protein), whose inactivation by phosphorylation reduces transcription of key enzymes of the glycolytic and lipogenic pathways.
R-HSA-5467333 APC truncation mutants are not K63 polyubiquitinated APC has been shown to be reversibly modified with K63-linked polyubiquitin chains. This modification is required for the assembly of the destruction complex and subsequent degradation of beta-catenin in the absence of WNT ligand. K63-polyubiquitination of APC is lacking in a number of colorectal cancer cell lines expressing truncated forms of APC, and these lines have aberrantly high beta-catenin levels and WNT pathway activation (Tran and Polakis, 2012).
R-HSA-5467337 APC truncation mutants have impaired AXIN binding Mutations in the APC tumor suppressor gene are common in colorectal and other cancers and cluster in the central mutation cluster region (MCR) of the gene (Miyoshi et al, 1992; Nagase and Nakamura, 1993; Dihlmann et al, 1999; reviewed in Bienz and Clevers, 2000). These mutations generally result in truncated proteins that destabilize the destruction complex and result in elevated WNT pathway activation (reviewed in Polakis, 2000).
R-HSA-179409 APC-Cdc20 mediated degradation of Nek2A Like Cyclin A, NIMA-related kinase 2A (Nek2A) is degraded during pro-metaphase in a checkpoint-independent manner.
R-HSA-174143 APC/C-mediated degradation of cell cycle proteins The Anaphase Promoting Complex or Cyclosome (APC/C) functions during mitosis to promote sister chromatid separation and mitotic exit through the degradation of mitotic cyclins and securin. This complex is also active in interphase insuring the appropriate length of the G1 phase (reviewed in Peters, 2002). The APC/C contains at least 12 subunits and functions as an ubiquitin-protein ligase (E3) promoting the multiubiquitination of its target proteins (see Gieffers et al., 2001).
In the ubiquitination reaction, ubiquitin is activated by the formation of a thioester bond with the (E1) ubiquitin activating enzyme then transferred to a cysteine residue within the ubiquitin conjugating enzyme (E2) and ultimately to a lysine residue within the target protein, with the aid of ubiquitin-protein ligase activity of the APC/C. The ubiquitin chains generated are believed to target proteins for destruction by the 26S proteasome (Reviewed in Peters, 1994 )
The activity of the APC/C is highly periodic during the cell cycle and is controlled by a combination of regulatory events. The APC/C is activated by phosphorylation and the regulated recruitment of activating subunits and is negatively regulated by sequestration by kinetochore-associated checkpoint proteins. The Emi1 protein associates with Cdh1 and Cdc20, inhibiting the APC/C between G1/S and prophase. RSSA1 may play a similar role in ihibiting the APC during early mitosis.
Following phosphorylation of the APC/C core subunits by mitotic kinases, the activating subunit, Cdc20 is recruited to the APC/C and is responsible for mitotic activities, including the initiation of sister chromatid separation and the timing of exit from mitosis (See Zachariae and Nasmyth, 1999). Substrates of the Cdc20:APC/C complex, which are recognized by a motif known as the destruction box (D box) include Cyclin A, Nek2, Securin and Cyclin B. Degradation of Securin and Cyclin B does not occur until the mitotic spindle checkpoint has been satisfied (see Castro et al. 2005).
Cdc20 is degraded late in mitosis (Reviewed in Owens and Hoyt, 2005). At this time the activating subunit, Cdh1, previously maintained in an inactive phosphorylated state by mitotic kinases, is dephosphorylated and associates with and activates the APC/C. The APC/C:Cdh1 complex recognizes substrates containing a D box, a KEN box (Pfleger and Kirschner, 2000) or a D box activated (DAD) domain (Castro et al., 2002) sequence and promotes the ordered degration of mitotic cyclins and other mitotic proteins culminating with its own ubiquitin-conjugating enzyme (E2) subunit UbcH10 (Rape et al., 2006). This ordered degradation promotes the stability of Cyclin A at the end of G1. This stabilization, in turn, promotes the phosphorylation of Cdh1 and its abrupt dissociation from the APC/C, allowing accumulation of cyclins for the next G1/S transition (Sorensen et al., 2001).
R-HSA-174048 APC/C:Cdc20 mediated degradation of Cyclin B The degradation of cyclin B1, which appears to occur at the mitotic spindle, is delayed until the metaphase /anaphase transition by the spindle assembly checkpoint and is required in order for sister chromatids to separate (Geley et al. 2001;Hagting et al, 2002).
R-HSA-174154 APC/C:Cdc20 mediated degradation of Securin The separation of sister chromatids in anaphase requires the destruction of the anaphase inhibitor, securin. Securin associates with and inactivates the protease, separase. Separase cleaves the cohesin subunit, Scc1 that is responsible for the cohesion of sister chromatids (reviewed in Nasmyth et al., 2000). Securin destruction begins at metaphase after the mitotic spindle checkpoint has been satisfied (Hagting et al., 2002).
R-HSA-176409 APC/C:Cdc20 mediated degradation of mitotic proteins Following phosphorylation of the APC/C core subunits by mitotic kinases, the activating protein, Cdc20 is recruited to the APC and promotes the multiubiquitination and subsequent degradation of the mitotic cyclins (Cyclin A and Cyclin B) as well as the protein securin which functions in sister chromatid cohesion. Timely degradation of these proteins is essential for sister chromatid separation and the proper timing of exit from mitosis (See Zachariae and Nasmyth, 1999). Cdc20 is degraded late in mitosis (Reviewed in Owens and Hoyt, 2005)
R-HSA-174178 APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 From late mitosis through G1 phase APC/C:Cdh1 insures the continued degradation of the mitotic proteins and during mitotic exit and G1 its substrates include Cdc20, Plk1, Aurora A, Cdc6 and Geminin (see Castro et al., 2005). Rape et al. have recently demonstrated that the order in which APC/C targeted proteins are degraded is determined by the processivity of multiubiquitination of these substrates. Processive substrates acquire a polyubiquitin chain upon binding to the APC/C once and are degraded. Distributive substrates bind, dissociate and reassociate with the APC/C multiple times before acquiring an ubiquitin chain of sufficient length to insure degradation. In addition, distributive substrates that dissociate from the APC/C with short ubiquitin chains are targeted for deubiquitination (Rape et al., 2006).
R-HSA-179419 APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint APC:CDC20 mediates the degradation of a number of cell cycle proteins including Cyclin A and Nek2A.
R-HSA-5649702 APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway NEIL1 and NEIL2 have a dual DNA glycosylase and beta/delta lyase activity. The AP (apurinic/apyrimidinic) site-directed lyase activity of NEIL1 and NEIL2 is their major physiological role, as they can act on AP sites generated spontaneously or by other DNA glycosylases. NEIL1 or NEIL2 cleave the damaged DNA strand 5' to the AP site, producing a 3' phosphate terminus (3'Pi) and a 5' deoxyribose phosphate terminus (5'dRP). DNA polymerase beta (POLB) excises 5'dRP residue but is unable to add the replacement nucleotide to DNA with the 3'Pi end. PNKP, a DNA 3' phosphatase, removes 3'Pi and enables POLB to incorporate the replacement nucleotide, which is followed by ligation of repaired DNA strand by XRCC1:LIG3 complex (Whitehouse et al. 2001, Wiederhold et al. 2004, Das et al. 2006).
R-HSA-180689 APOBEC3G mediated resistance to HIV-1 infection Representatives of the apolipoprotein B mRNA editing enzyme catalytic polypeptide 3 (APOBEC3) family provide innate resistance to exogeneous and endogenous retroviruses (see Cullen 2006 for a recent review). Humans and other primates encode a cluster of seven different cytidine deaminases with APOBEC3G, APOBEC3F and APOBEC3B having some anti HIV-1 activity. Our understanding is most complete for APOBEC3G which has been described first and the reactions described herein will focus on this representative enzyme.
APOBEC3G is a cytoplasmic protein which strongly restricts replication of Vif deficient HIV-1 (Sheehy 2002). It is expressed in cell populations that are susceptible to HIV infection (e.g., T-lymphocytes and macrophages). In the producer cell, APOBEC3G is incorporated into budding HIV-1 particles through an interaction with HIV-1 gag nucleocapsid (NC) protein in a RNA-dependent fashion.
Within the newly infected cell (= target cell), virus-associated APOBEC3G regulates the infectivity of HIV-1 by deaminating cytidine to uracil in the minus-strand viral DNA intermediate during reverse transcription. Deamination results in the induction of G-to-A hypermutations in the plus-strand viral DNA which subsequently can either be integrated as a non-functional provirus or degraded before integration.
R-HSA-5624958 ARL13B-mediated ciliary trafficking of INPP5E ARL13B is a ciliary-localized small GTPase with an atypical C-terminus containing a coiled coil domain and a proline rich domain (PRD) (Hori et al, 2008). Mutations in ARL13B are associated with the development of the ciliopathy Joubert's Syndrome (Cantagrel et al, 2008; Parisi et al, 2009). Studies in C. elegans and vertebrates suggest that ARL13B may play a role in stabilizing the interaction between the IFT A and B complexes and the kinesin-2 motors during anterograde traffic in the cilium (Cevik et al, 2010; Li et al, 2010; Cevik et al, 2013; reviewed in Li et al, 2012; Zhang et al, 2013). Recent work has shown an additional role for ARL13B in trafficking the inositol polyphosphate-5-phosphatase E (INPP5E) to the cilium through a network that also involves the phosphodiesterase PDE6D and the centriolar protein CEP164 (Humbert et al, 2012; Thomas et al, 2014; reviewed in Zhang et al, 2013). Mutations in INPP5E are also associated with the development of Joubert syndrome and other ciliopathies (Bielas et al, 2009; Jacoby et al, 2009; reviewed in Conduit et al, 2012).
R-HSA-170984 ARMS-mediated activation ARMS (Ankyrin-Rich Membrane Spanning/Kidins 220) is a 220kD tetraspanning adaptor protein which becomes rapidly tyrosine phosphorylated by active Trk receptors. ARMS is another adaptor protein which is involved in the activation of Rap1 and the subsequent prolonged activation of the MAPK cascade.
R-HSA-9717264 ASP-3026-resistant ALK mutants ASP3026 is a second generation tyrosine kinase inhibitor with activity against ALK fusions in non-small cell lung cancers (NSCLC) and anaplastic large cell lymphomas (ALCLs). This pathway describes ALK mutants that are resistant to inhibition by ASP3026 (Amin et al, 2016; Katayama et al, 2014; George et al, 2008; Mori et al, 2014; reviewed Roskoski, 2013; Lovly and Pao, 2012)
R-HSA-380994 ATF4 activates genes in response to endoplasmic reticulum stress ATF4 is a transcription factor and activates expression of IL-8, MCP1, IGFBP-1, CHOP, HERP1 and ATF3.
R-HSA-381183 ATF6 (ATF6-alpha) activates chaperone genes The N-terminal fragment of ATF6-alpha contains a bZIP domain and binds the sequence CCACG in ER Stress Response Elements (ERSEs). ATF6-alpha binds ERSEs together with the heterotrimeric transcription factor NF-Y, which binds the sequence CCAAT in the ERSEs, and together the two factors activate transcription of ER stress-responsive genes. Evidence from overexpression and knockdowns indicates that ATF6-alpha is a potent activator but its homolog ATF6-beta is not and ATF6-beta may actually reduce expression of ER stress proteins.
R-HSA-381033 ATF6 (ATF6-alpha) activates chaperones ATF6-alpha is a transmembrane protein that normally resides in the Endoplasmic Reticulum (ER) membrane. Here its luminal C-terminal domain is associated with BiP, shielding 2 Golgi-targeting regions and thus keeping ATF6-alpha in the ER. Upon interaction of BiP with unfolded proteins in the ER, ATF6-alpha dissociates and transits to the Golgi where it is cleaved by the S1P and S2P proteases that reside in the Golgi, releasing the N-terminal domain of ATF6-alpha into the cytosol. After transiting to the nucleus, the N-terminal domain acts as a transcription factor to activate genes encoding chaperones.
R-HSA-8874177 ATF6B (ATF6-beta) activates chaperones Like its homolog ATF6 (reviewed in Fox and Andrew 2015), ATF6B is activated by cleavage in response to endoplasmic reticulum (ER) stress (Haze et al. 2001). In unstressed cells, ATF6B spans the ER membrane where its lumenal domain probably forms a complex with HSPA5 (BiP, GRP78). During ER stress, HSPA5 dissociates from ATF6B exposing Golgi localization signals in the lumenal domain of ATF6B and causing ATF6B to traffic to the Golgi membrane. The Golgi-resident proteases MBTPS1 (S1P) and MBTPS2 (S2P) cleave ATF6B and release the cytoplasmic domain, which contains a transcription activation domain, a bZIP dimerization domain, and a nuclear localization signal (Haze et al. 2001). N-glycosylation in the lumenal domain of ATF6B is required for cleavage (Guan et al. 2009). The cytoplasmic fragment traffics to the nucleus where it acts as a weak transcription activator (Haze et al. 2001). By forming heterodimers with the strong activator ATF6, ATF6B acts as an inhibitory modulator of ATF6 (Thuerauf et al. 2004, Thuerauf et al. 2007).
R-HSA-1296025 ATP sensitive Potassium channels ATP sensitive K+ channels couple intracellular metabolism with membrane excitability. These channels are inhibited by ATP so are open in low metabolic states and close in high metabolic states, resulting in membrane depolarization triggering responses such as insulin secretion, modulation of vascular smooth muscle and cardioprotection. The channel comprises four Kir6.x subunits and four regulatory sulphonylurea receptors (SUR) (Akrouh et al, 2009).
R-HSA-450408 AUF1 (hnRNP D0) binds and destabilizes mRNA AUF1 (hnRNP D0) dimers bind U-rich regions of AU-rich elements (AREs) in the 3' untranslated regions of mRNAs. The binding causes AUF1 dimers to assemble into higher order tetrameric complexes. Diphosphorylated AUF1 bound to RNA recruits additional proteins, including eIF4G, polyA-binding protein, Hsp, Hsc70, Hsp27, NSEP-1, NSAP-1, and IMP-2 which target the mRNA and AUF1 for degradation. Unphosphorylated AUF1 is thought to be less able to recruit additional proteins. AUF1 also interacts directly or indirectly with HuR and the RNA-induced silencing complex (RISC).
AUF1 complexed with RNA and other proteins is ubiquitinated and targeted for destruction by the proteasome while the bound mRNA is degraded. Inhibition of ubiquitin addition to AUF1 blocks mRNA degradation. The mechanism by which ubiquitin-dependent proteolysis is coupled to mRNA degradation is unknown.
At least 4 isoforms of AUF1 exist: p45 (45 kDa) contains all exons, p42 lacks exon 2, p40 lacks exon 7, and p37 lacks exons 2 and 7. The presence of exon 7 in p42 and p45 seems to block ubiquitination while the absence of exon 7 (p37 and p40) targets AUF1 for ubiquitination and destabilizes bound RNAs. Lack of exon 2 (p37 and p42) is associated with higher affinity for RNA and 14-3-3sigma (SFN).
AUF1 binds and destabilizes mRNAs encoding Interleukin-1 beta (IL1B), Tumor Necrosis Factor alpha (TNFA), Cyclin-dependent kinase inhibitor 1 (CDNK1A, p21), Cyclin-D1 (CCND1), Granulocyte-macrophage colony stimulating factor (GM-CSF, CSF2), inducible Nitric oxide synthase (iNOS, NOS2), Proto-oncogene cFos (FOS), Myc proto-oncogene (MYC), Apoptosis regulator Bcl-2 (BCL2).
R-HSA-8854518 AURKA Activation by TPX2 TPX2 binds to aurora kinase A (AURKA) at centrosomes and promotes its activation by facilitating AURKA active conformation and autophosphorylation of the AURKA threonine residue T288 (Bayliss et al. 2003, Xu et al. 2011, Giubettini et al. 2011, Dodson and Bayliss 2012).
R-HSA-5467340 AXIN missense mutants destabilize the destruction complex Alterations in AXIN1 have been detected in a number of different cancers including liver and colorectal cancer and medullablastoma, among others (reviewed in Salahshor and Woodgett, 2005). Missense and nonsense mutations that disrupt or remove protein-protein interaction domains are common, and AXIN variants in cancers tend to disrupt the formation of a functional destruction complex (Satoh et al, 2000; Taniguchi et al, 2002; Webster et al, 2000; Shimizu et al, 2002).
R-HSA-2161522 Abacavir ADME Abacavir is a nucleoside analogue reverse transcriptase inhibitor with antiretroviral activity, widely used in combination with other drugs to treat HIV-1 infection (Yuen et al. 2008). Its uptake across the plasma membrane is mediated by organic cation transporters SLC22A1, 2, and 3; the transport proteins ABCB1 and ABCG2 mediate its efflux. Abacavir itself is a prodrug. Activation requires phosphorylation by a cytosolic adenosine phosphotransferase and deamination by ADAL deaminase to yield carbovir monophosphate. Cytosolic nucleotide kinases convert carbovir monophosphate to carbovir triphosphate, the active HIV reverse transcriptase inhibitor. Abacavir can be glucuronidated or oxidized to a 5'-carboxylate; these are the major forms in which it is excreted from the body.
R-HSA-2161541 Abacavir metabolism Abacavir activation proceeds steps of phosphorylation, deamination to yield carbovir monophosphate, and phosphorylation of the latter compound to yield the triphosphate. In addition, abacavir can be conjugated with glucuronide or oxidized to its 5'-carboxylate derivative, the two major forms in which it is excreted from the body (Yuen et al. 2008).
R-HSA-2161517 Abacavir transmembrane transport Cytosolic levels of abacavir are determined by the balance of its facilitated diffusion into the cell mediated by organic cation transporters SLC22A1, 2, and 3, and its ATP-dependent efflux from cells mediated by ABCG2 and ABCB1 (Klaasen and Aleksunes 2010; Pan et al. 2007; Shaik et al. 2007).
R-HSA-73930 Abasic sugar-phosphate removal via the single-nucleotide replacement pathway Abasic sugar phosphate removal via the single nucleotide replacement pathway requires displacement of DNA glycosylase by APEX1, APEX1-mediated endonucleolytic cleavage at the 5' side of the base free deoxyribose residue, recruitment of POLB to the AP site and excision of the abasic sugar phosphate (5'dRP) residue at the strand break (Lindahl and Wood, 1999).
R-HSA-9659787 Aberrant regulation of mitotic G1/S transition in cancer due to RB1 defects RB1 protein, also known as pRB or retinoblastoma protein, is a nuclear protein that plays a major role in the regulation of the G1/S transition during mitotic cell cycle in multicellular eukaryotes. RB1 performs this function by binding to activating E2Fs (E2F1, E2F2 and E2F3), and preventing transcriptional activation of E2F1/2/3 target genes, which include a number of genes involved in DNA synthesis. RB1 binds E2F1/2/3 through the so-called pocket region, which is formed by two parts, pocket domain A (amino acid residues 373-579) and pocket domain B (amino acid residues 640-771). Besides intact pocket domains, RB1 requires an intact nuclear localization signal (NLS) at its C-terminus (amino acid residues 860-876) to be fully functional (reviewed by Classon and Harlow 2002, Dick 2007). Functionally characterized RB1 mutations mostly affect pocket domains A and B and the NLS. RB1 mutations reported in cancer are, however, scattered over the entire RB1 coding sequence and the molecular consequences of the vast majority of these mutations have not been studied (reviewed by Dick 2007).
Many viral oncoproteins inactivate RB1 by competing with E2F1/2/3 for binding to the pocket region of RB1. RB1 protein is targeted by the large T antigen of the Simian virus 40 (SV40), the adenoviral E1A protein, and the E7 protein of oncogenic human papilloma viruses (HPVs) (reviewed by Classon and Harlow 2002).
R-HSA-9687139 Aberrant regulation of mitotic cell cycle due to RB1 defects RB1 was the first tumor suppressor gene discovered. Bi-allelic loss of function of the RB1 gene, located at the chromosomal band 13q14, is the underlying cause of both familial and sporadic retinoblastoma, a pediatric eye cancer (reviewed by Lohmann and Gallie 2000, Knudson 2001, Corson and Gallie 2007). Besides retinoblastoma, carriers of germline RB1 mutations are predisposed to an array of other cancers, called second primary tumors, such as pinealoblastoma, osteosarcoma, leiomyosarcoma, rhabdomyosarcoma and melanoma (reviewed by Lohmann and Gallie 2000).
Inactivating somatic mutations in the RB1 gene are frequent in bladder cancer (Cancer Genome Atlas Research Network 2014), osteosarcoma (Ren and Gu 2017), ovarian cancer (Liu et al. 1994, Kuo et al. 2009, Cancer Genome Atlas Research Network 2011), small-cell lung carcinoma (reviewed by Gazdar et al. 2017), liver cancer (Ahn et al. 2014, Bayard et al. 2018) and esophageal cancer (Gao et al. 2014, Kishino et al. 2016, Salem et al. 2018).
The vast majority of RB1 mutations in cancer represent complete genomic deletions or nonsense and frameshift mutations that are predicted to result in null alleles. Missense mutations are rare and usually result in partially active RB1 mutants. Functionally characterized RB1 missense mutations and inframe deletions mostly affect pocket domains A and B and the nuclear localization signal (NLS). RB1 missense mutations reported in cancer are, however, scattered over the entire RB1 coding sequence and the molecular consequences of the vast majority of these mutations have not been studied (reviewed by Dick 2007).
The RB1 protein product, also known as pRB or retinoblastoma protein, is a nuclear protein that plays a major role in the regulation of the G1/S transition during mitotic cell cycle in multicellular eukaryotes. RB1 performs this function by binding to activating E2Fs (E2F1, E2F2 and E2F3), and preventing transcriptional activation of E2F1/2/3 target genes, which include a number of genes involved in DNA synthesis (reviewed by Classon and Harlow 2002, Dick 2007). RB1 also regulates mitotic exit by acting on SKP2, a component of the SCF E3 ubiquitin ligase complex. RB1 facilitates degradation of SKP2 by the anaphase promoting complex/cyclosome (APC/C), thus preventing SKP2-mediated degradation of the cyclin-dependent kinase inhibitor CDKN1B (p27Kip1). RB1-dependent accumulation of p27Kip1 plays an important role in mitotic exit and RB1-mediated tumor suppression (reviewed by Dyson 2016).
In addition to its role in regulation of the G1/S transition and mitotic exit, RB1 also performs other, non-canonical, functions, such as its role in the maintenance of genomic stability, which is linked to its role in chromosome condensation during mitotic prophase. The impact of RB1 mutations on these E2F-independent functions, which are still important for RB1-mediated tumor suppression, has been poorly studied (reviewed by Chau and Wang 2003, Burkhart and Sage 2008, Manning and Dyson 2012, Dyson 2016, Dick et al. 2018).
R-HSA-9687136 Aberrant regulation of mitotic exit in cancer due to RB1 defects RB1 regulates mitotic exit by acting on SKP2, a component of the SCF E3 ubiquitin ligase complex. RB1 facilitates degradation of SKP2 by the anaphase promoting complex/cyclosome (APC/C), thus preventing SKP2-mediated degradation of the cyclin-dependent kinase inhibitor CDKN1B (p27Kip1). RB1-dependent accumulation of p27Kip1 plays an important role in mitotic exit and RB1-mediated tumor suppression (reviewed by Dyson 2016).
R-HSA-2978092 Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate Somatic mutations affecting arginine residue 132 of IDH1 (isocitrate dehydrogenase 1, a cytosolic enzyme that normally catalyzes the NADP+-dependent conversion of isocitrate to 2-oxoglutarate), are very commonly found in human glioblastomas (Parsons et al. 2008). These mutant proteins efficiently catalyze the NADPH-dependent reduction of 2-oxoglutarate to form 2-hydroxyglutarate. Cells expressing the mutant protein accumulate elevated levels of 2-hydroxyglutarate, probably in the cytosol as IDH1 is a cytosolic enzyme. The fate of the 2-hydroxyglutarate is unclear, but the high frequency with which the mutation is found in surveys of primary tumors is consistent with the possibility that it is advantageous to the tumor cells (Dang et al 2009).
R-HSA-167242 Abortive elongation of HIV-1 transcript in the absence of Tat This event was inferred from the corresponding Reactome human Poll II transcription elongation event. The details specific to HIV-1 transcription elongation are described below. In the absence of the HIV-1 Tat protein, the RNA Pol II complexes associated with the HIV-1 template are non-processive. RNA Pol II is arrested after promoter clearance by the negative transcriptional elongation factors DSIF and NELF as occurs during early elongation of endogenous templates (Wada et al, 1998; Yamaguchi et al. 1999). This arrest cannot be overcome by P-TEFb mediated phosphorylation in the absence of Tat however, and elongation aborts resulting in the accumulation of short transcripts (Kao et al., 1987).
R-HSA-156582 Acetylation N-acetyltransferases (NATs; EC 2.3.1.5) utilize acetyl Co-A in acetylation conjugation reactions. This is the preferred route of conjugating aromatic amines (R-NH2, converted to aromatic amides R-NH-COCH3) and hydrazines (R-NH-NH2, converted to R-NH-NH-COCH3). Aliphatic amines are not substrates for NAT. The basic reaction is
Acetyl-CoA + an arylamine = CoA + an N- acetylarylamine
CDK5-mediated phosphorylation of NTRK2 was suggested to influence the level of AKT activity, downstream mTOR signaling and DLG4 (PSD-95) expression, but further elucidation is needed (Lai et al. 2012).
Signaling by TRKB and CDK5 plays a role in inflammation induced hypersensitivity to heat-triggered pain in rats (Zhang et al. 2014). R-HSA-9028731 Activated NTRK2 signals through FRS2 and FRS3 Adapter proteins FRS2 and FRS3 can both bind to the cytoplasmic tail of activated NTRK2 (TRKB) receptor, which is followed by NTRK2-mediated phosphorylation of FRS2 and FRS3. NTRK2 signaling through FRS3 has been poorly characterized (Easton et al. 1999, Yuen and Mobley 1999, Dixon et al. 2006, Zeng et al. 2014). Phosphorylated FRS2 is known to recruit GRB2 (presumably in complex with SOS1) and PTPN11 (SHP2) to activated NTRK2, leading to augmentation of RAS signaling (Easton et al. 1999, Easton 2006). R-HSA-9032500 Activated NTRK2 signals through FYN In mouse brain, Fyn activation downstream of Bdnf-induced Ntrk2 (TrkB) signaling results in increased protein levels of AMPA receptor subunits Gria2 (GluR2), Gria3 (GluR3) and Gria1 (GluR1) without change in mRNA levels (Narisawa-Saito et al. 1999).
BDNF-mediated activation of NTRK2 increases phosphorylation of voltage gated sodium channels by FYN, resulting in decrease of sodium currents (Ahn et al. 2007).
FYN activation downstream of NTRK2 is implicated in olygodendrocyte myelination and contributes to BDNF-induced activation of ERK1/2 (MAPK3/1) through an unknown mechanism (Peckham et al. 2015).
Besides acting downstream of NTRK2, FYN and other SRC kinases, activated by other receptors such as GPCRs, may phosphorylate NTRK2 and enhance its catalytic activity (Rajagopal and Chao 2006, Huang and McNamara 2010).
R-HSA-9028335 Activated NTRK2 signals through PI3K Neurotrophin receptor NTRK2 (TRKB), activated by BDNF or NTF4, activates PI3K, resulting in formation of the PIP3 secondary messenger. PIP3 activates AKT signaling, and AKT signaling activates mTOR signaling (Yuen and Mobley 1999, Cao et al. 2013).
R-HSA-9026527 Activated NTRK2 signals through PLCG1 Activation of the neurotrophin receptor NTRK2 (TRKB) by BDNF or NTF4 triggers downstream PLCgamma (PLCG1) signaling, resulting in formation of secondary messengers DAG and IP3 (Eide et al. 1996, Minichiello et al. 1998, McCarthy and Feinstein 1999, Yuen and Mobley 1999, Minichiello et al. 2002, Yamada et al. 2002).
R-HSA-9026519 Activated NTRK2 signals through RAS Activation of the neurotrophin receptor NTRK2 (TRKB) by BDNF or NTF4 triggers downstream RAS signaling. The best studied mechanism for activation of RAS signaling downstream of NTRK2 is through SHC1-mediated recruitment of the GRB2:SOS1 complex, triggering SOS1-mediated guanine nucleotide exchange on RAS and formation of active RAS:GTP complexes (Minichiello et al. 1998, McCarthy and Feinstein 1999, Yuen and Mobley 1999).
R-HSA-9603381 Activated NTRK3 signals through PI3K The PI3K complex, composed of PIK3R1 and PIK3CA, co-immunoprecipitates with NTRK3 (TRKC), activated by NTF3 (NT-3) treatment (Yuen and Mobley 1999). Activation of NTRK3 correlates with activating phosphorylation of AKT, the main mediator of PI3K signaling (Tognon et al. 2001, Jin et al. 2008), and is dependent on PI3K activity (Tognon et al. 2001). NTRK3-mediated activation of PI3K signaling depends on SRC activation and the adaptor protein IRS1, but the exact mechanism is not known (Morrison et al. 2002, Lannon et al. 2004, Jin et al. 2008).
R-HSA-9034793 Activated NTRK3 signals through PLCG1 The receptor tyrosine kinase NTRK3 (TRKC), when activated by its ligand NTF3 (NT-3), induces PLCG1 phosphorylation, triggering PLCG1 signaling (Marsh and Palfrey 1996, Yuen and Mobley 1999).
R-HSA-9034864 Activated NTRK3 signals through RAS Upon activation by NTF3 (NT-3), the receptor tyrosine kinase NTRK3 (TRKC) triggers RAS signaling through adaptor proteins SHC1 and GRB2 (Marsh and Palfrey 1996, Gunn-Moore et al. 1997, Yuen and Mobley 1999). ERK activation downstream of NTRK3 may increase cell motility through WAVE. The mechanism is not known (Gromnitza et al. 2018).
R-HSA-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 PKN1, activated by phosphorylation at threonine T774, binds activated AR (androgen receptor) and promotes transcription from AR-regulated promoters. On one hand, phosphorylated PKN1 promotes the formation of a functional complex of AR with the transcriptional coactivator NCOA2 (TIF2) (Metzger et al. 2003). On the other hand, binding of phosphorylated PKN1, in complex with the activated AR, to androgen-reponsive promoters of KLK2 and KLK3 (PSA) genes, leads to PKN1-mediated histone phosphorylation. PKN1-phosphorylated histones recruit histone demethylases KDM4C (JMJD2C) and KDM1A (LSD1), and the ensuing demethylation of histones associated with the promoter regions of KLK2 and KLK3 genes increases their transcription (Metzger et al. 2005, Metzger et al. 2008).
R-HSA-2033519 Activated point mutants of FGFR2 Autosomal dominant mutations in FGFR2 are associated with the development of a range of skeletal disorders including Beare-Stevensen cutis gyrata syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome, Crouzon syndrome and Apert Syndrome (reveiwed in Burke, 1998; Webster and Donoghue 1997; Cunningham, 2007). Mutations that give rise to Crouzon, Jackson-Weiss and Pfeiffer syndromes tend to cluster in the third Ig-like domain of the receptor, either in exon IIIa (shared by the IIIb and the IIIc isoforms) or in the FGFR2c-specific exon IIIc. These mutations frequently involve creation or removal of a cysteine residue, leading to the formation of an unpaired cysteine residue that is thought to promote intramolecular dimerization and thus constitutive, ligand-independent activation (reviewed in Burke, 1998; Webster and Donoghue, 1997; Cunningham, 2007). Mutations in FGFR2 that give rise to Apert Syndrome cluster to the highly conserved Pro-Ser dipeptide in the IgII-Ig III linker; mutations in the paralogous residues of FGFR1 and 3 give rise to Pfeiffer and Muenke syndromes, respectively (Muenke, 1994; Wilkie, 1995; Bellus, 1996). Development of Beare-Stevensen cutis gyrata is associated with mutations in the transmembrane-proximal region of the receptor (Przylepa, 1996), and similar mutations in FGFR3 are linked to the development of thanatophoric dysplasia I (Tavormina, 1995a). These mutations all affect FGFR2 signaling without altering the intrinsic kinase activity of the receptor.
Activating point mutations have also been identified in FGFR2 in ~15% of endometrial cancers, as well as to a lesser extent in ovarian and gastric cancers (Dutt, 2008; Pollock, 2007; Byron, 2010; Jang, 2001). These mutations are found largely in the extracellular region and in the kinase domain of the receptor, and parallel activating mutations seen in autosomal dominant disorders described above.
Activating mutations in FGFR2 are thought to contribute to receptor activation through diverse mechanisms, including constitutive ligand-independent dimerization (Robertson, 1998), expanded range and affinity for ligand (Ibrahimi, 2004b; Yu, 2000) and enhanced kinase activity (Byron, 2008; Chen, 2007).
R-HSA-111452 Activation and oligomerization of BAK protein tBID binds to its mitochondrial partner BAK to release cytochrome c. Activated tBID results in an allosteric activation of BAK. This may induce its intramembranous oligomerization into a pore for cytochrome c efflux.
R-HSA-165158 Activation of AKT2 RAC serine/threonine-protein kinases (AKT, PKB) are serine/threonine kinases belonging to the cAMP-dependent protein kinase A/ protein kinase G/ protein kinase C (AGC) superfamily of protein kinases. They share structural homology within their catalytic domains and have similar mechanisms of activation. Mammals have three AKT genes, named RAC-alpha serine/threonine-protein kinase (AKT1, PKB, PKB-alpha), RAC-beta serine/threonine-protein kinase (AKT2, PKB-beta and RAC-gamma serine/threonine-protein kinase (AKT3, PKB-gamma, STK2). All share a conserved domain structure: an amino terminal pleckstrin homology (PH) domain, a central kinase domain and a carboxyl-terminal regulatory domain that contains a hydrophobic motif that is characteristic of AGC kinases. The PH domain interacts with membrane lipid products such as phosphatidylinositol (3,4,5) trisphosphate (PIP3) produced by phosphatidylinositol 3-kinase (PI3-kinase). Biochemical analysis. The PH domain of AKT binds to PIP3 and PIP2 with similar affinity (James et al. 1996, Frech et al. 1997). The kinase catalytic domain of Akt/PKB is highly similar to other AGC kinases (Peterson & Schreiber 1999). Phosphorylation of a conserved threonine residue in this region (T308 in AKT1) results in partial activation (Alessi et al. 1996). The carboxyl terminal extension has the hydrophobic motif FPQFSY. Phosphorylation of serine or threonine residue in this motif is necessary for full kinase activation. Deletion of this motif completely abolishes activity (Andjelković et al. 1997).
R-HSA-399710 Activation of AMPA receptors AMPA receptors are functionally either Ca permeable or Ca impermeable based on the subunit composition. Ca permeability is determined by GluR2 subunit which undergoes post-transcriptional RNA editing that changes glutamine (Q) at the pore to arginine (R). Incorporation of even a single subunit in the AMPA receptor confers Ca-limiting properties. Ca permeable AMPA receptors permit Ca and Na whereas Ca impermeable AMPA receptors permit only Na. In general, glutamatergic neurons contain Ca impermeable AMPA receptors and GABAergic interneurons contain Ca permeable AMPA receptors. However, some synapses do contain a mixture of Ca permeable and Ca impermeable AMPA receptors. GluR1-4 are encoded by four genes however, alternative splicing generates several functional subunits namely long and short forms of GluR1 and GluR2. GluR4 has long tail only and GluR3 has short tail only. Besides the differences in the tail length, flip/flop isoforms are generated by an interchangeable exon that codes the fourth membranous domain towards the C terminus. The fip/flop isoforms determine rate of desensitization/resensitization and the rate of channel closing. Receptors homomers or heteromers assembled from the combination of GluR1-4 subunits that vary in C tail length and flip/flop versions generates a whole battery of functionally distinct AMPA receptors.
R-HSA-9619483 Activation of AMPK downstream of NMDARs Activation of NMDA receptors (NMDARs) leads to activation of AMP-activated kinase (AMPK) in a CAMKK2-dependent manner. Overactivation of CAMKK2 or AMPK in neurons can lead to dendritic spine loss and is implicated in synaptotoxicity of beta-amyloids in Alzheimer's disease (Mairet-Coello et al. 2013).
R-HSA-176814 Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins APC/C:Cdc20 is first activated at the prometaphase/metaphase transition through phosphorylation of core subunits of the APC/C by mitotic kinases as well as recruitment of the APC/C activator protein Cdc20. APC/C:Cdc20 promotes the multiubiquitination and ordered degradation of Cyclin A and Nek2 degradation in prometaphase followed by Cyclin B and securin in metaphase (Reviewed in Castro et al., 2005).
R-HSA-176187 Activation of ATR in response to replication stress Genotoxic stress caused by DNA damage or stalled replication forks can lead to genomic instability. To guard against such instability, genotoxically-stressed cells activate checkpoint factors that halt or slow cell cycle progression. Among the pathways affected are DNA replication by reduction of replication origin firing, and mitosis by inhibiting activation of cyclin-dependent kinases (Cdks). A key factor involved in the response to stalled replication forks is the ATM- and rad3-related (ATR) kinase, a member of the phosphoinositide-3-kinase-related kinase (PIKK) family. Rather than responding to particular lesions in DNA, ATR and its binding partner ATRIP (ATR-interacting protein) sense replication fork stalling indirectly by associating with persistent ssDNA bound by RPA. These structures would be formed, for example, by dissociation of the replicative helicase from the leading or lagging strand DNA polymerase when the polymerase encounters a DNA lesion that blocks DNA synthesis. Along with phosphorylating the downstream transducer kinase Chk1 and the tumor suppressor p53, activated ATR modifies numerous factors that regulate cell cycle progression or the repair of DNA damage. The persistent ssDNA also stimulates recruitment of the RFC-like Rad17-Rfc2-5 alternative clamp-loading complex, which subsequently loads the Rad9-Hus1-Rad1 complex onto the DNA. The latter '9-1-1' complex serves to facilitate Chk1 binding to the stalled replication fork, where Chk1 is phosphorylated by ATR and thereby activated. Upon activation, Chk1 can phosphorylate additional substrates including the Cdc25 family of phosphatases (Cdc25A, Cdc25B, and Cdc25C). These enzymes catalyze the removal of inhibitory phosphate residues from cyclin-dependent kinases (Cdks), allowing their activation. In particular, Cdc25A primarily functions at the G1/S transition to dephosphorylate Cdk2 at Thr 14 and Tyr 15, thus positively regulating the Cdk2-cyclin E complex for S-phase entry. Cdc25A also has mitotic functions. Phosphorylation of Cdc25A at Ser125 by Chk1 leads to Cdc25A ubiquitination and degradation, thus inhibiting DNA replication origin firing. In contrast, Cdc25B and Cdc25C regulate the onset of mitosis through dephosphorylation and activation of Cdk1-cyclin B complexes. In response to replication stress, Chk1 phosphorylates Cdc25B and Cdc25C leading to Cdc25B/C complex formation with 14-3-3 proteins. As these complexes are sequestered in the cytoplasm, they are unable to activate the nuclear Cdk1-cyclin B complex for mitotic entry.
These events are outlined in the figure. Persistent single-stranded DNA associated with RPA binds claspin (A) and ATR:ATRIP (B), leading to claspin phosphorylation (C). In parallel, the same single-stranded DNA:RPA complex binds RAD17:RFC (D), enabling the loading of RAD9:HUS1:RAD1 (9-1-1) complex onto the DNA (E). The resulting complex of proteins can then repeatedly bind (F) and phosphorylate (G) CHK1, activating multiple copies of CHK1. R-HSA-111447 Activation of BAD and translocation to mitochondria The switching on/off of its phosphorylation by growth/survival factors regulates BAD activity. BAD remains sequestered by 14-3-3 scaffold proteins after phosphorylation by Akt1. Calcineurin activates BAD by dephosphorylation. R-HSA-114452 Activation of BH3-only proteins The BH3-only members act as sentinels that selectively trigger apoptosis in response to developmental cues or stress-signals like DNA damages. Widely expressed mammalian BH3-only proteins are thought to act by binding to and neutralizing their pro-survival counterparts. Activation of BH3-only proteins directly or indirectly results in the activation of proapoptotic BAX and BAK to trigger cell death. Anti-apoptotic BCL-2 or BCL-XL may bind and sequester BH3-only molecules to prevent BAX, BAK activation. The individual BH3-only members are held in check by various mechanisms with in the cells. They are recruited for death duties in response to death cues by diverse activation processes.The mechanisms involved in activation and release of BH3-only proteins for apoptosis will be discussed in this section.
The following figure has been reproduced here with the kind permission from the authors.
R-HSA-111446 Activation of BIM and translocation to mitochondria BIM acts as a sentinel to check the integrity of the cytoskeleton. It exists as two variant proteins: BIM-EL and BIM-L. In healthy cells, these two isoforms are sequestered to the dynein motor complex on microtubules via the dynein light chain DLC1. JNK or MAPK8 releases BIM in response to UV irradiation by phosphorylation.
R-HSA-139910 Activation of BMF and translocation to mitochondria In healthy cells, BMF is bound to the myosin V motor complex through its interaction with DLC2. UV irradiation or anoikis induces MAPK8 (JNK) to phosphorylate Dynein Light Chain 2 (DLC2) to release BMF.
R-HSA-174577 Activation of C3 and C5 The 3 pathways of complement activation converge on the cleavage of C3 by C3 convertases. C3 convertase cleaves C3 into C3a and C3b - a central step of complement activation. C3a remains in the fluid phase and acts as an anaphylatoxin, whereas C3b can form additional C3 convertases hastening the production of C3b. Besides, C3b binds to C3 convertases to form C5 convertase, which can act as an opsonin, or is degraded into fragments which cannot form an active convertase.
R-HSA-451308 Activation of Ca-permeable Kainate Receptor Kainate receptors that are assembled with subunits GRIK1-5, are Ca2+ permeable if GRIK1 and GRIK2 are not edited at the Q/R or other sites.
These channels permit Ca2+ upon activation by glutamate or other agonists.
R-HSA-1296041 Activation of G protein gated Potassium channels Activation of Kir 3 channels occurs after binding of G beta gamma subunits of GPCR. Activation of Kir3/GIRK leads to K+ efflux. The dissociation of GPCR into G alpha and G beta gamma subunits is activated by the activation of GABA B receptor by GABA binding.
R-HSA-991365 Activation of GABAB receptors GABA B receptors are metabotropic receptors that are functionally linked to C type G protein coupled receptors.? GABA B receptors are activated upon ligand binding. The GABA B1 subunit binds ligand and GABA B2 subunit modulates the activity of adenylate cyclase via the intracellular loop.? GABA B receptors show inhibitory activity via Galpha/G0 subunits via the inhibition of adenylate cyclase or via the activity of Gbeta/gamma subunits that mediate the inhibition of voltage gated Ca2+ channels.
R-HSA-5619507 Activation of HOX genes during differentiation Hox genes encode proteins that contain the DNA-binding homeobox motif and control early patterning of segments in the embryo as well as later events in development (reviewed in Rezsohazy et al. 2015). Mammals have 39 Hox genes arrayed in 4 linear clusters, with each cluster containing 9 to 11 genes. Based on homologies, the genes have been assigned to 13 paralogous groups. The nomenclature of Hox genes uses a letter to indicate the cluster and a number to indicate the paralog group. For example, HOXA4 is the gene in cluster A that is most similar with genes of paralog group 4 from other clusters.
One of the most striking aspects of mammalian Hox gene function is the mechanism of their activation during embryogenesis: the order of genes in a cluster correlates with the timing and location of their activation such that genes at the 3' end of a cluster are activated first and genes at the 5' end of a cluster are activated last. (5' and 3' refer to the transcriptional orientation of the genes in the cluster.) Because development of segments of the embryo proceeds from anterior to posterior this means that the anterior boundaries of expression of 3' genes are more anterior (rostral) and the anterior boundaries of expression of 5' genes are more posterior (caudal). Expression of HOX genes initiates in the posterior primitive streak at the beginning of gastrulation at approximately E7.5 in mouse. As gastrulation proceeds, further 5' genes are sequentially activated and they too undergo the same chromatin changes and migration. After formation of the axis of the embryo, similar waves of activation of HOXA and HOXD clusters occur in developing limbs beginning at about E9. Retinoids, especially all trans retinoic acid (atRA), participate in initiating the process via retinoid receptors. Other factors such as FGFs and Wnt, also regulate Hox expression. After activation, Hox genes participate in maintaining their own expression (autoregulation), activating later, 5' Hox genes, and repressing prior, 3' Hox genes (crossregulation). Differentiation of embryonal carcinoma cells and embryonic stem cells in response to retinoic acid is used to model the process in vitro (reviewed in Gudas et al. 2013).
Activation of Hox genes is accompanied by a change from bivalent chromatin to euchromatin (reviewed in Soshnikova and Duboule 2009). Bivalent chromatin has extensive methylation of lysine-9 on histone H3 (H3K9me3), a repressive mark, with interspersed punctate regions of methylation of lysine-4 on histone H3 (H3K4me2, H3K4me3), an activating mark. Euchromatization initiates at the 3' ends of clusters and proceeds towards the 5' ends, with the euchromatin migrating to an active region of the nucleus (reviewed in Montavon and Duboule 2013). This change in chromatin reflects a loss of H3K27me3 and a gain of H3K4me2,3. Polycomb repressive complexes bind H3K27me3 and are responsible for maintenance of repression, KDM6A and KDM6B histone demethylases remove H3K27me3, and members of the trithorax family of histone methylases (KMT2A, KMT2C, KMT2D) methylate H3K4.
R-HSA-936964 Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) Cell stimulation with viral double-stranded (ds) RNA and bacterial lipopolysaccharide (LPS) activate Toll-like receptors 3 (TLR3) and TLR4, respectively, triggering the activation the activation of two IKK-related serine/threonine kinases, TANK-binding kinase 1 (TBK1) and IκB kinase ε (IKKε, IKBKE) which directly phosphorylate interferon regulatory factor 3 (IRF3) and IRF7 promoting their dimerization and translocation into the nucleus. Although both kinases show structural and functional similarities, it seems that TBK1 and IKBKE differ in their regulation of downstream signaling events of TLR3/TLR4.
IRF3 activation and interferon β (IFNβ) production by poly(I:C), a synthetic analog of dsRNA, are decreased in TBK1-deficient mouse fibroblasts, whereas normal activation was observed in the IKBKE-deficient fibroblasts. However, in double-deficient mouse fibroblasts, the activation of IRF3 is completely abolished, suggesting a partially redundant functions of TBK1 and IKKε (IKBKE) (Hemmi H et al., 2004).
The poly(I:C)-induced phosphorylation of TBK1 and IRF3 was abolished in TRIF (TICAM1)-knockout human keratinocyte HACAT cells (Bakshi S et al., 2017). TICAM1 is utilized as an adaptor protein by TLR3 and TLR4 (Yamamoto M et al., 2003).
TLR3 recruits and activates PI3 kinase (PI3K), which activates the downstream kinase, Akt, leading to full phosphorylation and activation of IRF3 (Sarkar SN et al., 2004). When PI3K is not recruited to TLR3 or its activity is blocked, IRF3 is only partially phosphorylated and fails to bind the promoter of the target gene (Sarkar SN et al., 2004).
R-HSA-1592389 Activation of Matrix Metalloproteinases The matrix metalloproteinases (MMPs), previously known as matrixins, are classically known to be involved in the turnover of extracellular matrix (ECM) components. However, recent high throughput proteomics analyses have revealed that ~80% of MMP substrates are non-ECM proteins including cytokines, growth factor binding protiens, and receptors. It is now clear that MMPs regulate ECM turnover not only by cleaving ECM components, but also by the regulation of cell signalling, and that some MMPs are beneficial and may be drug anti-targets. Thus, MMPs have important roles in many processes including embryo development, morphogenesis, tissue homeostasis and remodeling. They are implicated in several diseases such as arthritis, periodontitis, glomerulonephritis, atherosclerosis, tissue ulceration, and cancer cell invasion and metastasis. All MMPs are synthesized as preproenzymes. Alternate splice forms are known, leading to nuclear localization of select MMPs. Most are secreted from the cell, or in the case of membrane type (MT) MMPs become plasma membrane associated, as inactive proenzymes. Their subsequent activation is a key regulatory step, with requirements specific to MMP subtype.
R-HSA-1169091 Activation of NF-kappaB in B cells DAG and calcium activate protein kinase C beta (PKC-beta, Kochs et al. 1991) which phosphorylates CARMA1 and other proteins (Sommer et al. 2005). Phosphorylated CARMA1 recruits BCL10 and MALT1 to form the CBM complex (Sommer et al. 2005, Tanner et al. 2007) which, in turn, recruits the kinase TAK1 and the IKK complex (Sommer et al. 2005, Shinohara et al. 2005 using chicken cells). TAK1 phosphorylates the IKK-beta subunit, activating it (Wang et al. 2001). The IKK complex then phosphorylates IkB complexed with NF-kappaB dimers in the cytosol (Zandi et al. 1998, Burke et al. 1999, Heilker et al. 1999), resulting in the degradation of IkB (Miyamoto et al. 1994, Traenckner et al. 1994, Alkalay et al. 1995, DiDonato et al. 1995, Li et al. 1995, Lin et al. 1995, Scherer et al. 1995, Chen et al. 1995). NF-kappaB dimers are thereby released and are translocated to the nucleus where they activate transcription (Baeuerle and Baltimore 1988, Blank et al. 1991, Ghosh et al. 2008, Fagerlund et al. 2008).
R-HSA-2980767 Activation of NIMA Kinases NEK9, NEK6, NEK7 NEK6 and NEK7 are activated during mitosis by another NIMA family kinase, NEK9 (Belham et al. 2003, Richards et al. 2009), which is activated by CDK1- and PLK1-mediated phosphorylation (Roig et al. 2002, Bertran et al. 2011).
R-HSA-442755 Activation of NMDA receptors and postsynaptic events NMDA receptors are a subtype of ionotropic glutamate receptors that are specifically activated by a glutamate agonist N-methyl-D-aspartate (NMDA). Activation of NMDA receptors involves opening of the ion channel that allows the influx of Ca2+. NMDA receptors are central to activity dependent changes in synaptic strength and are predominantly involved in the synaptic plasticity that pertains to learning and memory. A unique feature of NMDA receptors, unlike other glutamate receptors, is the requirement for dual activation, both voltage-dependent and ligand-dependent activation. The ligand-dependent activation of NMDA receptors requires co-activation by two ligands, glutamate and glycine. However, at resting membrane potential, the pore of ligand-bound NMDA receptors is blocked by Mg2+. The voltage dependent Mg2+ block is relieved upon depolarization of the post-synaptic membrane. NMDA receptors are coincidence detectors, and are activated only if there is a simultaneous activation of both pre- and post-synaptic cell. Upon activation, NMDA receptors allow the influx of Ca2+ that initiates various molecular signaling cascades involved in the processes of learning and memory. For review, please refer to Cohen and Greenberg 2008, Hardingham and Bading 2010, Traynelis et al. 2010, and Paoletti et al. 2013.
R-HSA-111448 Activation of NOXA and translocation to mitochondria NOXA is transactivated in a p53-dependent manner and by E2F1. Activated NOXA is translocated to mitochondria.
R-HSA-451307 Activation of Na-permeable kainate receptors Kainate receptors that are formed by subunits GRIK1 and or GRIK2 that are edited at the Q/R and other editing sites in GRIK2 are Ca2+ impermeable. They permit the passage of Na+ ions. Glutamine in GRIK1 at position 636 is replaced by arginine by an editing step which occurs posttranscriptioanlly. GRIK2 is glutamine 621 is edited to arginine. GRIK2 is also edited at 571 (Y/C) where a tyrosine residue is changed to cysteine and 567 (I/V) where an isoleucine is changed to valine. All three sites are edited postranscriptionally. A fully edited GRIK2 at all three sites is impermeable to calcium ions.
R-HSA-2151209 Activation of PPARGC1A (PGC-1alpha) by phosphorylation The transcriptional coactivator PPARGC1A (PGC-1alpha), one of the master regulators of mitochondrial biogenesis, is activated by phosphorylation. Energy depletion causes a reduction in ATP and an increase in AMP which activates AMPK. AMPK in turn phosphorylates PPARGC1A. Likewise, p38 MAPK is activated by muscle contraction (possibly via calcium and CaMKII) and phosphorylates PPARGC1A. PPARGC1A does not bind DNA directly, but rather interacts with other transcription factors. Deacetylation of PPARGC1A by SIRT1 appears to follow phosphorylation however the role of deacetylation is unresolved (Canto et al. 2009, Gurd et al. 2011, Philp et al. 2011)
R-HSA-139915 Activation of PUMA and translocation to mitochondria Puma is transactivated in a p53-dependent manner and by E2F1. Activated Puma is translocated to mitochondria.
R-HSA-428540 Activation of RAC1 A low level of RAC1 activity is essential to maintain axon outgrowth. ROBO activation recruits SOS, a dual specificity GEF, to the plasma membrane via Dock homolog NCK (NCK1 or NCK2) to activate RAC1 during midline repulsion.
R-HSA-9619229 Activation of RAC1 downstream of NMDARs Activation of calcium/calmodulin-dependent kinase kinases, CaMKKs (CAMKK1 and CAMKK2), upon calcium influx through activated NMDA receptors, leads to activation of the cytosolic calcium/calmodulin kinase CaMKI (CAMK1). One of the CAMK1 targets is the RAC1 guanine nucleotide exchange factor ARHGEF7 (beta-Pix). Activation of RAC1 is involved in NMDA-receptor triggered synaptogenesis (Saneyoshi et al. 2008).
R-HSA-1169092 Activation of RAS in B cells RasGRP1 and RasGRP3 bind diacylglycerol at the plasma membrane (Lorenzo et al. 2001) and are phosphorylated by protein kinase C (Teixeira et al. 2003, Zheng et al. 2005). Phosphorylated RasGRP1 (Roose et al. 2007) and RasGRP3 (Ohba et al. 2000, Yamashita et al. 2000, Rebhun et al. 2000, Lorenzo et al. 2001) then catalyze the exchange of GDP for GTP bound by RAS, thereby activating RAS.
R-HSA-5635838 Activation of SMO Activation of the transmembrane protein SMO in response to Hh stimulation is a major control point in the Hh signaling pathway (reviewed in Ayers and Therond, 2010; Jiang and Hui, 2008). In the absence of ligand, SMO is inhibited in an unknown manner by the Hh receptor PTCH. PTCH regulates SMO in a non-stoichiometric manner and there is little evidence that endogenous PTCH and SMO interact directly (Taipale et al, 2002; reviewed in Huangfu and Anderson, 2006). PTCH may regulate SMO activity by controlling the flux of sterol-related SMO agonists and/or antagonists, although this has not been fully substantiated (Khaliullina et al, 2009; reviewed in Rohatgi and Scott, 2007; Briscoe and Therond, 2013).
PTCH-mediated inhibition of SMO is relieved upon ligand stimulation of PTCH, but the mechanisms for this relief are again unknown. SMO and PTCH appear to have opposing localizations in both the 'off' and 'on' state, with PTCH exiting and SMO entering the cilium upon Hh pathway activation (Denef et al, 2000; Rohatgi et al, 2007; reviewed in Goetz and Anderson, 2010; Hui and Angers, 2011). Activation of SMO involves a conserved phosphorylation-mediated conformational change in the C-terminal tails that destabilizes an intramolecular interaction and promotes the interaction between adjacent tails in the SMO dimer. In Drosophila, this phosphorylation is mediated by PKA and CK1, while in vertebrates it appears to involve ADRBK1/GRK2 and CSNK1A1. Sequential phosphorylations along multiple serine and threonine motifs in the SMO C-terminal tail appear to allow a graded response to Hh ligand concentration in both flies and vertebrates (Zhao et al, 2007; Chen et al, 2010; Chen et al, 2011). In flies, Smo C-terminal tail phosphorylation promotes an association with the Hedgehog signaling complex (HSC) through interaction with the scaffolding kinesin-2 like protein Cos2, activating the Fu kinase and ultimately releasing uncleaved Ci from the complex (Zhang et al, 2005; Ogden et al, 2003; Lum et al, 2003; reviewed in Mukhopadhyay and Rohatgi, 2014). In vertebrates, SMO C-terminal tail phosphorylation and conformational change is linked to its KIF7-dependent ciliary accumulation (Chen et al, 2011; Zhao et al, 2007; Chen et al, 2010). In the cilium, SMO is restricted to a transition-zone proximal region known as the EvC zone (Yang et al, 2012; Blair et al, 2011; Pusapati et al, 2014; reviewed in Eggenschwiler 2012). Both SMO phosphorylation and its ciliary localization are required to promote the Hh-dependent dissociation of the GLI:SUFU complex, ultimately allowing full-length GLI transcription factors to translocate to the nucleus to activate Hh-responsive genes (reviewed in Briscoe and Therond, 2013).
R-HSA-187015 Activation of TRKA receptors Trk receptors can either be activated by neurotrophins or by two G-protein-coupled receptors (GPCRs) although the biological relevance of GPCRs remains to be shown.
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis In mammals, anterior Hox genes may be defined as paralog groups 1 to 4 (Natale et al. 2011), which are involved in development of the hindbrain through sequential expression in the rhombomeres, transient segments of the neural tube that form during development of the hindbrain (reviewed in Alexander et al. 2009, Soshnikova and Duboule 2009, Tumpel et al. 2009, Mallo et al. 2010, Andrey and Duboule 2014). Hox gene activation during mammalian development has been most thoroughly studied in mouse embryos and the results have been extended to human development by in vitro experiments with human embryonal carcinoma cells and human embryonic stem cells.
Expression of a typical anterior Hox gene has an anterior boundary located at the junction between two rhombomeres and continues caudally to regulate segmentation and segmental fate in ectoderm, mesoderm, and endoderm. Anterior boundaries of expression of successive Hox paralog groups are generally separated from each other by 2 rhombomeres. For example, HOXB2 is expressed in rhombomere 3 (r3) and caudally while HOXB3 is expressed in r5 and caudally. Exceptions exist, however, as HOXA1, HOXA2, and HOXB1 do not follow the rule and HOXD1 and HOXC4 are not expressed in rhombomeres. Hox genes within a Hox cluster are expressed colinearly: the gene at the 3' end of the cluster is expressed earliest, and hence most anteriorly, then genes 5' are activated sequentially in the same order as they occur in the cluster.
Activation of expression occurs epigenetically by loss of polycomb repressive complexes and change of bivalent chromatin to active chromatin through, in part, the actions of trithorax family proteins (reviewed in Soshnikova and Duboule 2009). Hox gene expression initiates in the posterior primitive streak that will contribute to extraembryonic mesoderm. Expression then extends anteriorly into the cells that will become the embryo, where expression is first observed in presumptive lateral plate mesoderm and is transmitted to both paraxial mesoderm and neurectoderm formed by gastrulation along the primitive streak (reviewed in Deschamps et al. 1999, Casaca et al. 2014).
Prior to establishment of the rhombomeres, expression of HOXA1 and HOXB1 is initiated near the future site of r3 and caudally by a gradient of retinoic acid (RA). (Mechanisms of retinoic acid signaling are reviewed in Cunningham and Duester 2015.) The RA is generated by the ALDH1A2 (RALDH2) enzyme located in somites flanking the caudal hindbrain and degraded by CYP26 enzymes expressed initially in anterior neural ectoderm of the early gastrula and then throughout most of the hindbrain (reviewed in White and Schilling 2008). HOXA1 with PBX1,2 and MEIS2 directly activate transcription of ALDH1A2 to maintain retinoic acid synthesis in the somitic mesoderm (Vitobello et al. 2011). Differentiation of embryonal carcinoma cells and embryonic stem cells in response to retinoic acid is used to model the process of differentiation in vitro (reviewed in Soprano et al. 2007, Gudas et al. 2013).
HOXA1 appears to set the anterior limit of HOXB1 expression (Barrow et al. 2000). HOXB1 initiates expression of EGR2 (KROX20) in presumptive r3. EGR2 then activates HOXA2 expression in r3 and r5 while HOXB1, together with PBX1 and MEIS:PKNOX1 (MEIS:PREP), activates expression of HOXA2 in r4 and caudal rhombomeres. AP-2 transcription factors maintain expression of HOXA2 in neural crest cells (Maconochie et al. 1999). HOXB1 also activates expression of HOXB2 in r3 and caudal rhombomeres. EGR2 negatively regulates HOXB1 so that by the time rhombomeres appear, HOXB1 is restricted to r4 and HOXA1 is no longer detectable (Barrow et al. 2000). EGR2 and MAFB (Kreisler) then activate HOXA3 and HOXB3 in r5 and caudal rhombomeres. Retinoic acid activates HOXA4, HOXB4, and HOXD4 in r7, the final rhombomere. HOX proteins, in turn, activate expression of genes in combination with other factors, notably members of the TALE family of transcription factors (PBX, PREP, and MEIS, reviewed in Schulte and Frank 2014, Rezsohazy et al. 2015). HOX proteins also participate in non-transcriptional interactions (reviewed in Rezsohazy 2014). In zebrafish, Xenopus, and chicken factors such as Meis3, Fgf3, Fgf8, and vHNF regulate anterior hox genes (reviewed in Schulte and Frank 2014), however less is known about the roles of homologous factors in mammals.
Mutations in HOXA1 in humans have been observed to cause developmental abnormalities located mostly in the head and neck region (Tischfield et al. 2005, Bosley et al. 2008). A missense mutation in HOXA2 causes microtia, hearing impairment, and partially cleft palate (Alasti et al. 2008). A missense mutation in HOXB1 causes a similar phenotype to the Hoxb1 null mutation in mice: bilateral facial palsy, hearing loss, and strabismus (improper alignment of the eyes) (Webb et al. 2012).
R-HSA-111459 Activation of caspases through apoptosome-mediated cleavage Procaspase-3 and 7 are cleaved by the apoptosome.
R-HSA-2426168 Activation of gene expression by SREBF (SREBP) After transiting to the nucleus SREBPs (SREBP1A/1C/2, SREBFs) bind short sequences, sterol regulatory elements (SREs), in the promoters of target genes (reviewed in Eberle et al. 2004, Weber et al. 2004). SREBPs alone are relatively weak activators of transcription, with SREBP1C being significantly weaker than SREBP1A or SREBP2. In combination with other transcription factors such as SP1 and NF-Y the SREBPs are much stronger activators. SREBP1C seems to more specifically target genes involved in fatty acid synthesis while SREBP2 seems to target genes involved in cholesterol synthesis (Pai et al. 1998).
R-HSA-451326 Activation of kainate receptors upon glutamate binding Kainate receptors are found both in the presynaptc terminals and the postsynaptic neurons.
Kainate receptor activation could lead to either ionotropic activity (influx of Ca2+ or Na+ and K+) in the postsynaptic neuron or coupling of the receptor with G proteins in the presynaptic and the postsynaptic neurons.
Kainate receptors are tetramers made from subunits GRIK1-5 or GluR5-7 and KA1-2. Activation of kainate receptors made from GRIK1 or KA2 release Ca2+ from the intracellular stores in a G protein-dependent manner. The G protein involved in this process is sensitive to pertussis toxin.
R-HSA-450341 Activation of the AP-1 family of transcription factors Activator protein-1 (AP-1) is a collective term referring to a group of transcription factors that bind to promoters of target genes in a sequence-specific manner. AP-1 family consists of hetero- and homodimers of bZIP (basic region leucine zipper) proteins, mainly of Jun-Jun, Jun-Fos or Jun-ATF.
AP-1 members are involved in the regulation of a number of cellular processes including cell growth, proliferation, survival, apoptosis, differentiation, cell migration. The ability of a single transcription factor to determine a cell fate critically depends on the relative abundance of AP-1 subunits, the composition of AP-1 dimers, the quality of stimulus, the cell type, the co-factor assembly.
AP-1 activity is regulated on multiple levels; transcriptional, translational and post-translational control mechanisms contribute to the balanced production of AP-1 proteins and their functions. Briefly, regulation occurs through:
In addition to its role in energy generation, the citric acid cycle is a source of carbon skeletons for amino acid metabolism and other biosynthetic processes. One such process included here is the interconversion of 2-hydroxyglutarate, probably derived from porphyrin and amino acid metabolism, and 2-oxoglutarate (alpha-ketoglutarate), a citric acid cycle intermediate.
R-HSA-5423646 Aflatoxin activation and detoxification Aflatoxins are among the principal mycotoxins produced as secondary metabolites by the molds Aspergillus flavus and Aspergillus parasiticus that contaminate economically important food and feed crops (Wild & Turner 2002). Aflatoxin B1 (AFB1) is the most potent naturally occurring carcinogen known and is also an immunosuppressant. It is a potent hepatocarcinogenic agent in many species, and has been implicated in the etiology of human hepatocellular carcinoma. Poultry, especially turkeys, are extremely sensitive to the toxic and carcinogenic action of AFB1 present in animal feed, resulting in multi-million dollar losses to the industry. Discerning the biochemical and molecular mechanisms of this extreme sensitivity of poultry to AFB1 will help with the development of new strategies to increase aflatoxin resistance (Rawal et al. 2010, Diaz & Murcia 2011).
AFB1 has one major genotoxic metabolic fate, conversion to AFXBO, and several others that are less mutagenic but that can still be quite toxic. AFB1 can be oxidised to the toxic AFB1 exo 8,9 epoxide (AFXBO) product by several cytochrome P450 enzymes, especially P450 3A4 in the liver. This 8,9 epoxide can react with the N7 atom of a guanyl base of DNA to produce adducts by intercalating between DNA base pairs. The exo epoxide is unstable in solution, however, and can react spontaneously to form a diol that is no longer reactive with DNA. The diol product in turn undergoes base-catalysed rearrangement to a dialdehyde that can react with protein lysine residues. AFB1 can also be metabolised to products (AFQ1, AFM1, AFM1E) which have far less genotoxic consequences than AFB1. The main route of detoxification of AFB1 is conjugation of its reactive 8,9-epoxide form with glutathione (GSH). This reaction is carried out by trimeric glutathione transferases (GSTs), providing a chemoprotective mechanism against toxicity. Glutathione conjugates are usually excreted as mercapturic acids in urine (Guengerich et al. 1998, Hamid et al. 2013). The main metabolic routes of aflatoxin in humans are described here.
R-HSA-9646399 Aggrephagy When the capacity of the proteosome to degrade misfolded proteins is limited, the alternate route to eliminate denatured proteins is via forming aggresomes - a process known as aggrephagy. Aggresome formation starts with ubiquitination of misfolded proteins following transport to the microtubule-organizing center (MTOC) with the help of dynein motor proteins. At the MTOC the cargo is encapsulated with intermediate filament proteins to result in the aggresome. Subsequently, this aggresome recruits chaperones that result in its autophagic elimination (Garcia Mata R et al. 2002).
R-HSA-351143 Agmatine biosynthesis Agmatine is an amine that is formed by decarboxylation of L-arginine by the enzyme arginine decarboxylase (ADC) and hydrolyzed by the enzyme agmatinase to putrescine. Agmatine binds to several target receptors in the brain and has been proposed as a novel neuromodulator (Reghunathan 2006). Agmatine has the potential to serve in the coordination of the early and repair phase pathways of arginine in inflammation (Satriano, 2003).
R-HSA-8964540 Alanine metabolism The interconversion of alanine and pyruvate, annotated here, is a key connection among the processes of protein turnover and energy metabolism in the human body (Felig 1975; Owen et al. 1979).
R-HSA-9730737 Alkylating DNA damage induced by chemotherapeutic drugs This pathway describes how chemotherapeutic drugs commonly used in cancer treatment produce alkylating DNA damage that is repaired through the base excision repair (BER) pathway. For review, please refer to Fu et al. 2012.
R-HSA-1462054 Alpha-defensins Humans have 7 alpha defensin genes plus 5 pseudogenes (see HGNC at http://www.genenames.org/genefamilies/DEFA). Alpha-defensins have six cysteines linked 1-6, 2-4, 3-5. The canonical sequence of alpha-defensins in humans is x1-2CXCRx2-3Cx3Ex3GxCx3Gx5CCx1-4, where x represents any amino acid residue.
Human alpha-defensins 1-4 are often called human neutrophil peptides (HNP1-4) as they were initially identified in neutrophil primary (azurophilic) granules. Alpha-defensins 5 and 6 (HD5, HD6) are products of Paneth cells. HNP-1 and -3 peptides are 30 residues long, differing only in the first amino acid. They are encoded by the genes DEFA1 and DEFA3 respectively. These exhibit copy number polymorphism, with some individuals having 4-14 copies per diploid genome, while 10-37% of individuals have no copies of DEFA3 (Aldred et al. 2005, Linzmier & Ganz 2005, Ballana et al. 2007). HNP-4, encoded by DEFA4, is 33 amino acids long of which 22 differ from the other HNPs (Wilde et al. 1989). It is a minor component of neutrophil granules compared to HNP1-3. In contrast to DEFA1 and DEFA3, the genes for HNP-4, HD-5 and HD-6 are only found as two copies per diploid genome (Linzmeier & Ganz 2005). HNP-2 is 29 amino acids in length and is the proteolytic product of cleavage of the N-terminal amino acid from either HNP-1 and/or HNP-3 (Selsted et al. 1985).
R-HSA-389599 Alpha-oxidation of phytanate Phytanic acid arises through ruminant metabolism of chlorophyll and enters the human diet as a constituent of dairy products (Baxter 1968). It can act as an agonist for PPAR and other nuclear hormone receptors, but its normal role in human physiology, if any, is unclear. It is catabolized via a five-step alpha-oxidation reaction sequence that yields pristanoyl-CoA, which is turn is a substrate for beta-oxidation. These reactions take place in the peroxisomal matrix and their failure is associated with Refsum disease (Wanders et al. 2003).
R-HSA-9645460 Alpha-protein kinase 1 signaling pathway Immune recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRR) often activates proinflammatory nuclear factor kappa B (NF-κB) signalling. Lipopolysaccharide (LPS) is a well-known PAMP produced by gram-negative bacteria. LPS is recognized by toll like receptor 4 (TLR4) and is a strong activator of NF-κB inflammatory responses (Akashi S et al. 2003). LPS is also recognized in the cytosol by mouse caspase-11 and related human caspase-4 and caspase-5, which stimulate pyroptosis, a proinflammatory form of cell death (Kayagaki N et al. 2011; Shi J et al. 2015). Key metabolic intermediates in LPS biosynthesis, d-glycero-β-d-manno-heptose 1,7-bisphosphate (HBP) and ADP L-glycero-β-d-manno-heptose (ADP-heptose) were reported to activate the NF-κB pathway and trigger the innate immune responses (Milivojevic M et al. 2017; Zimmermann S et al. 2017; Zhou P et al. 2018; García-Weber D; 2018). ADP-heptose but not HBP can enter host cells autonomously (Zhou P et al. 2018). During infection, ADP-heptose or HBP translocate into the host cytosol where their presence is sensed by alpha-protein kinase 1 (ALPK1) (Zimmermann S et al. 2017; Zhou P et al. 2018). ADP-heptose directly binds and activates ALPK1 (Garcia-Weber D et al. 2018; Zhou P et al. 2018); instead, HBP is converted by host-derived adenylyltransferases, such as nicotinamide nucleotide adenylyltransferases, to ADP-heptose 7-P, a substrate which can then activate ALPK1 (Zhou P et al. 2018). The ADP-heptose binding to ALPK1 is thought to trigger conformational changes and stimulate the kinase domain of ALPK1 (Zhou P et al. 2018). ALPK1 kinase activity in turn leads to the phosphorylation-dependent oligomerization of the tumor necrosis factor (TNF-α) receptor–associated factor (TRAF)–interacting protein with the forkhead-associated domain (TIFA) (Zimmermann S et al. 2017; Zhou P et al. 2018). This process activates TRAF6 oligomerization and ubiquitination, and the recruitment of transforming growth factor β-activated kinase 1 (TAK1)-binding protein 2 (TAB2), a component of the TAK1 (MAP3K7) complex (Ea CK et al. 2004; Gaudet RG et al. 2017). This TIFA oligomer signaling platform was given the term: TIFAsome. TIFAsome-activated TAK1 induces NF-κB nuclear translocation and proinflammatory gene expression. The ALPK1-TIFA signaling pathway has been identified in human embryonic kidney cells, intestinal epithelial cells, gastric cells and cervical cancer cells (Gaudet RG et al. 2015, 2017; Stein SC et al. 2017; Gall A et al. 2017; Zimmermann S et al. 2017; Milivojevic M et al. 2017; Zhou P et al. 2018). In vivo studies demonstrate that ADP-heptose and Burkholderia cenocepacia trigger massive inflammatory responses with increased production of several NF-κB-dependent cytokines and chemokines in wild type (WT), but not in Alpk1-/- mice (Zhou P et al. 2018).
This Reactome module describes ALPK1 as a cytosolic innate immune receptor for bacterial ADP-heptose. R-HSA-9006821 Alternative Lengthening of Telomeres (ALT) Alternative lengthening of telomeres (ALT) is a homologous recombination repair-directed telomere synthesis that takes place in 5-15% of tumors. ALT positive tumors often harbor loss-of-function mutations in ATRX (Alpha thalassemia mental retardation X-linked) or, more rarely, DAXX (Death domain-associated protein 6) chromatin remodeling factors, which may act to inhibit DNA recombination at telomere ends (reviewed by Gocha et al. 2013). The nuclear receptor complex NuRD-ZNF827 contributes to the recruitment of homologous recombination (HR) machinery to telomeres (Conomos et al. 2014). ALT is most prevalent in subsets of sarcomas, including osteosarcomas and some soft tissue sarcomas, brain cancers and neuroblastomas (Heaphy et al. 2011, Arora and Azzalin 2015). For review, please refer to Nabetani and Ishikawa 2011, Pickett and Reddel 2015, Verma and Greenberg 2016, Amorim et al. 2016, Sommer and Royle 2020, Zhang and Zou 2020. R-HSA-173736 Alternative complement activation The proteins participating in alternative pathway activation are C3 (and C3b), the factors B, D, and properdin. In the first place, alternative pathway activation is a positive feedback mechanism to increase C3b. When C3b binds covalently to sugars on a cell surface, it can become protected. Then Factor B binds to C3b. In the presence of Factor D, bound Factor B is cleaved to Ba and Bb. Bb contains the active site for a C3 convertase. Properdin then binds to C3bBb to stabilize the C3bBb convertase on cell surface leading to cleavage of C3. Finally, a C3bBb3b complex forms and this is a C5 convertase. R-HSA-140179 Amine Oxidase reactions Human amine oxidases (AO) catalyze the oxidative deamination of biogenic amines (neurotransmitters such as serotonin, noradrenaline, the hormone adrenaline and polyamines such as the spermines) and xenobiotic amines (exogenous dietary tyramine and phenylethylamine). The basic reaction is the oxidative cleavage of the alpha-H to form an imine product with the concomitant reduction of a FAD cofactor. The imine product then hydrolyses to an aldehyde and ammonia (or amine for secondary and tertiary amine substrates). Reduced FAD is reoxidized to form hydrogen peroxide to complete the catalytic cycle.
The reaction can be summarized as
RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2
The resultant hydrogen peroxide is the source of the most toxic free radical, the hydroxyl radical (.OH). This free radical is produced in the Fenton reaction with the use of ferrous (Fe2+) iron.
R-HSA-375280 Amine ligand-binding receptors The class A (rhodopsin-like) GPCRs that bind to classical biogenic amine ligands are annotated here. The amines involved (acetylcholine, adrenaline, noradrenaline, dopamine, serotonin and histamine) can all act as neurotransmitters in humans. The so-called 'trace amines', used when referring to p-tyramine, beta-phenylethylamine, tryptamine and octopamine, can also bind to recently-discovered GPCRs. R-HSA-156587 Amino Acid conjugation Xenobiotics that contain either a carboxylic group or an aromatic hydroxylamine group are possible substrates for amino acid conjugation. Xenobiotics with a carboxylic group conjugate with an amino group of amino acids such as glycine, taurine and glutamine. The hydroxylamine group conjugates with the carboxylic group of amino acids such as proline and serine. The amino acid is first activated by an aminoacyl-tRNA-synthetase which then reacts with the hydroxylamine group to form a reactive N-ester. N-esters can degrade to form electrophilic nitrenium (R-N+-R') and carbonium (R-C+H2) ions. The pyrolysis product of tryptophan, an N-hydroxy intermediate, can potentially form these reactive electrophilic ions. R-HSA-352230 Amino acid transport across the plasma membrane Amino acid transport across plasma membranes is critical to the uptake of these molecules from the gut, to their reabsortion in the kidney proximal tubulues, and to their distribution to cells in which they are required for the synthesis of proteins and of amino acid derived small molecules such as neurotransmitters. Physiological studies have defined 18 "systems" that mediate amino acid transport, each characterized by its amino acid substrates, as well as its pH sensitivity and its association (or not) with ion transport. More recently, molecular cloning studies have allowed the identification of the plasma membrane transport proteins that mediate these reactions. Amino acid uptake mediated by 17 of these transporters is annotated here (Broer 2008). R-HSA-9639288 Amino acids regulate mTORC1 The mTORC1 complex acts as an integrator that regulates translation, lipid synthesis, autophagy, and cell growth in response to multiple inputs, notably glucose, oxygen, amino acids, and growth factors such as insulin (reviewed in Sabatini 2017, Meng et al. 2018, Kim and Guan 2019).AMPs have also been referred to as cationic host defense peptides, anionic antimicrobial peptides/proteins, cationic amphipathic peptides, cationic AMPs, host defense peptides and alpha-helical antimicrobial peptides (Brown KL & Hancock RE 2006; Harris F et al. 2009; Groenink J et al. 1999; Bradshaw J 2003; Riedl S et al. 2011; Huang Y et al. 2010).
The Reactome module describes the interaction events of various types of human AMPs, such as cathelicidin, histatins and neutrophil serine proteases, with conserved patterns of microbial membranes at the host-pathogen interface. The module includes also proteolytic processing events for dermcidin (DCD) and cathelicidin (CAMP) that become functional upon cleavage. In addition, the module highlights an AMP-associated ability of the host to control metal quota at inflammation sites to influence host-pathogen interactions.
R-HSA-1169410 Antiviral mechanism by IFN-stimulated genes Interferons activate JAK–STAT signaling, which leads to the transcriptional induction of hundreds of IFN-stimulated genes (ISGs). The ISG-encoded proteins include direct effectors which inhibit viral infection through diverse mechanisms as well as factors that promote adaptive immune responses. The ISG proteins generated by IFN pathways plays key roles in the induction of innate and adaptive immune responses.
R-HSA-109581 Apoptosis Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of "cell-death", and the mechanisms of various apoptotic pathways are still being revealed today.
The two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptors
The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation.
The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.
In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes.
R-HSA-140342 Apoptosis induced DNA fragmentation DNA fragmentation in response to apoptotic signals is achieved, in part, through the activity of apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) (reviewed in Widlak and Garrard, 2005). In non-apoptotic cells, DFF is a nuclear heterodimer consisting of a 45 kD chaperone and inhibitor subunit (DFF45)/inhibitor of CAD (ICAD-L)] and a 40 kD nuclease subunit (DFF40/CAD)( Liu et al. 1997, 1998; Enari et al. 1998). During apoptosis, activated caspase-3 or -7 cleave DFF45/ICAD releasing active DFF40/CAD nuclease. The activity of DFF is tightly controlled at multiple stages. During translation, DFF45/ICAD, Hsp70, and Hsp40 proteins play a role in insuring the appropriate folding of DFF40 during translation(Sakahira and Nagata, 2002). The nuclease activity of DFF40 is enhanced by the chromosomal proteins histone H1, Topoisomerase II and HMGB1/2(Widlak et al., 2000). In addition, the inhibitors (DFF45/35; ICAD-S/L) are produced in stoichiometric excess (Widlak et al., 2003).
R-HSA-351906 Apoptotic cleavage of cell adhesion proteins Apoptotic cells show dramatic rearrangements of tight junctions, adherens junctions, and desmosomes (Abreu et al., 2000). Desmosome-specific members of the cadherin superfamily of cell adhesion molecules including desmoglein-3, plakophilin-1 and desmoplakin are cleaved by caspases after onset of apoptosis (Weiske et al., 2001). Cleavage results in the disruption of the desmosome structure and thus contributes to cell rounding and disintegration of the intermediate filament system (Weiske et al., 2001).
R-HSA-111465 Apoptotic cleavage of cellular proteins Apoptotic cell death is achieved by the caspase-mediated cleavage of various vital proteins. Among caspase targets are proteins such as E-cadherin, Beta-catenin, alpha fodrin, GAS2, FADK, alpha adducin, HIP-55, and desmoglein involved in cell adhesion and maintenance of the cytoskeletal architecture. Cleavage of proteins such as APC and CIAP1 can further stimulate apoptosis by produce proapoptotic proteins (reviewed in Fischer et al., 2003. See also Wee et al., 2006 and the CASVM Caspase Substrates Database: http://www.casbase.org/casvm/squery/index.html ).
R-HSA-75153 Apoptotic execution phase In the execution phase of apoptosis, effector caspases cleave vital cellular proteins leading to the morphological changes that characterize apoptosis. These changes include destruction of the nucleus and other organelles, DNA fragmentation, chromatin condensation, cell shrinkage and cell detachment and membrane blebbing (reviewed in Fischer et al., 2003).
R-HSA-111471 Apoptotic factor-mediated response In response to apoptotic signals, mitochondrial proteins are released into the cytosol and activate both caspase-dependent and -independent cell death pathways. Cytochrome c induces apoptosome formation, AIF and endonuclease G function in caspase independent apoptotic nuclear DNA damage. Smac/DIABLO and HtrA2/OMI promote both caspase activation and caspase-independent cytotoxicity (Saelens et al., 2004).
R-HSA-445717 Aquaporin-mediated transport Aquaporins (AQP's) are six-pass transmembrane proteins that form channels in membranes. Each monomer contains a central channel formed in part by two asparagine-proline-alanine motifs (NPA boxes) that confer selectivity for water and/or solutes. The monomers assemble into tetramers. During passive transport by Aquaporins most aquaporins (i.e. AQP0/MIP, AQP1, AQP2, AQP3, AQP4, AQP5, AQP7, AQP8, AQP9, AQP10) transport water into and out of cells according to the osmotic gradient across the membrane. Four aquaporins (the aquaglyceroporins AQP3, AQP7, AQP9, AQP10) conduct glycerol, three aquaporins (AQP7, AQP9, AQP10) conduct urea, and one aquaporin (AQP6) conducts anions, especially nitrate. AQP8 also conducts ammonia in addition to water.
AQP11 and AQP12, classified as group III aquaporins, were identified as a result of the genome sequencing project and are characterized by having variations in the first NPA box when compared to more traditional aquaporins. Additionally, a conserved cysteine residue is present about 9 amino acids downstream from the second NPA box and this cysteine is considered indicative of group III aquaporins. Purified AQP11 incorporated into liposomes showed water transport. Knockout mice lacking AQP11 had fatal cyst formation in the proximal tubule of the kidney. Exogenously expressed AQP12 showed intracellular localization. AQP12 is expressed exclusively in pancreatic acinar cells.
Aquaporins are important in fluid and solute transport in various tissues. During Transport of glycerol from adipocytes to the liver by Aquaporins, glycerol generated by triglyceride hydrolysis is exported from adipocytes by AQP7 and is imported into liver cells via AQP9. AQP1 plays a role in forming cerebrospinal fluid and AQP1, AQP4, and AQP9 appear to be important in maintaining fluid balance in the brain. AQP0, AQP1, AQP3, AQP4, AQP8, AQP9, and AQP11 play roles in the physiology of the hepatobiliary tract.
In the kidney, water and solutes are passed out of the bloodstream and into the proximal tubule via the slit-like structure formed by nephrin in the glomerulus. Water is reabsorbed from the filtrate during its transit through the proximal tubule, the descending loop of Henle, the distal convoluted tubule, and the collecting duct. Aquaporin-1 (AQP1) in the proximal tubule and the descending thin limb of Henle is responsible for about 90% of reabsorption (as estimated from mouse knockouts of AQP1). AQP1 is located on both the apical and basolateral surface of epithelial cells and thus transports water through the epithelium and back into the bloodstream. In the collecting duct epithelial cells have AQP2 on their apical surfaces and AQP3 and AQP4 on their basolateral surfaces to transport water across the epithelium. Vasopressin regulates renal water homeostasis via Aquaporins by regulating the permeability of the epithelium through activation of a signaling cascade leading to the phosphorylation of AQP2 and its translocation from intracellular vesicles to the apical membrane of collecting duct cells.
Here, three views of aquaporin-mediated transport have been annotated: a generic view of transport mediated by the various families of aquaporins independent of tissue type (Passive transport by Aquaporins), a view of the role of specific aquaporins in maintenance of renal water balance (Vasopressin regulates renal water homeostasis via Aquaporins), and a view of the role of specific aquaporins in glycerol transport from adipocytes to the liver (Transport of glycerol from adipocytes to the liver by Aquaporins).
R-HSA-2142753 Arachidonate metabolism Eicosanoids, oxygenated, 20-carbon fatty acids, are autocrine and paracrine signaling molecules that modulate physiological processes including pain, fever, inflammation, blood clot formation, smooth muscle contraction and relaxation, and the release of gastric acid. Eicosanoids are synthesized in humans primarily from arachidonate (all-cis 5,8,11,14-eicosatetraenoate) that is released from membrane phospholipids. Once released, arachidonate is acted on by prostaglandin G/H synthases (PTGS, also known as cyclooxygenases (COX)) to form prostaglandins and thromboxanes, by arachidonate lipoxygenases (ALOX) to form leukotrienes, epoxygenases (cytochrome P450s and epoxide hydrolase) to form epoxides such as 15-eicosatetraenoic acids, and omega-hydrolases (cytochrome P450s) to form hydroxyeicosatetraenoates (Buczynski et al. 2009, Vance & Vance 2008).
Levels of free arachidonate in the cell are normally very low so the rate of synthesis of eicosanoids is determined primarily by the activity of phospholipase A2, which mediates phospholipid cleavage to generate free arachidonate. The enzymes involved in arachidonate metabolism are typically constitutively expressed so the subset of these enzymes expressed by a cell determines the range of eicosanoids it can synthesize.
Eicosanoids are unstable, undergoing conversion to inactive forms with half-times under physiological conditions of seconds or minutes. Many of these reactions appear to be spontaneous.
R-HSA-426048 Arachidonate production from DAG Diacylglycerol (DAG) is an important source of arachidonic acid, a signalling molecule and the precursor of the prostaglandins. In human platelet almost all the DAG produced from phosphatidylinositol degradation contains arachidonate (Takamura et al. 1987). DAG is hydrolysed by DAG lipase to 2-arachidonylglycerol (2-AG) which is further hydrolysed by monoacylglycerol lipase. 2-AG is an agonist of cannabinoid receptor 1.
R-HSA-211957 Aromatic amines can be N-hydroxylated or N-dealkylated by CYP1A2 CYP1A2 oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. It is most active in catalyzing N-hydroxylation or N-dealkylation reactions.
R-HSA-8937144 Aryl hydrocarbon receptor signalling The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that belongs to the basic helix-loop-helix/PER-ARNT-SIM family of DNA binding proteins and controls the expression of a diverse set of genes. Two major types of environmental compounds can activate AHR signaling: halogenated aromatic hydrocarbons such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and polycyclic aromatic hydrocarbons (PAH) such as benzo(a)pyrene. Unliganded AHR forms a complex in the cytosol with two copies of 90kD heat shock protein (HSP90AB1), one X-associated protein (AIP), and one p23 molecular chaperone protein (PTGES3). After ligand binding and activation, the AHR complex translocates to the nucleus, disassociates from the chaperone subunits, dimerises with the aryl hydrocarbon receptor nuclear translocator (ARNT) and transactivates target genes via binding to xenobiotic response elements (XREs) in their promoter regions. AHR targets genes of Phase I and Phase II metabolism, such as cytochrome P450 1A1 (CYP1A1), cytochorme P450 1B1 (CYP1B1), NAD(P)H:quinone oxidoreductase I (NQO1) and aldehyde dehydrogenase 3 (ALHD3A1). This is thought to be an organism's response to foreign chemical exposure and normally, foreign chemicals are made less reactive by the induction and therefore increased activity of these enzymes (Beischlag et al. 2008).
AHR itself is regulated by the aryl hydrocarbon receptor repressor (AHRR, aka BHLHE77, KIAA1234), an evolutionarily conserved bHLH-PAS protein that inhibits both xenobiotic-induced and constitutively active AHR transcriptional activity in many species. AHRR resides predominantly in the nuclear compartment where it competes with AHR for binding to ARNT. As a result, there is competition between AHR:ARNT and AHRR:ARNT complexes for binding to XREs in target genes and AHRR can repress the transcription activity of AHR (Hahn et al. 2009, Haarmann-Stemmann & Abel 2006).
R-HSA-446203 Asparagine N-linked glycosylation N-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 revealed that about 50% of the proteins in the Swiss-Prot database at the time were N-glycosylated (Apweiler et al. 1999). It is now established that the majority of the proteins in the secretory pathway require glycosylation in order to achieve proper folding.
The addition of an N-glycan to a protein can have several roles (Shental-Bechor & Levy 2009). First, glycans enhance the solubility and stability of the proteins in the ER, the golgi and on the outside of the cell membrane, where the composition of the medium is strongly hydrophilic and where proteins, that are mostly hydrophobic, have difficulty folding properly. Second, N-glycans are used as signal molecules during the folding and transport process of the protein: they have the role of labels to determine when a protein must interact with a chaperon, be transported to the golgi, or targeted for degradation in case of major folding defects. Third, and most importantly, N-glycans on completely folded proteins are involved in a wide range of processes: they help determine the specificity of membrane receptors in innate immunity or in cell-to-cell interactions, they can change the properties of hormones and secreted proteins, or of the proteins in the vesicular system inside the cell.
All N-linked glycans are derived from a common 14-sugar oligosaccharide synthesized in the ER, which is attached co-translationally to a protein while this is being translated inside the reticulum. The process of the synthesis of this glycan, known as Synthesis of the N-glycan precursor or LLO, constitutes one of the most conserved pathways in eukaryotes, and has been also observed in some eubacteria. The attachment usually happens on an asparagine residue within the consensus sequence asparagine-X-threonine by an complex called oligosaccharyl transferase (OST).
After being attached to an unfolded protein, the glycan is used as a label molecule in the folding process (also known as Calnexin/Calreticulin cycle) (Lederkremer 2009). The majority of the glycoproteins in the ER require at least one glycosylated residue in order to achieve proper folding, even if it has been shown that a smaller portion of the proteins in the ER can be folded without this modification.
Once the glycoprotein has achieved proper folding, it is transported via the cis-Golgi through all the Golgi compartments, where the glycan is further modified according to the properties of the glycoprotein. This process involves relatively few enzymes but due to its combinatorial nature, can lead to several millions of different possible modifications. The exact topography of this network of reactions has not been established yet, representing one of the major challenges after the sequencing of the human genome (Hossler et al. 2006).
Since N-glycosylation is involved in an great number of different processes, from cell-cell interaction to folding control, mutations in one of the genes involved in glycan assembly and/or modification can lead to severe development problems (often affecting the central nervous system). All the diseases in genes involved in glycosylation are collectively known as Congenital Disorders of Glycosylation (CDG) (Sparks et al. 2003), and classified as CDG type I for the genes in the LLO synthesis pathway, and CDG type II for the others.
R-HSA-8963693 Aspartate and asparagine metabolism These reactions mediate the synthesis of aspartate and asparagine from glutamate, TCA cycle intermediates, and ammonia and and allow the utilization of carbon atoms from these amino acids for glucose synthesis under fasting conditions (Felig 1975; Owen et al. 1979).
R-HSA-9749641 Aspirin ADME In water aspirin (acetylsalicylic acid, ASA) dissolves, dissociating into the acetylsalicylate ion (ASA-). ASA- is an anti-clotting agent and nonsteroidal anti-inflammatory drug (NSAID); the therapeutic effects are mediated through its interaction with PTGS enzymes. On a molar basis ASA- (a) is more potent as an analgesic/anti-inflammatory agent, (b) has greater gastric ulcerogenic activity, and (c) is much more effective as an inhibitor of prostaglandin biosynthesis and platelet aggregation than salicylate (ST) (Flower 1974; Mills et al, 1974; Rainsford 1975; Rainsford 1977).
Acetylsalicylic acid is only slightly soluble in conditions being found in the stomach mucosa, mostly because of unavailability of sufficient amount of solvent. The absorption, as well as the absorbing area, increases in the small intestine. Further increased absorption is achieved by dissolving tablets before ingestion or usage of ASA salts (Dressman et al, 2012). Practically 100% of therapeutic aspirin doses are taken up, mostly by intestinal mucosal cells (Artursson & Karlsson, 1991; Yee 1997).
Only a few percent of ASA- remain unchanged, the rest is hydrolyzed to salicylate (ST). The major route of ST catabolism is conjugation with glycine to form salicyluric acid. This accounts for 20–65% of the products. Conjugation to glucuronides (ester and ether) removes up to 42% of ST. Finally, a minor part also gets hydroxylated by cytochromes (Hutt et al, 1986).
R-HSA-175474 Assembly Of The HIV Virion Virion assembly packages all the components required for infectivity. These steps include two copies of the positive sense genomic viral RNA, cellular tRNALys, the viral envelope (Env) protein, the Gag polyprotein, and the three viral enzymes: protease (PR), reverse transcriptase (RT), and integrase (IN). The viral enzymes are packaged as domains within the Gag-Pro-Pol polyprotein.
R-HSA-9609736 Assembly and cell surface presentation of NMDA receptors N-methyl-D-aspartate receptors (NMDARs) are tetramers that consist of two GluN1 (GRIN1) subunits and two subunits that belong to either the GluN2 (GRIN2) subfamily (GluN2A, GluN2B, GluN2C and GluN2D) or the GluN3 (GRIN3) subfamily (GluN3A and GluN3B). The GluN2/GluN3 subunits in the NMDA tetramer can either be identical, constituting an NMDA di-heteromer (di-heterotetramer), which consists of two subunit types, GluN1 and one of GluN2s/GluN3s, or they can be two different GluN2/GluN3 proteins, constituting an NMDA tri-heteromer (tri-heterotetramer), which consists of three subunit types, GluN1 and two of GluN2s/GluN3s (Monyer et al. 1992, Wafford et al. 1993, Sheng et al. 1994, Dunah et al. 1998, Perez-Otano et al. 2001, Chatterton et al. 2002, Matsuda et al. 2002, Yamakura et al. 2005, Nilsson et al. 2007, Hansen et al. 2014, Kaiser et al. 2018, Bhattacharya et al. 2018, Bhattacharya and Traynelis 2018).
NMDA tetramers assemble in the endoplasmic reticulum and traffic to the plasma membrane as part of transport vesicles (McIlhinney et al. 1998, Perez-Otano et al. 2001). NMDA receptor subunits undergo N-glycosylation, which impacts their trafficking from the endoplasmic reticulum to the plasma membrane. Trafficking efficiency may vary among different subunits of NMDARs (Lichnereva et al. 2015). Mechanistic details, such as glycosyl transferases involved and the type of sugar side chains added, are not known.
As there are eight splicing isoforms of GluN1, four different GluN2 and two different GluN3 proteins, many different combinations of NMDAR subunits are possible, but only a handful of distinct NMDAR receptors have been experimentally confirmed and functionally studied. The composition of NMDARs affects trafficking, spatial (including synaptic) localization, ligand preference, channel conductivity and downstream signal transmission. Prevalent NMDARs differ at different stages of neuronal development, in different regions of the central nervous system, and at different levels of neuronal activity. For review, please refer to Lau and Zukin 2007, Traynelis et al. 2010, Paoletti et al. 2013, Pérez-Otaño et al. 2016, Iacobucci and Popescu 2017.
R-HSA-9820962 Assembly and release of respiratory syncytial virus (RSV) virions A mature virion of the respiratory syncytial virus (RSV) consists of the ribonucleoprotein complex (RNP) surrounded by the protein matrix and a lipid bilayer envelope. The RNP is composed of the genomic negative sense single-stranded (-ssRNA) that is tightly associated with the N protein (nucleoprotein) and the RNA-dependent RNA polymerase complex (RdRP). The RdRP consists of the L protein subunit (large polymerase subunit), the P protein subunit (phosphoprotein polymerase cofactor), and the M2-1 protein, which acts as a transcription processivity factor. The matrix consists of the M (matrix) protein. The M2-1 protein serves as the bridge between the RNP and the M protein. The matrix supports the viral envelope. The viral envelope contains three embedded viral proteins: fusion protein (F), attachment protein (G), and a small hydrophobic protein (SH). The M protein associates with the cytoplasmic domain of the F protein. The SH protein forms a pentameric ion channel in the viral envelope and is thought to delay apoptosis of infected cells. The assembly and budding of RSV virions primarily occurs at the apical surface of ciliated airway epithelial cells where viral filaments containing RNPs form. The budding of RSV virions requires interactions between viral proteins, host cytoskeletal proteins, and membrane. For review, please refer to Shaikh and Crowe 2013, and Battles and McLellan 2019.
Based on the findings that P, M, and F proteins are sufficient for formation of viral‑like particles (VLPs), P protein, particularly its highly phosphorylated serine/threonine‑rich region between amino acids 39 and 57 that likely interacts with M and/or F proteins, may play an important role in the assembly (Meshram and Oomens 2019).
R-HSA-168316 Assembly of Viral Components at the Budding Site Following synthesis on membrane-bound ribosomes, the three viral integral membrane proteins, HA (hemagglutinin), NA (neuraminidase) and M2 (ion channel) enter the host endoplasmic reticulum (ER) where all three are folded and HA and NA are glycosylated. Subsequently HA is assembled into a trimer. HA, NA and M2 are transported to the Golgi apparatus where cysteine residues on HA and M2 are palmitoylated. Furin cleaves HA into HA1 and HA2 subunits and all three proteins are directed to the virus assembly site on the apical plasma membrane via apical sorting signals. The signals for HA and NA reside on the transmembrane domains (TMD) while the sorting signal for M2 is not yet characterized. The TMDs of HA and NA also contain the signals for lipid raft association. Lipid rafts are non-ionic detergent-resistant lipid microdomains within the plasma membrane that are rich in sphingolipids and cholesterol. Examination of purified virus particles indicates that influenza virus buds preferentially from these microdomains.
R-HSA-8963889 Assembly of active LPL and LIPC lipase complexes Lipoprotein lipase (LPL) and hepatic triacylglycerol lipase (LIPC) enzymes on the lumenal surfaces of capillary endothelia mediate the hydrolysis of triglyceride molecules in circulating lipoprotein particles.
LPL is widely expressed in the body and is especially abundant in adipocytes and skeletal and cardiac myocytes. Activation of the protein requires glycosylation, dimerization, and glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 (GPIHBP1), which delivers it to heparan sulfate proteoglycan (HSPG) associated with the plasma membrane. It is inactivated by proteolytic cleavage (Berryman & Bensadoun 1995; Sukonina et al. 2006; Young et al. 2011).
Expression of the LPL gene is transcriptionally regulated by Cyclic AMP-responsive element-binding protein 3-like protein 3 (CREB3L3), which also regulates the expression of APOA4, APOA5, APOC2, CIDEC and FGF21 (Lee et al. 2011).
Maturation of LIPC enzyme requires association with LMF1 protein (or possibly, inferred from sequence similarity, LMF2). Heparin binding stabilizes LIPC in its active dimeric form (Babilonia-Rosa & Neher 2014).
R-HSA-2022090 Assembly of collagen fibrils and other multimeric structures Collagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular space. For fibrillar collagens namely types I, II, III, V, XI, XXIV and XXVII (Gordon & Hahn 2010, Ricard-Blum 2011) secretion is concomitant with processing of the N and C terminal collagen propeptides. These processed molecules are known as tropocollagens, considered to be the units of higher order collagen structures. They form within the extracellular space via a process that can proceed spontaneously, but in the cellular environment is regulated by many collagen binding proteins such as the FACIT (Fibril Associated Collagens with Interrupted Triple helices) family collagens and Small Leucine-Rich Proteoglycans (SLRPs). The architecture formed ultimately depends on the collagen subtype and the cellular conditions. Structures include the well-known fibrils and fibres formed by the major structural collagens type I and II plus several different types of supramolecular assembly (Bruckner 2010). The mechanical and physical properties of tissues depend on the spatial arrangement and composition of these collagen-containing structures (Kadler et al. 1996, Shoulders & Raines 2009, Birk & Bruckner 2011).
Fibrillar collagen structures are frequently heterotypic, composed of a major collagen type in association with smaller amounts of other types, e.g. type I collagen fibrils are associated with types III and V, while type II fibrils frequently contain types IX and XI (Wess 2005). Fibres composed exclusively of a single collagen type probably do not exist, as type I and II fibrils require collagens V and XI respectively as nucleators (Kadler et al. 2008, Wenstrup et al. 2011). Much of the structural understanding of collagen fibrils has been obtained with fibril-forming collagens, particularly type I, but some central features are believed to apply to at least the other fibrillar collagen subtypes (Wess 2005). Fibril diameter and length varies considerably, depending on the tissue and collagen types (Fang et al. 2012). The reasons for this are poorly understood (Wess 2005).
Some tissues such as skin have fibres that are approximately the same diameter while others such as tendon or cartilage have a bimodal distribution of thick and thin fibrils. Mature type I collagen fibrils in tendon are up to 1 cm in length, with a diameter of approx. 500 nm. An individual fibrillar collagen triple helix is less than 1.5 nm in diameter and around 300 nm long; collagen molecules must assemble to give rise to the higher-order fibril structure, a process known as fibrillogenesis, prevented by the presence of C-terminal propeptides (Kadler et al. 1987). In electron micrographs, fibrils have a banded appearance, due to regular gaps where fewer collagen molecules overlap, which occur because the fibrils are aligned in a quarter-stagger arrangement (Hodge & Petruska 1963). Collagen microfibrils are believed to have a quasi-hexagonal unit cell, with tropocollagen arranged to form supertwisted, right-handed microfibrils that interdigitate with neighbouring microfibrils, leading to a spiral-like structure for the mature collagen fibril (Orgel et al. 2006, Holmes & Kadler 2006).
Neighbouring tropocollagen monomers interact with each other and are cross-linked covalently by lysyl oxidase (Orgel et al. 2000, Maki 2006). Mature collagen fibrils are stabilized by lysyl oxidase-mediated cross-links. Hydroxylysyl pyridinoline and lysyl pyridinoline cross-links form between (hydroxy) lysine and hydroxylysine residues in bone and cartilage (Eyre et al. 1984). Arginoline cross-links can form in cartilage (Eyre et al. 2010); mature bovine articular cartilage contains roughly equimolar amounts of arginoline and hydroxylysyl pyridinoline based on peptide yields. Mature collagen fibrils in skin are stabilized by the lysyl oxidase-mediated cross-link histidinohydroxylysinonorleucine (Yamauch et al. 1987). Due to the quarter-staggered arrangement of collagen molecules in a fibril, telopeptides most often interact with the triple helix of a neighbouring collagen molecule in the fibril, except for collagen molecules in register staggered by 4D from another collagen molecule. Fibril aggregation in vitro can be unipolar or bipolar, influenced by temperature and levels of C-proteinase, suggesting a role for the N- and C- propeptides in regulation of the aggregation process (Kadler et al. 1996). In vivo, collagen molecules at the fibril surface may retain their N-propeptides, suggesting that this may limit further accretion, or alternatively represents a transient stage in a model whereby fibrils grow in diameter through a cycle of deposition, cleavage and further deposition (Chapman 1989).
In vivo, fibrils are often composed from more than one type of collagen. Type III collagen is found associated with type I collagen in dermal fibrils, with the collagen III on the periphery, suggesting a regulatory role (Fleischmajer et al. 1990). Type V collagen associates with type I collagen fibrils, where it may limit fibril diameter (Birk et al. 1990, White et al. 1997). Type IX associates with the surface of narrow diameter collagen II fibrils in cartilage and the cornea (Wu et al. 1992, Eyre et al. 2004). Highly specific patterns of crosslinking sites suggest that collagen IX functions in interfibrillar networking (Wess 2005). Type XII and XIV collagens are localized near the surface of banded collagen I fibrils (Nishiyama et al. 1994). Certain fibril-associated collagens with interrupted triple helices (FACITs) associate with the surface of collagen fibrils, where they may serve to limit fibril fusion and thereby regulate fibril diameter (Gordon & Hahn 2010). Collagen XV, a member of the multiplexin family, is almost exclusively associated with the fibrillar collagen network, in very close proximity to the basement membrane. In human tissues collagen XV is seen linking banded collagen fibers subjacent to the basement membrane (Amenta et al. 2005). Type XIV collagen, SLRPs and discoidin domain receptors also regulate fibrillogenesis (Ansorge et al. 2009, Kalamajski et al. 2010, Flynn et al. 2010).
Collagen IX is cross-linked to the surface of collagen type II fibrils (Eyre et al. 1987). Type XII and XIV collagens are found in association with type I (Walchli et al. 1994) and type II (Watt et al. 1992, Eyre 2002) fibrils in cartilage. They are thought to associate non-covalently via their COL1/NC1 domains (Watt et al. 1992, Eyre 2002).
Some non-fibrillar collagens form supramolecular assemblies that are distinct from typical fibrils. Collagen VII forms anchoring fibrils, composed of antiparallel dimers that connect the dermis to the epidermis (Bruckner-Tuderman 2009). During fibrillogenesis, the nascent type VII procollagen molecules dimerize in an antiparallel manner. The C-propeptides are then removed by Bone morphogenetic protein 1 (Rattenholl et al. 2002) and the processed antiparallel dimers aggregate laterally. Collagens VIII and X form hexagonal networks and collagen VI forms beaded filament (Gordon & Hahn 2010, Ricard-Blum et al. 2011).
R-HSA-68616 Assembly of the ORC complex at the origin of replication Human ORC1 can associate with DNA origin of replication sites independently of other origin of replication complex (ORC) subunits (Hoshina et al. 2013; Eladl et al. 2021). ORC1 localizes to condensed chromosomes during early mitosis (M phase) and serves as a nucleating center for the assembly of the ORC and, subsequently, the pre-replication complex. ORC1 remains associated with late replication origins throughout late G1. Upon S phase entry, ORC1 undergoes ubiquitin-mediated degradation, leading to dissociation of the ORC from chromatin (Kara et al. 2015).
Most human replication origins contain guanine (G)-rich sequences which may form G-quadruplex (G4) structures (Besnard et al. 2012) and these G4 structures may mediate the recognition of replication origins by ORC1 (Hoshina et al. 2013; Eladl et al. 2021). Besides binding to nucleosome-free replication origin DNA, ORC1 interacts with neighboring nucleosomes (Hizume et al. 2013), in particular with nucleosomes containing histone H4 dimethylated at lysine 21 (H4K20me2 mark), which is enriched at replication origins. Binding of ORC1 to H4K20me2 facilitates ORC1 binding to replication origins and ORC chromatin loading (Kuo et al. 2012, Zhang et al. 2015).
ORC1 binding sites are universally associated with transcription start sites (TSSs) of coding and non-coding RNAs. Replication origins associated with moderate to high transcription level TSSs (belonging to coding RNAs) fire in early S phase, while those associated with low transcription level TSSs (belonging to non-coding RNAs) fire throughout the S phase (Dellino et al. 2013).
ORC2 forms a heterodimer with ORC3, which is a prerequisite for the association of ORC5 and, subsequently, ORC4 (Ranjan and Gossen 2006; Siddiqui and Stillman 2007). ORC1 binds to the ORC(2-5) complex in the nucleus to form a stable ORC(1-5) complex (Radichev et al. 2006; Ghosh et al. 2011). ORC1 is necessary for the association of the ORC(2-5) complex to chromatin (Radichev et al. 2006). The ORC(2-5) complex exhibits a tightly autoinhibited conformation, with the winged-helix domain (WHD) of ORC2 completely blocking the central DNA-binding channel. Binding of ORC1 remodels the WHD of ORC2, moving it away from the central channel and partially relieving the autoinhibition (Cheng et al. 2020, Jaremko et al. 2020). ORC6 associates with the ORC(1-5) complex to form the ORC(1-6) complex (Ghosh et al. 2011). The association of ORC6 with the ORC(1-5) complex is weak and it frequently does not co-immunoprecipitate with the other ORC(1-5) subunits. ORC4 is the only ORC(1-5) subunit that was shown to directly bind to ORC6 (Radichev et al. 2006). Some ORC6 mutations reported in Meier-Gorlin syndrome were shown to interfere with ORC6 incorporation into the ORC (Balasov et al. 2015).
R-HSA-9683439 Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) In a sequence of ten reactions, mature non-structural proteins (nsp) generated by cleavage of the SARS-CoV-1 pp1a / pp1ab polyproteins are assembled to form a replication – transcription complex (Fung & Liu 2019; Kirchdoerfer & Ward 2019).
R-HSA-9694271 Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
In a sequence of ten reactions, mature non-structural proteins (nsp) generated by cleavage of the SARS-CoV-1 pp1a / pp1ab polyproteins are assembled to form the RTC (Fung & Liu 2019; Kirchdoerfer & Ward 2019). Six of these ten steps have been directly studied in SARS-CoV-2: binding of nsp7 to nsp8 (Gao et al. 2020, Li et al. 2020, Konkolova et al. 2020), recruitment of nsp12 (Gao et al. 2020, Hillen et al. 2020, Li et al. 2020, Yin et al. 2020), binding of nsp14 and nsp10 (Li et al. 2020), binding of nsp13 to nsp12 (Chen et al. 2020) formation of the nsp15 hexamer (Kim et al. 2020), and binding of nsp16 to nsp12 (Li et al. 2020, Rosas-Lemus et al. 2020, Viswanathan et al. 2020).
R-HSA-68867 Assembly of the pre-replicative complex DNA replication pre-initiation in eukaryotic cells begins with the formation of the pre-replicative complex (pre-RC) during the late M phase and continues in the G1 phase of the mitotic cell cycle, a process also called DNA replication origin licensing. The association of initiation proteins (ORC, Cdc6, Cdt1, Mcm2-7) with the origin of replication in both S. cerevisiae and humans has been demonstrated by chromatin immunoprecipitation experiments. In S. cerevisiae, pre-replicative complexes are assembled from late M to G1. In mammalian cells as well, pre-replicative complexes are assembled from late M to G1, as shown by biochemical fractionation and immunostaining. There are significant sequence similarities among some of the proteins in the pre-replicative complex. The ORC subunits Orc1, Orc4 and Orc5 are homologous to one another and to Cdc6. The six subunits of the Mcm2-7 complex are homologous to one another. In addition, Orc1, Orc4, Orc5, Cdc6, and the Mcm2-7 subunits, are members of the AAA+ superfamily of ATPases. Since the initial identification of these pre-RC components other factors that participate in this complex have been found, including Cdt1 in human, Xenopus, S. pombe, and S. cerevisiae cells.
R-HSA-390471 Association of TriC/CCT with target proteins during biosynthesis TRiC has broad recognition specificities, but in the cell it interacts with only a defined set of substrates (Yam et al. 2008). Many of its substrates that are targeted during biosynthesis are conserved between mammals and yeast (Yam et al. 2008).
R-HSA-210455 Astrocytic Glutamate-Glutamine Uptake And Metabolism In astrocytic glutamate-glutamine cycle, the excess glutamate released by the pre-synaptic neuron in the synaptic cleft is transported into the astrocyte by a family glutamate transporters called the excitatory amino acid transporters 1 and 2, EAAT1 and EAAT2. Astrocytes carrying these transporters exist in close apposition to the synapse to clear excess glutamate to prevent excessive activation of neurons and hence neuronal death. Glutamate in astrocytes is converted to glutamine by glutamine synthetase. Glutamine is then transported into the extracellular space by system N transporters. The glutamate in the extracellular space is available for neuronal uptake.
R-HSA-4608870 Asymmetric localization of PCP proteins One of the hallmarks of the Planar Cell Polarity pathway is the asymmetric distribution of proteins on opposite membranes of a single cell. In Drosophila, Stbm and Pk (homologues to the human VANGL1/2 and PRICKLE1/2/3) colocalize opposite Fz, Dsh and Dgo (FZD, DVL, and ANKRD6, respectively). The two complexes antagonize each other, with Fz:Dsh:Dgo acting to promote signaling downstream of Dsh, while the Stbm:Pk complex restricts this signaling (reviewed in Seifert and Mlodzik, 2007). Asymmetric localization of some PCP proteins is also seen in vertebrates (Montcouquiol et al, 2003, 2006; Wang et al, 2006, Narimatsu et al, 2009) although the patterns of localization differ from that of flies. The details of how localization is established and how the asymmetrical distribution of proteins is translated into gross morphological processes remain to be fully elucidated.
R-HSA-9754706 Atorvastatin ADME Atorvastatin (ATV, brand name Lipitor), is a lipid-lowering drug of the statin class of medications. It inhibits the endogenous production of cholesterol in the liver, thereby lowering abnormally high cholesterol and lipid levels, and ultimately reducing the risk of cardiovascular disease. Statins inhibit the enzyme hydroxymethylglutaryl-coenzyme A reductase (HMGCR) , which catalyzes the critical step in cholesterol biosynthesis of HMG-CoA conversion to mevalonic acid. Statins are the most commonly prescribed medication for treating abnormal lipid levels (Malhotra & Goa 2001). ATV and its hydroxy-metabolites collectively inhibit HMGCR to reduce circulating low-density lipoprotein cholesterol.
ATV is transported in the blood almost exclusively bound to plasma proteins (>98%) (Lennernas 2003), and is subject to pre‑systemic clearance at the gastrointestinal tract and to first‑pass hepatic clearance, which explains its low systemic bioavailability (~12%) (Garcia et al. 2003). Organic anion transporters OATP1B1, OATP1B3 and OATP2B1, encoded by SLCO1B1, SLCO1B3, and SLCO2B1, respectively are expressed on the sinusoidal membrane of hepatocytes and can facilitate the liver uptake of drugs such as ATV (Kalliokoski & Niemi 2009).
In hepatocytes (and to a lesser extent, the GI tract), ATV can be hydroxylated by cytochrome P450 3A4 (CYP3A4) to hydroxy-metabolites, or undergo lactonization via an unstable acyl glucuronide intermediate to ATV lactone (ATVL) mediated by UGT1A3 and 1A1. ATVL may also be hydroxylated by CYP3A4 to hydroxylactone-metabolites. The lactone metabolites are inactive against HMGCR, but can be hydrolyzed via paraoxonases (PONs) to their corresponding hydroxy acids, which are active against HMGCR. Elimination of ATV and its metabolites is principally biliary with apparently no significant enterohepatic recirculation. Half-life (t1/2) is approximately 14 h for atorvastatin and 20–30 h for its metabolites (Schachter 2005).
R-HSA-9694614 Attachment and Entry This COVID-19 event has been created by a combination of computational inference (see https://reactome.org/documentation/inferred-events) from SARS-CoV-1 data and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
Coronavirus replication is initiated by the binding of S protein to the cell surface receptor(s). The S protein is composed of two functional domains, S1 (bulb) which mediates receptor binding and S2 (stalk) which mediates membrane fusion. Specific interaction between S1 and the cognate receptor triggers a drastic conformational change in S2, leading to fusion between the virus envelope and the cellular membrane and release of the viral nucleocapsid into the host cell cytosol. Receptor binding is the major determinant of the host range and tissue tropism for a coronavirus. Some human coronaviruses (HCoVs) have adopted cell surface enzymes as receptors, angiotensin converting enzyme 2 (ACE2) for SARS-CoV-2 (reviewed by Jackson et al, 2022), SARS-CoV-1, and HCoV NL63. The receptor-bound S protein is activated by cleavage into S1 and S2, mediated by one of two host proteases, the endosomal cysteine protease cathepsin L and another trypsin like serine protease. Type II transmembrane serine proteases TMPRSS2 and TMPRSS11D have also been implicated in the activation of S protein of SARS-CoV-2. Host factors may play additional roles in viral entry (not annotated here). Valosin containing protein (VCP) contributes by a poorly understood mechanism to the release of coronavirus from early endosomes. Host factors may also restrict the attachment and entry of HCoV.
R-HSA-9678110 Attachment and Entry Coronavirus replication is initiated by the binding of S protein to the cell surface receptor(s). The S protein is composed of two functional domains, S1 (bulb) which mediates receptor binding and S2 (stalk) which mediates membrane fusion. Specific interaction between S1 and the cognate receptor triggers a drastic conformational change in S2, leading to fusion between the virus envelope and the cellular membrane and release of the viral nucleocapsid into the host cell cytosol. Receptor binding is the major determinant of the host range and tissue tropism for a coronavirus. Some human coronaviruses (HCoVs ) have adopted cell surface enzymes as receptors, angiotensin converting enzyme 2 (ACE2) for SARS-CoV-1 and HCoV NL63. The receptor-bound S protein is activated by cleavage into S1 and S2, mediated by one of two of two host proteases, the endosomal cysteine protease cathepsin L and another trypsin like serine protease. Type II transmembrane serine proteases TMPRSS2 and TMPRSS11D have also been implicated in the activation of S protein of SARS-CoV-1. Host factors may play additional roles in viral entry (not annotated here). Valosin containing protein (VCP) contributes by a poorly understood mechanism to the release of coronavirus from early endosomes. Host factors may also restrict the attachment and entry of HCoV. Some interferon inducible transmembrane proteins (IFITMs) exhibited broad spectrum antiviral functions against various RNA viruses including SARS-CoV-1 while others may facilitate HCoV entry into host cells (Fung & Liu 2019).
R-HSA-162791 Attachment of GPI anchor to uPAR The mature form of urokinase plasminogen activator receptor (uPAR) is attached to the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor (Ploug et al. 1991). As nascent uPAR polypeptide moves into the lumen of the endoplasmic reticulum, it is attacked by a transamidase complex that cleaves the uPAR polypeptide after residue 305, releasing the carboxyterminal peptide of uPAR and replacing it with an acylated GPI moiety. In a second step, the GPI moiety is deacylated, yielding a uPAR-GPI conjugate that can be efficiently transported to the Golgi apparatus.
R-HSA-3371568 Attenuation phase Attenuation of the heat shock transcriptional response occurs during continuous exposure to intermediate heat shock conditions or upon recovery from stress (Abravaya et al. 1991). The attenuation phase of HSF1 cycle involves the transcriptional silencing of HSF1 bound to HSE, the release of HSF1 trimers from HSE and dissociation of HSF1 trimers to monomers. HSF1-driven heat stress associated transcription was shown to depend on inducible and reversible acetylation of HSF1 at Lys80, which negatively regulates DNA binding activity of HSF1 (Westerheide SD et al. 2009). In addition, the attenuation of HSF1 activation takes place when enough HSP70/HSP40 is produced to saturate exposed hydrophobic regions of proteins damaged as a result of heat exposure. The excess HSP70/HSP40 binds to HSF1 trimer, which leads to its dissociation from the promoter and conversion to the inactive monomeric form (Abravaya et al. 1991; Shi Y et al. 1998). Interaction of HSP70 with the transcriptional corepressor repressor element 1-silencing transcription factor corepressor (CoREST) assists in terminating heat-shock response (Gomez AV et al. 2008). HSF1 DNA-binding and transactivation activity were also inhibited upon interaction of HSF1-binding protein (HSBP1) with active trimeric HSF1(Satyal SH et al. 1998).
R-HSA-174084 Autodegradation of Cdh1 by Cdh1:APC/C Cdh1 is degraded by the APC/C during in G1 and G0. This auto-regulation may contribute to reducing the levels of Cdh1 levels during G1 and G0 (Listovsky et al., 2004).
R-HSA-349425 Autodegradation of the E3 ubiquitin ligase COP1 COP1 is one of several E3 ubiquitin ligases responsible for the tight regulation of p53 abundance. Following DNA damage, COP1 dissociates from p53 and is inactivated by autodegradation via a pathway involving ATM phosphorylation of COP1 on Ser(387), autoubiquitination and proteasome mediated degradation. Destruction of COP1 results in abrogation of the ubiquitination and degradation of p53 (Dornan et al., 2006).
R-HSA-177539 Autointegration results in viral DNA circles In this pathway, the viral integration machinery uses a site within the viral DNA as an integration target. This results in a covalent rearrangment of the viral DNA. The resulting DNA forms are not substrates for integration.
It has been suggested that the cellular BAF protein binds to viral DNA and diminishes autointegration by coating and condensing the viral DNA, thereby making it a less efficient integration target.
R-HSA-9612973 Autophagy Autophagy is an intracellular degradation process that is triggered by cellular stresses. There are three primary types of autophagy - macroautophagy, chaperone-mediated autophagy (CMA) and late endosomal microautophagy. Despite being morphologically distinct, all three processes culminate in the delivery of cargo to the lysosome for degradation and recycling (Parzych KR et al, 2014). In macroautophagy a double membrane compartment sequesters the cargo and delivers it to the lysosome. Chaperones are used to deliver specific cargo proteins to the lysosome in CMA. In microautophagy invaginations of the endosomal membrane are used to capture cargo from the cytosol. Autophagy can target a wide range of entities ranging from bulk proteins and lipids to cell organelles and pathogens giving rise to several subclasses such as mitophagy, lipophagy, xenophagy, etc. (Shibutani ST 2014 et al).
R-HSA-422475 Axon guidance Axon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, which senses the guidance cues in the environment through guidance cue receptors and responds by undergoing cytoskeletal changes that determine the direction of axon growth.
Guidance cues present in the surrounding environment provide the necessary directional information for the trip. These extrinsic cues have been divided into attractive or repulsive signals that tell the growth cone where and where not to grow.
Genetic and biochemical studies have led to the identification of highly conserved families of guidance molecules and their receptors that guide axons. These include netrins, Slits, semaphorins, and ephrins, and their cognate receptors, DCC and or uncoordinated-5 (UNC5), roundabouts (Robo), neuropilin and Eph. In addition, many other classes of adhesion molecules are also used by growth cones to navigate properly which include NCAM and L1CAM.
For review of axon guidance, please refer to Russel and Bashaw 2018, Chedotal 2019, Suter and Jaworski 2019).
Axon guidance cues and their receptors are implicated in cancer progression (Biankin et al. 2012), where they likely contribute to cell migration and angiogenesis (reviewed by Mehlen et al. 2011).
R-HSA-193634 Axonal growth inhibition (RHOA activation) p75NTR can also form a receptor complex with the Nogo receptor (NgR). Such complexes mediates axonal outgrowth inhibitory signals of MDGIs (myelin-derived growth-inhibitors), such as Nogo66, myelin-associated glycoprotein (MAG), and oligodendrocyte myelin glycoprotein (OMGP).
R-HSA-209563 Axonal growth stimulation Complex formation between p75NTR and RHOA can leads to inhibition of RHOA activity and axonal growth.
R-HSA-9748787 Azathioprine ADME Thiopurines were originally developed for cancer treatment in the early 1950s, with 6-mercaptopurine (6MP) being the first thiopurine approved by the FDA for the treatment of leukaemia, just two years after its discovery. Azathioprine (AZA), a prodrug of 6MP, was developed by the addition of a nitroimidazol group a few years later to bypass the high first-pass metabolism of 6MP due to oxidation in intestinal cells by xanthine oxidase (XDH). AZA is a thiopurine prodrug, and its pharmacological action is based on the release of the active metabolite 6-mercaptopurine (6MP) which is further metabolised to pharmacoligically active 6-thioguanine nucleotides (6-TGNs). These 6-TGNs achieve their cytotoxic effects in one of four ways
1. Incorporation of 6-thioguanosine triphosphate (6TGTP) into RNA
2. Incorporation of 6-thiodeoxyguanosine triphosphate (6TdGTP) into DNA
3. Inhibition of de novo purine synthesis by methylmercaptopurine nucleotides such as methylthioinosine monophosphate (meTIMP)
4. Inhibition of RAC1 by 6TGTP which induces apoptosis in activated T-cells.
While AZA has been supplanted as an antitumour drug, it remains useful as an immunosuppressant antimetabolite drug indicated to treat rheumatoid arthritis, Crohn's disease, ulcerative colitis, cancer and to prevent rejection in kidney transplant patients (Axelrad et al. 2016, Tominaga et al. 2021).
The molecular steps of AZA metabolism are described in this pathway (Cuffari et al. 1996, Dubinsky 2004). Briefly, oral AZA is rapidly converted to 6MP. Initial 6MP metabolism occurs along competing catabolic (XDH, TPMT) and anabolic (HPRT) enzymatic pathways. Once formed, 6-thiosine 5′-monophosphate (6TIMP) is further metabolized by inosine monophosphate dehydrogenase (IMPDH) and guanosine monophosphate synthetase (GMPS) to 6-thioguanosine 5′monophosphate (6TGMP). 6TGMP is then converted to the pharmacologically-active di- and tri- derivatives by their respective kinases.
R-HSA-5250924 B-WICH complex positively regulates rRNA expression The B-WICH complex is a large 3 Mdalton complex containing SMARCA5 (SNF2H), BAZ1B (WSTF), ERCC6 (CSB), MYO1C (Nuclear myosin 1c), SF3B1, DEK, MYBBP1A, and DDX21 (Cavellan et al. 2006, Percipalle et al. 2006, Vintermist et al. 2001, Sarshad et al. 2013, Shen et al. 2013, reviewed in Percipalle and Farrants 2006). B-WICH is found at active rRNA genes as well as at 5S rRNA and 7SL RNA genes. B-WICH appears to remodel chromatin and recruit histone acetyltransferases that modify histones to transcriptionally active states.
R-HSA-5620922 BBSome-mediated cargo-targeting to cilium The BBSome is a stable complex consisting of 7 Bardet-Biedl proteins (BBS1, 2, 4, 5, 7, 8 and 9) and BBIP10 that has roles in promoting IFT and trafficking proteins to the cilum (Blacque et al, 2004; Nachury et al, 2007; Loktev et al, 2008; Jin et al, 2010; reviewed in Sung and Leroux 2013). The BBSome is the primary effector of ARL6/BBS3, a small GTPase that binds the BBSome in complex with associated membrane proteins that are destined for the ciliary membrane (Jin et al, 2010; Nachury et al, 2007; Zhang et al, 2011; Seo et al, 2011). Components of the BBSome are enriched in TPR and beta-propeller motifs and are thought to form a linear coat on membranes that functions with ARL6 to target proteins to the cilium (Jin et al, 2010; reviewed in Nachury et al, 2010).
R-HSA-9859138 BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV The mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKDH) complex catalyzes the reactions of alpha-ketoisocaproate, alpha-keto beta-methylvalerate, or alpha-ketoisovalerate with CoA and NAD+ to form isovaleryl-CoA, alpha-methylbutyryl-CoA, or isobutyryl-CoA, respectively, and CO2 and NADH (Chuang and Shih, 2001). While bovine and microbial BCKD complexes have been characterized most extensively (Reed and Hackert 1990), structural studies of individual components and subcomplexes of human BCKD have confirmed their structures and roles in the overall oxidative decarboxylation process and have related these features to the disruptive effects of mutations on branched-chain amino acid metabolism in vivo: E1a and E1b components (AEvarsson et al., 2000), E2 (Chang et al., 2002), and E3 (DLD)(Brautigam et al., 2005). In addition, structural studies have confirmed the lipoylation of lysine residue 105 in E2 protein (Chang et al., 2002) and the loss of an aminoterminal mitochondrial transport sequence from mature E3 protein (Brautigam et al., 2005). Loss of mitochondrial transport sequences from proteins E1a, E1b, and E2 has been demonstrated by sequence analysis (Wynn et al., 1999). Defects in E1a, E1b, and E2 may cause so-called maple syrup urine disease, with accumulation of the abovementioned amino acids and their corresponding keto acids, leading to encephalopathy and progressive neurodegeneration (MSUD, MIM:248600; reviewed in Xu et al., 2020). Defects in the E3 (DLD) subunit, shared with other ketoacid dehydrogenase complexes, typically present as neonatal lactic acidosis due to lack of pyruvate dehydrogenase activity although symptoms of BCKDH deficiency may also be present.
R-HSA-9024909 BDNF activates NTRK2 (TRKB) signaling Signaling by the neurotrophin receptor tyrosine kinase NTRK2 (TRKB) can be activated by binding to brain-derived neurotrophic factor (BDNF), which functions as a ligand for NTRK2 (Soppet et al. 1991, Klein et al. 1991). Binding to BDNF triggers NTRK2 dimerization (Ohira et al. 2001) and trans-autophosphorylation of NTRK2 dimers on conserved tyrosine residues in the cytoplasmic tail of the receptor (Guiton et al. 1994, Minichiello et al. 1998, McCarty and Feinstein 1999). Phosphorylated tyrosine residues subsequently serve as docking sites for recruitment of effector proteins that trigger downstream signaling cascades.
R-HSA-111453 BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members Bcl-2 interacts with tBid (Yi et al. 2003), BIM (Puthalakath et al. 1999), PUMA (Nakano and Vousden 2001), NOXA (Oda et al. 2000), BAD (Yang et al. 2005), BMF (Puthalakath et al. 2001), resulting in inactivation of BCL2. Binding of BCL2 to tBID inhibits BID-induced cytochrome C release and apoptosis (Yi et al. 2003). BH3 only proteins associate with and inactivate anti-apoptotic BCL-XL.
R-HSA-1368108 BMAL1:CLOCK,NPAS2 activates circadian gene expression As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) and BMAL1:NPAS2 (ARNTL:NPAS2) heterodimers bind to sequence elements (E boxes) in the promoters of target genes and enhance transcription (Gekakis et al. 1998, reviewed in Munoz and Baler 2003).
R-HSA-9824439 Bacterial Infection Pathways Bacterial infection pathways aim to capture molecular mechanisms of human bacterial diseases related to bacterial adhesion to and invasion of human host cells and tissues, toxigenicity (interaction of bacterially-produced toxins with the human host), and evasion of the host's immune defense.
Bacterial infection pathways currently include some metabolic processes mediated by intracellular Mycobacterium tuberculosis, the actions of clostridial, anthrax, and diphtheria toxins, and the entry of Listeria monocytogenes into human cells.
Clostridial toxins are produced by anaerobic spore-forming gram-positive bacilli of the genus Clostridium. Clostridium tetani causes tetanus, Clostridium botulinum causes botulism, Clostridium perfringens causes gas gangrene, and Clostridium difficile causes pseudomembranous colitis. The anthrax toxin is produced by the aerobic spore-forming gram-positive bacilli of the species Bacillus anthracis. The diphtheria toxin is produced by aerobic nonspore-forming gram-positive bacilli of the species Corynebacterium diphtheriae infected with the bacterial virus corynephage beta. Enterobacterial toxins are produced by pathogenic strains of Enterobacteriaceae, aerobic gram-negative bacilli that are part of normal intestinal flora, such as Escherichia coli.
Mycobacterium tuberculosis bacteria are acid-fast, aerobic, nonspore-forming bacilli that cause tuberculosis, a wide-spread disease that usually affects the lungs.
Listeria monocytogenes bacteria are aerobic nonspore-forming gram-positive bacilli that cause listeriosis.
R-HSA-73884 Base Excision Repair Of the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of the numerous individual glycosylases, each of which recognizes and removes a specific modified base(s) from DNA. BER is responsible for the repair of the most prevalent types of DNA lesions, oxidatively damaged DNA bases, which arise as a consequence of reactive oxygen species generated by normal mitochondrial metabolism or by oxidative free radicals resulting from ionizing radiation, lipid peroxidation or activated phagocytic cells. BER is a two-step process initiated by one of the DNA glycosylases that recognizes a specific modified base(s) and removes that base through the catalytic cleavage of the glycosydic bond, leaving an abasic site without disruption of the phosphate-sugar DNA backbone. Subsequently, abasic sites are resolved by a series of enzymes that cleave the backbone, insert the replacement residue(s), and ligate the DNA strand. BER may occur by either a single-nucleotide replacement pathway or a multiple-nucleotide patch replacement pathway, depending on the structure of the terminal sugar phosphate residue. The glycosylases found in human cells recognize "foreign adducts" and not standard functional modifications such as DNA methylation (Lindahl and Wood 1999, Sokhansanj et al. 2002).
R-HSA-73929 Base-Excision Repair, AP Site Formation Base excision repair is initiated by DNA glycosylases that hydrolytically cleave the base-deoxyribose glycosyl bond of a damaged nucleotide residue, releasing the damaged base (Lindahl and Wood 1999, Sokhansanj et al. 2002).
R-HSA-210991 Basigin interactions Basigin is a widely expressed transmembrane glycoprotein that belongs to the Ig superfamily and is highly enriched on the surface of epithelial cells. Basigin is involved in intercellular interactions involved in various immunologic phenomena, differentiation, and development, but a major function of basigin is stimulation of synthesis of several matrix metalloproteinases. Basigin also induces angiogenesis via stimulation of VEGF production.
Basigin has an extracellular region with two Ig-like domains of which the N-term Ig-like domain is involved in interactions. It undergoes interactions between basigin molecules on opposing cells or on neighbouring cells. It also interacts with a variety of other proteins like caveolin-1, cyclophilins, integrins and annexin II that play important roles in cell proliferation, energy metabolism, migration, adhesion and motion, especially in cancer metastasis.
R-HSA-1461957 Beta defensins Humans have 38 beta-defensin genes plus 9-10 pseudogenes (details available on the HGNC website at http://www.genenames.org/genefamilies/DEFB). Many beta-defensins are encoded by recently duplicated genes giving rise to identical transcripts. Nomenclature is confusing and currently in transition. Uniprot recommended names are used throughout this pathway.
Many beta-defensins show expression that correlates with infection (Sahl et al. 2005, Pazgier et al. 2006). All so far characterized beta-defensins, i.e. beta-defensin 1 (hBD1), 4A (hBD2), 103 (hBD3), 104 (hBD4), 106 (hBD6), 118 (hBD18) and 128 (hBD28) have antimicrobial properties (Pazgier et al. 2006). For beta-defensins 4A, 103 and 118 (hBD2, 3, and 18) this has been shown to correlate with membrane permeabilization effects (Antcheva et al. 2004, Sahl et al. 2005, Yenugu et al. 2004). Electrostatic interaction and disruption of microbial membranes is widely believed to the primary mechanism of action for beta-defensins. Two models explain how membrane disruption takes place, the 'pore model' which postulates that beta-defensins form transmembrane pores in a similar manner to alpha-defensins, and the 'carpet model', which suggests that beta-defensins act as detergents. Beta-defensins contain 6 conserved cysteine residues that in beta-defensins 1, 4A and 103 (hBD1-3) are experimentally confirmed to be cross-linked 1-5, 2-4, 3-6. The canonical sequence for beta-defensins is x2-10Cx5-6(G/A)xCX3-4Cx9-13Cx4-7CCxn. Structurally they are similar to alpha-defensins but with much shorter pre-regions. Though dimerization of some beta-defensins has been reported this is not the case for all and it is unclear whether it is required for function. The majority of functional studies have focused on beta-defensin 103 (hBD3), which has the most significant antimicrobial activity at physiological salt concentrations (Harder et al. 2001). Beta-defensin 103 is highly cationic with a net charge of +11 e0. It exhibits broad-spectrum antimicrobial activity against gram-positive bacteria and some gram-negative bacteria (Harder et al. 2001), though some species are highly resistant (Sahly et al. 2003). Sensitivity correlates with lipid composition of the membrane, with more negatively-charged lipids correlating with larger beta-defensin 103-induced changes in membrane capacitance (Bohling et al. 2006). Though membrane disruption is widely believed to be the primary mechanism of action of beta-defensins they have other antimicrobial properties, such as inhibition of cell wall biosynthesis (Sass et al. 2010), and chemoattractant effects (Yang et al. 1999, Niyonsaba et al. 2002, 2004). The chemotactic activity of beta-defensins 1, 4A and 103 (hBD1-3) for memory T cells and immature DCs is mediated through binding to the chemokine receptor CCR6 and probably another unidentified Gi-coupled receptor (Yang et al. 1999, 2000).
Like defensins, the human cathelicidin LL37 peptide is rich in positively-charged residues (Lehrer & Ganz 2002).
Expression of certain beta-defensins can be induced in response to various signals, such as bacteria, pathogen-associated molecular patterns (PAMPs), or proinflammatory cytokines (Ganz 2003, Yang et al. 2004). Like the alpha-defensins, copy number variation has been reported for DEFB4, DEFB103 and DEFB104 with individuals having 2-12 copies per diploid genome. In contrast DEFB1 does not show such variation but exhibits a number of SNPs (Hollox et al. 2003, Linzmier & Ganz 2005).
R-HSA-77352 Beta oxidation of butanoyl-CoA to acetyl-CoA The seventh and final pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid butanoyl-CoA and at the third step produces acetoacetyl-CoA, which can be used to generate 2 acetyl-CoA molecules or can be turned toward the synthesis of ketone bodies pathway. Four enzymatic steps are required starting with SCAD CoA dehydrogenase (Short Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD). The final enzymatic step, creating two acetyl-CoA molecules requires a specific ketoacyl-CoA thiolase, Acetoacetyl-CoA thiolase.
R-HSA-77346 Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA The fourth pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid decanoyl-CoA and produces octanoyl-CoA. Four enzymatic steps are required starting with MCAD CoA dehydrogenase (Medium Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein. Note that the 3-hydroxyacyl-CoA dehydrogenase activity of SCHAD is not actually limited to short chain fatty acids, in fact SCHAD has a broad substrate specificity.
R-HSA-77350 Beta oxidation of hexanoyl-CoA to butanoyl-CoA The sixth pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid hexanoyl-CoA and produces butanoyl-CoA. Four enzymatic steps are required starting with SCAD CoA dehydrogenase (Short Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein.
R-HSA-77310 Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA The third pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid lauroyl-CoA and produces decanoyl-CoA. Four enzymatic steps are required starting with LCAD CoA dehydrogenase (Long Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein. Note that the 3-hydroxyacyl-CoA dehydrogenase activity of SCHAD is not actually limited to short chain fatty acids, in fact SCHAD has a broad substrate specificity.
R-HSA-77285 Beta oxidation of myristoyl-CoA to lauroyl-CoA The second pass through the beta-oxidation spiral starts with the saturated fatty acid myristoyl-CoA (from the first swing through the beta oxidation spiral) and produces lauroyl-CoA. Four enzymatic steps are required starting with LCAD CoA dehydrogenase (Long Chain) activity, followed by three enzymatic steps, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, and ketoacyl-CoA thiolase activities, all present in the mitochondrial membrane associated trifunctional protein.
R-HSA-77348 Beta oxidation of octanoyl-CoA to hexanoyl-CoA The fifth pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid octanoyl-CoA and produces hexanoyl-CoA. Four enzymatic steps are required starting with MCAD CoA dehydrogenase (Medium Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein.
R-HSA-77305 Beta oxidation of palmitoyl-CoA to myristoyl-CoA This first pass through the beta-oxidation spiral starts with the saturated fatty acid palmitoyl-CoA and produces myristoyl-CoA. Four enzymatic steps are required, starting with VLCAD CoA dehydrogenase (Very Long Chain) activity, followed by three enzymatic steps, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, and ketoacyl-CoA thiolase activities, all present in the mitochondrial membrane associated trifunctional protein.
R-HSA-3858494 Beta-catenin independent WNT signaling Humans and mice have 19 identified WNT proteins that were originally classified as either 'canonical' or 'non-canonical' depending upon whether they were able to transform the mouse mammary epithelial cell line C57MG and to induce secondary axis formation in Xenopus (Wong et al, 1994; Du et al, 1995). So-called canonical WNTs, including Wnt1, 3, 3a and 7, initiate signaling pathways that destabilize the destruction complex and allow beta-catenin to accumulate and translocate to the nucleus where it promotes transcription (reviewed in Saito-Diaz et al, 2013). Non-canonical WNTs, including Wnt 2, 4, 5a, 5b, 6, 7b, and Wnt11 activate beta-catenin-independent responses that regulate many aspects of morphogenesis and development, often by impinging on the cytoskeleton (reviewed in van Amerongen, 2012). Two of the main beta-catenin-independent pathways are the Planar Cell Polarity (PCP) pathway, which controls the establishment of polarity in the plane of a field of cells, and the WNT/Ca2+ pathway, which promotes the release of intracellular calcium and regulates numerous downstream effectors (reviewed in Gao, 2012; De, 2011).
R-HSA-196299 Beta-catenin phosphorylation cascade Degradation of beta-catenin is initiated following amino-terminal serine/threonine phosphorylation. Phosphorylation of B-catenin at S45 by CK1 alpha primes the subsequent sequential GSK-3-mediated phosphorylation at Thr41, Ser37 and Ser33 (Amit et al., 2002 ; Lui et al., 2002).
R-HSA-9915355 Beta-ketothiolase deficiency ACAT1 is a mitochondrial enzyme that plays a role in metabolism of ketone bodies and isoleucine catabolism (Fukao et al, 1991; Haapalainen et al, 2007; reviewed in Fukao et al, 2019). As part of isoleucine catabolism in the mitochondria, ACAT1 catalyzes the thiolytic degradation of alpha-methylacetoacetyl-CoA to propionyl-CoA and acetyl-CoA (Fukao et al, 1991; Happalainen et al, 2007). Mutations in ACAT1 that affect protein stability and enzymatic activity are associated with beta-ketothiolase deficiency, also known as alpha-methylacetoacetic aciduria, an inborn error of metabolism that is identified by the presence of isoleucine intermediate metabolites in bodily fluids (Daum et al, 1973; Schutgens et al, 1982; Fukao et al, 1991; Fukao et al, 1992; Wakazono et al, 1995; Fukao et al, 1998; Sakurai et al, 2007; reviewed in Korman, 2006; Fukao et al, 2019). Neonatal onset is rare and most affected individuals present between 6 and 18 months with metabolic acidosis, lethargy, vomiting and sometimes coma (reviewed in Korman, 2006). As with other disorders of branched-chain metabolism, there is not a direct correlation between genotype and severity of phenotypic presentation (reviewed in Korman, 2006).
R-HSA-389887 Beta-oxidation of pristanoyl-CoA Pristanoyl-CoA, generated in the peroxisome by alpha-oxidation of dietary phytanic acid, is further catabolized by three cycles of peroxisomal beta-oxidation to yield 4,8-dimethylnonanoyl-CoA, acetyl-CoA and two molecules of propionyl-CoA. These molecules in turn are converted to carnitine conjugates, which can be transported to mitochondria (Wanders and Waterham 2006, Verhoeven et al. 1998, Ferdinandusse et al. 1999).
R-HSA-390247 Beta-oxidation of very long chain fatty acids Linear fatty acids containing more than 18 carbons are broken down by beta-oxidation in peroxisomes to yield acetyl-CoA and medium chain-length fatty acyl CoA's such as octanoyl-CoA (Wanders and Waterham 2006).
R-HSA-425381 Bicarbonate transporters Respiratory oxidation in the mitochondria produces carbon dioxide (CO2) as a waste product. CO2 is in equilibrium with bicarbonate (HCO3-) and is the body's central pH buffering system. HCO3- is charged so cannot move across membranes unaided. The bicarbonate transport proteins move bicarbonate across the membrane. There are 14 genes which encode these transport proteins in mammals. Applying the Human Genome Organization's sytematic nomenclature to human genes, the bicarbonate transporters belong to the SLC4A and SLC26A families. Within SLC4A, there are two distinct subfamilies, functionally corresponding to the electroneutral Cl-/HCO3- exchangers and Na+-coupled HCO3- co-transporters (Romero MF et al, 2004; Cordat E and Casey JR, 2009).
R-HSA-194068 Bile acid and bile salt metabolism In a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily. Newly synthesized bile salts are secreted into the bile and released into the small intestine where they emulsify dietary fats (Russell 2003). About 95% of the bile salts in the intestine are recovered and returned to the liver (Kullak-Ublick et al. 2004; Trauner and Boyer 2002). The major pathway for bile salt synthesis in the liver begins with the conversion of cholesterol to 7alpha-hydroxycholesterol. Bile salt synthesis can also begin with the synthesis of an oxysterol - 24-hydroxycholesterol or 27-hydroxycholesterol. In the body, the initial steps of these two pathways occur in extrahepatic tissues, generating intermediates that are transported to the liver and converted to bile salts via the 7alpha-hydroxycholesterol pathway. These extrahepatic pathways contribute little to the total synthesis of bile salts, but are thought to play important roles in extrahepatic cholesterol homeostasis (Javitt 2002).
R-HSA-2173782 Binding and Uptake of Ligands by Scavenger Receptors Scavenger receptors bind free extracellular ligands as the initial step in clearance of the ligands from the body (reviewed in Ascenzi et al. 2005, Areschoug and Gordon 2009, Nielsen et al. 2010). Some scavenger receptors, such as the CD163-haptoglobin system, are specific for only one ligand. Others, such as the SCARA receptors (SR-A receptors) are less specific, binding several ligands which share a common property, such as polyanionic charges.
Brown and Goldstein originated the idea of receptors dedicated to scavenging aberrant molecules such as modified low density lipoprotein particles (Goldstein et al. 1979) and such receptors have been shown to participate in pathological processes such as atherosclerosis. Based on homology, scavenger receptors have been categorized into classes A-H (reviewed in Murphy et al. 2005).
R-HSA-173107 Binding and entry of HIV virion HIV enters cells by fusion at the cell surface, that results in a productive infection. The envelope (Env) protein of HIV mediates entry. Env is composed of a surface subunit, gp120, and a transmembrane subunit, gp41, which assemble as heterotrimers on the virion surface.The trimeric, surface gp120 protein (SU) on the virion engages CD4 on the host cell, inducing conformational changes that promote binding to select chemokine receptors CCR5 and CXCR4.
The sequential interplay between SU, CD4 and chemokine coreceptors prompts a conformational change in the transmembrane gp41. This coiled coil protein, assembled as a trimer on the virion membrane, springs open to project three peptide fusion domains that 'harpoon' the lipid bilayer of the target cell. A hairpin structure (also referred to as a "coiled coil bundle") is subsequently formed when the extracellular portion of gp41 collapses, and this hairpin formation promotes the fusion of virion and target cell membranes by bringing them into close proximity. Virion and target cell membrane fusion leads to the release of HIV viral cores into the cell interior.
R-HSA-4411364 Binding of TCF/LEF:CTNNB1 to target gene promoters The genes regulated by beta-catenin and TCF/LEF are involved in a diverse range of functions in cellular proliferation, differentiation, embryogenesis and tissue homeostasis, and include transcription factors, cell cycle regulators, growth factors, proteinases and inflammatory cytokines, among others (reviewed in Vlad et al, 2008). A number of WNT signaling components are themselves positively or negatively regulated targets of TCF/LEF-dependent transcription, establishing feedback loops to enhance or restrict signaling (see for instance, Khan et al 2007; Chamorro et al, 2005; Roose et al, 1999; Lustig et al, 2002). Other than a few of these general feedback targets (e.g. Axin2), most target genes are cell- and/or tissue-specific. A list of WNT/beta-catenin-dependent target genes is maintained at http://www.standford.edu/group/nusselab/cgi-bin/wnt/target_genes.
R-HSA-141333 Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB Human monoamine oxidases (MAOs) are flavin-containing enzymes that are present on the outer mitochondrial membrane and act on primary, secondary and tertiary amines. In contrast to the P450s which have a large number of isozymes, MAOs number only two isozymes, MAO-A and MAO-B. These gene products share over 70% sequence identity, are approximately 59KDa in size and have overlapping substrates (for example dopamine, tryamine and tryptamine) but each form also has distinct substrate specificities. MAO-A (primary type in fibroblasts) preferentially oxidises serotonin (5-Hydroxytryptamine) whereas MAO-B (primary type in platelets) prefers phenylethylamine. MAOs are of particular clinical interest because of the use of MAO inhibitors (MAOI) as antidepressants or in the treatment of neurodegenerative diseases Benedetti 2001, Beedham 1997).
R-HSA-211859 Biological oxidations All organisms are constantly exposed to foreign chemicals every day. These can be man-made (drugs, industrial chemicals) or natural (alkaloids, toxins from plants and animals). Uptake is usually via ingestion but inhalation and transdermal routes are also common.
The very nature of many chemicals that make them suitable for uptake by these routes, in other words their lipophilicty (favours fat solubility) is also the main reason organisms have developed mechanisms that convert them to hydrophilic (favours water solubility) compounds which are readily excreted via bile and urine. Otherwise, lipophilic chemicals would accumulate in the body and overwhelm defense mechanisms. This process is called biotransformation and is catalyzed by enzymes mainly in the liver of higher organisms but a number of other organs have considerable ability to process xenobiotica such as kidneys, gut and lungs. As well as xenobiotics, many endogenous compounds are commonly eliminated by this process.
This mechanism is of ancient origin and a major factor for its development in animals is plants. Most animals are plant eaters and thus are subject to a huge variety of chemical compounds which plants produce to stop themselves being eaten. This complex set of enzymes have several features which make them ideal for biotransformation;
(1) metabolites of the parent chemical are usually made more water soluble so it favours rapid excretion via bile and urine
(2) the enzymes possess broad and overlapping specificity to be able to deal with newly exposed chemicals
(3) metabolites of the parent generally don't have adverse biological effects.
In the real world however, all these criteria have exceptions. Many chemicals are transformed into reactive metabolites. In pharmacology, the metabolites of some parent drugs exert the desired pharmacological effect but in the case of polycyclic aromatic hydrocarbons (PAHs), which can undergo epoxidation, it results in the formation of an electrophile which can attack proteins and DNA.
Metabolism of xenobiotica occurs in several steps called Phase 1 (functionalization) and Phase 2 (conjugation). To improve water solubility, a functional group is added to or exposed on the chemical in one or more steps (Phase 1) to which hydrophilic conjugating species can be added (Phase 2). Functional groups can either be electrophilic (epoxides, carbonyl groups) or nucleophilic (hydroxyls, amino and sulfhydryl groups, carboxylic groups) (see picture).
Once chemicals undergo functionalization, the electrophilic or nucleophilic species can be detrimental to biological systems. Electrophiles can react with electron-rich macromolecules such as proteins, DNA and RNA by covalent interaction whilst nucleophiles have the potential to interact with biological receptors. That's why conjugation is so important as it mops up these potentially reactive species.
Many chemicals, when exposed to certain metabolizing enzymes can induce those enzymes, a process called enzyme induction. The effect of this is that these chemicals accelerate their own biotransformation and excretion. The reverse is also true where some chemicals cause enzyme inhibition. Some other factors that alter enzyme levels are sex, age and genetic predisposition. Between species, there can be considerable differences in biotransformation ability which is a problem faced by drug researchers interpreting toxicological results to humans.
R-HSA-2466712 Biosynthesis of A2E, implicated in retinal degradation Lipofuscin is a yellow-brown pigment grain composed mainly of lipids but also sugars and certain metals. Accumulation of lipofuscin is associated with degenerative diseases such as Alzheimer's disease, Parkinson's disease, chronic obstructive pulmonary disease and retinal macular degeneration.
A prominent component of lipofuscin in retinal pigment epithelial (RPE) cells is the bisretinoid A2E (di-retinoid-pyridinium-ethanolamine), the end-product of the condensation of 2 molecules of all-trans-retinal (atRAL) and phosphatidylethanolamine (PE) in photoreceptor outer disc membranes. Once formed, A2E is phagocytosed, together with outer segments (Kevany & Palczewski 2010), to RPE where it accumulates. There is no evidence as yet to indicate that A2E can be catabolised (Sparrow et al. 2012, Sparrow et al. 2010). A simplified biosynthetic pathway for A2E is described here.
R-HSA-9018676 Biosynthesis of D-series resolvins The D-series resolvins (RvD1-6) are biosynthesised from the precursor ω-3 fatty acid docosahexaenoic acid (DHA), either via aspirin-triggered cylcooxygenase catalysis (17(R) AT-RvDs) or via the lipoxygenase pathway (described here) forming the epimeric 17(S)-RvD1-6 resolvins (Serhan et al. 2014, Bannenberg & Serhan 2010).
R-HSA-9018677 Biosynthesis of DHA-derived SPMs Docosahexaenoic acid (DHA), a major ω-3 polyunsaturated fatty acid (PUFA) found in fish oil is the source of D-series resolvins (RvDs), one of the specialized proresolving mediators (SPMs) that show potent anti-inflammatory and pro-resolving actions (Molfino et al. 2017). The biosynthesis of RvDs occurs mainly during the process of inflammation when endothelial cells interact with leukocytes. Dietary DHA circulates in plasma or is present in cellular membranes as it can easily integrate into membranes. On injury or infection, DHA moves with edema into the tissue sites of acute inflammation where it is converted to exudate RvDs to interact with local immune cells (Kasuga et al. 2008). The initial transformation of DHA by aspirin-acetylated cyclooxygenase-2 or cyclooxygenase-mediated catalysis can produce stereospecific D-resolvins (18(R)- or 18(S)-RvDs respectively). Combinations of oxidation, reduction and hydrolysis reactions determine the type of D-resolvin formed (RvD1-6) (Serhan et al. 2002, Serhan & Petasis 2011, Serhan et al. 2014).
R-HSA-9026395 Biosynthesis of DHA-derived sulfido conjugates The polyunsaturated fatty acid (PUFA) ω-3 docosahexaenoic acid (DHA) is a precursor for the production of novel sulfido-peptide conjugated mediators with structural similarity to the cysteinyl-leukotrienes and with novel biological properties. They are produced from specialised proresolving mediators (SPMs) in human macrophages and are termed protectin conjugates in tissue regeneration (PCTR), resolvin conjugates in tissue regeneration (RCTR), and maresin conjugates in tissue regeneration (MCTR) because they regulate mechanisms in inflammation resolution as well as tissue regeneration (Dalli et al. 2014, 2015, 2016, Serhan et al. 2017). Their biosynthesis is descibed in this section.
R-HSA-9018683 Biosynthesis of DPA-derived SPMs Docosapentaenoic acid (DPA), a C22:5 long-chain ω3 or ω6 polyunsaturated fatty acid (PUFA), is found in algal and fish oils, created via linoleic acid metabolism and is a metabolite in DHA metabolism. It can be acted upon by lipoxygenases to produce mono-, di- and tri-hydroxy derivatives in neutrophils and macrophages. These DPA derivatives are another branch of the specialised proresolving mediators (SPMs) produced from long-chain fatty acids which have anti-inflammatory properties, even though mechanisms of their anti-inflammatory action have not been fully elucidated (Bannenberg & Serhan 2010, Dangi et al. 2010, Vik et al. 2017, Hansen et al. 2017).
The biosynthesis of SPMs derived from the two isomers of DPA, DPAn-6 (cis-4,7,10,13,16-docosapentaenoic acid) and DPAn-3 (cis-7,10,13,16,19-docosapentaenoic acid), is described here. The only difference between the two isomers is the position of the first double bond; ω-3 for DPAn-3 and ω-6 for DPAn-6. The products of these isomers were characterised by analogy in structure and action to docosahexaenoic acid (DHA)-derived and eicosapentaenoic acid (EPA)-derived resolvins, protectins and maresins (Serhan et al. 2002, Bannenberg & Serhan 2010, Serhan et al. 2015).
R-HSA-9025094 Biosynthesis of DPAn-3 SPMs The polyunsaturated fatty acid (PUFA) ω-3 cis-7,10,13,16,19-docosapentaenoic acid (DPAn-3) is an intermediate in the biosynthesis of docosahexaenoic acid (DHA) from eicosapentaenoic acid (EPA) and is also a precursor for the production of novel bioactive mediators. The proposed biosynthesis of specialised proresolving mediators (SPMs) derived from DPAn-3 is described here (Dalli et al. 2013, Hansen et al. 2017, Vik et al. 2017). The products of the ω-3 isomer were characterised based on DHA (docosahexaenoic acid) derived resolvins, protectins and maresins (Serhan et al. 2002, Bannenberg & Serhan 2010). The same biosynthetic route as DHA-derived SPMs is probably how DPAn-3 products are also formed (Dalli et al. 2013).
R-HSA-9026403 Biosynthesis of DPAn-3-derived 13-series resolvins Neutrophils adherence to the vascular endothelium is a critical and early event in the innate immune response to injury or invading pathogens (Sadik et al. 2011). Studies of the lipid fraction from neutrophil-endothelial cell cultures resulted in the discovery of four novel specialised proresolving mediators (SPMs) (Dalli et al. 2015). Results from LC/MS-MS metabololipidomics using a chemically-synthesised precursor (13(R)-hydroxy-DPAn-3) identified four mediators generated from this precursor.
The polyunsaturated fatty acid (PUFA) ω-3 cis-7,10,13,16,19-docosapentaenoic acid (DPAn-3) is an intermediate in the biosynthesis of docosahexaenoic acid (DHA) from eicosapentaenoic acid (EPA) and is also a precursor for the production of novel bioactive mediators. DPAn-3 can form this precursor when acted upon by cyclooxygenase 2 (COX2). Thus these novel 13-series resolvins (RvT1-4) originate from DPAn-3 (Primdahl et al. 2016). In E. coli-infected mice, RvTs accelerated resolution of inflammation and increased survival. RvTs also regulated human and mouse phagocyte responses, stimulating bacterial phagocytosis and regulating inflammasome components (Dalli et al. 2015). The biosynthetic routes of these RvTs are described here. RvT formation requires neutrophil-endothelial cell interaction and is thought to proceed via a two-step process; COX2 hydroxylates DPAn-3 to 13(R)-DPAn-3 which trafficks to adjacent neutrophils where it is lipoxygenated by 5-lipoxygenase to RvT1-4 (Vik et al. 2017).
R-HSA-9026290 Biosynthesis of DPAn-3-derived maresins The polyunsaturated fatty acid (PUFA) ω-3 cis-7,10,13,16,19-docosapentaenoic acid (DPAn-3) is an intermediate in the biosynthesis of docosahexaenoic acid (DHA) from eicosapentaenoic acid (EPA) and is also a precursor for the production of novel bioactive mediators.The proposed biosynthesis of maresins derived from DPAn-3 is described here (Dalli et al. 2013, Hansen et al. 2017, Vik et al. 2017). 12-lipoxygenase oxygenates DPAn-3 to its 14(S) hydroperoxy epimer from which maresins are formed via a combination of oxygenation, reduction and hydrolysis reactions (Dalli et al. 2013). The products of the ω-3 isomer were characterised based on docosahexaenoic acid (DHA)-derived maresins (Serhan et al. 2015) and were demonstrated to have similar potent systemic anti-inflammatory and tissue protective actions as DHA-derived specialised proresolving mediators (SPMs) (Dalli et al. 2013). The same biosynthetic route as DHA-derived SPMs is probably how DPAn-3 products are also formed (Dalli et al. 2013).
R-HSA-9026286 Biosynthesis of DPAn-3-derived protectins and resolvins The polyunsaturated fatty acid (PUFA) ω-3 cis-7,10,13,16,19-docosapentaenoic acid (DPAn-3) is an intermediate in the biosynthesis of docosahexaenoic acid (DHA) from eicosapentaenoic acid (EPA) and is also a precursor for the production of novel bioactive mediators. The proposed biosynthesis of resolvins and protectins derived from DPAn-3 is described here (Dalli et al. 2013, Hansen et al. 2017, Vik et al. 2017). 15-lipoxygenase oxygenates DPAn-3 to its 17(S) hydroperoxy epimer from which resolvins and protectins are formed via a combination of oxygenation, reduction and hydrolysis reactions (Dalli et al. 2013). The products of the ω-3 isomer were characterised based on docosahexaenoic acid (DHA)-derived resolvins and protectins (Serhan et al. 2002) and were demonstrated to have similar potent systemic anti-inflammatory and tissue protective actions as DHA-derived specialised proresolving mediators (SPMs) (Dalli et al. 2013). The same biosynthetic route as DHA-derived SPMs is probably how DPAn-3 products are also formed (Dalli et al. 2013).
R-HSA-9025106 Biosynthesis of DPAn-6 SPMs The biosynthesis of specialised proresolving mediators (SPMs) derived from the ω-6 isomer of DPA, DPAn-6 (cis-4,7,10,13,16-docosapentaenoic acid) is described here (Dangi et al. 2010). The products of the ω-6 isomer were characterised by analogy in structure and action to docosahexaenoic acid (DHA)-derived and eicosapentaenoic acid (EPA)-derived resolvins (Serhan et al. 2002, Bannenberg & Serhan 2010).
R-HSA-9023661 Biosynthesis of E-series 18(R)-resolvins Eicosapentaenoic acid (EPA), a major ω-3 polyunsaturated fatty acid (PUFA) found in fish oil is the source of E-series resolvins, one of the specialized proresolving mediators (SPMs) that show potent anti-inflammatory and pro-resolving actions (Molfino et al. 2017, Calder 2017). The initial transformation of EPA can be mediated by either cytochrome P450s or aspirin-acetylated cyclooxygenase-2, resulting in 18(R)- and 18(S)-stereospecific E-resolvins. Combinations of oxidation, reduction and hydrolysis reactions determine the type of E-resolvin formed (RvE1, RvE2 or RvE3) (Serhan & Petasis 2011). Aspirin acetylation of cyclooxygenase isoforms results in changed activities. Acetylation of cyclooxygenase-1 results in its inhibition and thereby halting production of inflammatory mediators. However, acetylation of cyclooxygenase-2 transforms its enzyme activity from a cyclooxygenase to a lipoxygenase, thereby blocking prostaglandin biosynthesis and, additionally, initiating the production of SPMs (Arita et al. 2005, Kyriakopoulos et al. 2017). The biosynthesis of 18(R) E-resolvins is described here.
R-HSA-9018896 Biosynthesis of E-series 18(S)-resolvins Eicosapentaenoic acid (EPA), a major ω-3 polyunsaturated fatty acid (PUFA) found in fish oil is the source of E-series resolvins, one of the specialized proresolving mediators (SPMs) that show potent anti-inflammatory and pro-resolving actions (Molfino et al. 2017, Calder 2017). The initial transformation of EPA can be mediated by either cytochrome P450s and/or aspirin-acetylated cyclooxygenase-2, resulting in stereospecific formation of 18(R)- and 18(S) E-resolvins. Combinations of oxidation, reduction and hydrolysis reactions determine the type of E-resolvin formed (RvE1, RvE2 or RvE3) (Serhan & Petasis 2011). Aspirin acetylation of cyclooxygenase isoforms results in changed activities. Acetylation of cyclooxygenase-1 results in its inhibition and thereby halting production of inflammatory mediators. However, acetylation of cyclooxygenase-2 transforms its enzyme activity from a cyclooxygenase to a lipoxygenase, thereby blocking prostaglandin biosynthesis and, additionally, initiating the production of SPMs (Arita et al. 2005, Kyriakopoulos et al. 2017). The biosynthesis of 18(S) E-resolvins is described here.
R-HSA-9018679 Biosynthesis of EPA-derived SPMs Eicosapentaenoic acid (EPA), a major ω-3 polyunsaturated fatty acid (PUFA) found in fish oil is the source of E-series resolvins (RvEs), one of the specialized proresolving mediators (SPMs) that show potent anti-inflammatory and pro-resolving actions (Molfino et al. 2017). The biosynthesis of RvEs occurs mainly during the process of inflammation when endothelial cells interact with leukocytes. EPA, circulating in plasma or released/mobilised from damaged cellular membranes on injury or infection, moves with edema into the tissue sites of acute inflammation where it is converted to exudate RvEs to interact with local immune cells (Kasuga et al. 2008). The initial transformation of EPA by aspirin-acetylated cyclooxygenase 2- and/or cytochrome P450-mediated catalysis can produce stereospecific resolvins (18(R)- or 18(S)-RvEs). Combinations of oxidation, reduction and hydrolysis reactions determine the type of resolvin formed (RvE1, RvE2 or RvE3) (Serhan et al. 2000, 2002, Serhan & Petasis 2011, Maehre et al. 2015).
R-HSA-2142700 Biosynthesis of Lipoxins (LX) Lipoxins A4 (LXA4) and B4 (LXB4), structurally characterized from human neutrophils incubated with 15-hydroperoxy-eicosatetraenoic acid (15-HpETE), each contain three hydroxyl moieties and a conjugated tetraene. The third hydroxyl of LXA4 is positioned at C-6, and of LXB4 at C-14. The action of arachidonate 5-lipoxygenase (ALOX5), in concert with an arachidonate 12-lipoxygenase (ALOX12) or arachidonate 15-lipoxygenase (ALOX15) activity, has been shown to produce lipoxins by three distinct pathways. Neutrophil ALOX5 can produce and secrete leukotriene A4 (LTA4) that is taken up by platelets, where it is acted upon by ALOX12 to form lipoxins. Likewise, ALOX15s can generate either 15-hydroperoxy-eicosatetraenoic acid (15-HpETE) or 15-hydro-eicosatetraenoic acid (15-HETE) that can be taken up by monocytes and neutrophils, where highly expressed ALOX5 uses it to generate lipoxins. Finally, aspirin acetylated prostaglandin G/H synthase 2 (PTGS2), rendered unable to synthesize prostaglandins, can act as a 15-lipoxygenase. This leads to the formation of 15R-HETE and culminates in creation of epi-lipoxins, which have altered stereochemistry at the C-15 hydroxyl but similar biological potency (Chiang et al. 2006, Buczynski et al. 2009, Vance & Vance 2008, Stsiapanava et al. 2017).
R-HSA-9020265 Biosynthesis of aspirin-triggered D-series resolvins The D-series resolvins (RvD1-6) are biosynthesised from the precursor ω-3 fatty acid docosahexaenoic acid (DHA), either via the lipoxygenase pathway (17(S)-RvDs) or via aspirin-triggered cylcooxygenase catalysis (described here) forming the epimeric 17(R)-RvD1-6 resolvins (Serhan et al. 2014, Bannenberg & Serhan 2010).
R-HSA-9027604 Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives Electrophilic oxo-derivatives of ω-3 polyunsaturated fatty acids (ω-3 PUFAs) are generated in macrophages and neutrophils in response to inflammation and oxidative stress to promote the resolution of inflammation. Being electrophilic, these derivatives reversibly bind to nucleophilic residues on target proteins (thiolates of cysteines and amino groups of histidine and lysine), triggering the activation of cytoprotective pathways. These include the Nrf2 antioxidant response, the heat shock response and the peroxisome proliferator activated receptor γ (PPARγ) and suppressing the NF-κB proinflammatory pathway (Cipollina 2015). Thus, these electrophilic derivatives transduce anti-inflammatory actions rather than suppress the production of pro-inflammatory arachidonic acid metabolites. An oxo-derivative of EPA has been shown to ablate leukemia stem cells in mice, which may represent a novel chemoprotective action for some oxo-derivatives (Hedge et al. 2011, Finch et al. 2015). In humans, dietary supplementation with ω-3 PUFAs has been reported to increase the formation of oxo-derivatives (Yates et al. 2014). The enzymes cyclooxygenases (COX), lipoxygenases (LOs) and cytochromes P450s, acting alone or in concerted transcellular biosynthesis, initially form epoxy or hydroxy intermediates of ω-3 PUFAs docosahexaenoic acid (DHA), docosapentaenoic acid (DPAn-3) and eicosapentaenoic acid (EPA) before these are further oxidised to electrophilic α,β-unsaturated keto-derivatives by cellular dehydrogenases.
R-HSA-9026762 Biosynthesis of maresin conjugates in tissue regeneration (MCTR) Resolution of inflammation is carried out by endogenous mediators termed specialised proresolving mediators (SPMs). Macrophages are central to the acute inflammatory response, governing both initiation and resolution phases, depending on the macrophage subtype activated. Human macrophages involved in resolution produce a family of bioactive peptide-conjugated mediators called maresin conjugates in tissue regeneration (MCTR). These mediators stimulate human phagocytotic functions, promote the resolution of bacterial infections, counterregulate the production of proinflammatory mediators and promote tissue repair and regeneration (Dalli et al. 2016). The proposed biosynthetic pathway is as follows. The maresin epoxide intermediate 13(S),14(S)-epoxy-MaR (13(S),14(S)-epoxy-docosahexaenoic acid) can be converted to MCTR1 (13(R)-glutathionyl, 14(S)-hydroxy-docosahexaenoic acid) by LTC4S and GSTM4. MCTR1 can be converted to MCTR2 (13(R)-cysteinylglycinyl, 14(S)-hydroxy-docosahexaenoic acid) by γ-glutamyl transferase (GGT). Finally, a dipeptidase can cleave the cysteinyl-glycinyl bond of MCTR2 to give MCTR3 (13(R)-cysteinyl, 14(S)-hydroxy-docosahexaenoic acid) (Dalli et al. 2016, Serhan et al. 2017).
R-HSA-9027307 Biosynthesis of maresin-like SPMs Maresin-like mediators MaR-L1, Mar-L2 and 14,21-dihydroxy docosahexaenoic acids are normally synthesized by leukocytes, platelets and macrophages, via the pathways described here. Impaired production of these specialised proresolving mediators (SPMs) in diabetic skin wounds is associated with impaired macrophage function and delayed or absent wound healing (Brem & Tomic-Canic 2007, Boniakowski et al 2017). Macrophages play critical roles in wound healing by mechanisms as yet unknown. They are active in both the initiation (M1 macrophage phenotype) and the resolution (M2 macrophage phenotype) of inflammatory processes. In a pathological state, the switch from the M1 phenotype macrophage to the M2 phenotype macrophage may be delayed or fail to occur, which can result in chronic low-grade inflammation. This macrophage phenotype skewing toward an inflammatory phenotype has been implicated in the pathogenesis of type 2 diabetes (T2D) and the non-healing of diabetic wounds (Boniakowski et al 2017, Pradhan et al. 2009).
Administration of maresin-like SPMs to diabetic mice with induced wounds have been shown to act as autocrine/paracrine factors in restoring reparative functions of macrophages (Hong et al. 2014, Tian et al. 2011a, 2011b, Lu et al. 2010, Hellman et al. 2012).
R-HSA-9018682 Biosynthesis of maresins Maresins 1 and 2 (MaR1 and MaR2) are derived through the action of lipoxygenase 12 on the ω-3 fatty acid docosahexaenoic acid (DHA). MaRs are mainly produced by macrophages hence the derivation of the name from MAcrophage mediator RESolving INflammation. MaR1 exhibits potent anti-inflammatory, pro-resolving, analgesic and wound healing activities. Major cellular targets for the actions of MaR1 are vascular smooth muscle (VSM) cells and vascular endothelial cells. In these cells MaR1 attenuates the adhesion of monocytes to the endothelium induced by TNF-alpha. Maresin 1 also inhibits the production of reactive oxygen species by both VSM and endothelial cells. The major mechanism through which MaR1 exerts these effects is through down-regulation of the transcription factor, nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB). MaR2 has been shown to reduce neutrophil infiltration and to enhance macrophage-mediated phagocytosis of dead and dying cells, a process termed efferocytosis. Two related structures, the maresin-like mediators (MaR-L1 and MaR-L2), are generated when the maresins produced by macrophages are released and acted upon by leukocytes and platelets (Hong et al. 2014). These, together with 14,21-dihydroxy-DHAs, rescue the reparative function of diabetes-impaired macrophages in diabetic wound healing (Hong et al. 2014, Tian et al. 2011, Boniakowski et al. 2017).
R-HSA-9026766 Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) Activated human macrophages and PMNs are able to produce 17-series sulfido-conjugated specialised proresolving mediators (SPMs) that are able to resolve acute inflammation and promote tissue regeneration. The ω-3 polyunsaturated fatty acid docosahexaenoic acid (DHA) is the source of these novel SPMs termed resolvin conjugates in tissue regeneration (RCTR) and protectin conjugates in tissue regeneration (PCTR). protectin conjugate in tissue regeneration PCTR and RCTR are thus named because they share proposed biosynthetic pathways, structural features, and biological actions with the DHA-derived protectins and resolvins (respectively) as well as displaying potent tissue-regenerative actions (Serhan et al. 2014).
The proposed biosynthetic pathways for PCTRs and RCTRs are described here (Dalli et al. 2015, Serhan et al. 2017). Mammalian lipoxygenases insert molecular oxygen predominantly in the S-stereochemistry, so the hydroxy groups at the 7- and 17-positions are presumed to be in the S-configuration. The R-containing diastereomers of these products may also possess biological activity in the resolution of inflammation and tissue regeneration but they are not described here.
R-HSA-9018681 Biosynthesis of protectins Docosahexaenoic acid (DHA), a major ω-3 polyunsaturated fatty acid (PUFA) found in fish oil is the source of protectins (PDs), one of the specialized proresolving mediators (SPMs) that show potent anti-inflammatory and pro-resolving actions (Molfino et al. 2017, Balas & Durand 2016). The switch from synthesis of pro-inflammatory eicosanoids, such as the prostaglandins and the thromboxanes, to the pro-resolving lipoxins, resolvins and protectins, occurs via induction of the 15-lipoxygenase enzyme.
Protectin, identified as (N)PD1 (N signifies neuroprotectin when produced in neural tissues) is derived from DHA through the actions of 15-lipoxygenase then enzymatic hydrolysis. Aspirin can also trigger the formation of epimeric protectin (AT-PD1) (Serhan et al. 2015). An additional protectin (DX) is formed through the sequential actions of two lipoxygenase reactions. The biosynthesis of these protectins is described here (Balas & Durand 2016, Balas et al. 2014, Serhan et al. 2014, Serhan et al. 2015).
R-HSA-9018678 Biosynthesis of specialized proresolving mediators (SPMs) A host’s normal protective response to tissue injury or pathogenic infection is acute inflammation. The condition of acute inflammation is created by the release of pro-inflammatory lipid mediators such as leukotrienes (LTs) and prostaglandins (PGs) that launch a series of signaling cascades to destroy invading pathogens and to repair damaged tissue (Libby 2007). The potent chemotactic agent leukotriene B4 (LTB4) promotes the recruitment of neutrophils (PMNs) to inflamed tissues, while the prostaglandins E2 and D2 (PGE2 and PGD2) further accelerate the inflammatory process. If left unchecked, the inflammatory response can initiate chronic systemic inflammatory disorders associated with cardiovascular disease, rheumatoid arthritis, periodontal disease, asthma, diabetes, inflammatory bowel disease (IBD), Alzheimer’s disease and age-related macular degeneration (AMD). The specific role by which inflammation contributes to their pathogenesis is not fully understood.
To prevent the onset of chronic inflammation, a lipid mediator class switch is thought to occur from the initial actions of pro-inflammatory lipid mediators to the anti-inflammatory and pro-resolving actions of lipoxins, resolvins, protectins and maresins (collectively called specialized proresolving mediators (SPMs)). Nanopicogram quantities of different lipid mediators are generated at different times during the evolution of the inflammatory response and these mediators coincide with distinct cellular events. The class switch activates leukocyte translational regulation of the enzymes required to produce pro-resolving lipid mediators (Levy et al. 2001). Each family of these PSMs exert specialized actions, including blocking neutrophil recruitment, promoting the recruitment and activation of monocytes, as well as mediating the nonphlogistic phagocytosis and lymphatic clearance of apoptotic neutrophils by activated macrophages (ie without inducing inflammation) and mediating tissue regeneration. Eventually, through the combined actions of these mediators, the resolution of inflammation is completed and homeostasis is reached (Serhan 2010, Bannenberg & Serhan 2010, Freire & Van Dyke 2013, Serhan et al. 2014).
SPMs are derived from polyunsaturated fatty acids (PUFAs) (Molfino et al. 2017). PUFAs of the ω-3 series are essential nutrients since they cannot be produced by humans (Duvall & Levy 2016) and are primarily found in dietary fish oils (Calder 2013) and in plants (Baker et al. 2016). The ω-3 PUFAs eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and docosapentaenoic acid (DPAn-3) circulate in the bloodstream after dietary intake and are easily incorporated into cellular membranes in a time- and dose-dependent manner (Calder 2009), as well as being present in inflammatory exudates (Kasuga et al. 2008). They can be mobilised by phospholipase A2 from cellular membranes on injury or infection when they are converted to exudate SPMs (Serhan et al. 2002) to interact with local immune cells (Kasuga et al. 2008). EPA is the source for E-series resolvins while DHA is the source for D-series resolvins, protectins, maresins and sulfido conjugates in tissue regeneration mediators (Serhan et al. 2017). The ω-6 fatty acid arachidonic acid (AA) is the source for lipoxins. ω-3 or ω-6 PUFA docosapentaenoic acids (DPAn-3 and DPAn-6) are the sources of DPA-derived resolvins, protectins and maresins (Vik et al. 2017). Aspirin can also trigger the production of epimeric SPMs via acetylated PTGS2 (prostaglandin G/H synthase, COX2) (Serhan & Chiang 2002). Combinations of oxidation, reduction and hydrolysis can generate numerous SPMs. Electrophilic oxo-derivatives of ω-3 PUFAs are a class of oxidised derivatives that are generated in macrophages and neutrophils by the actions of 5-lipoxygenase, cyclooxygenase-2 and acetylated cyclooxygenase-2, followed by dehydrogenation. Being electrophilic, oxo-derivative SPMs reversibly bind to nucleophilic residues on target proteins, triggering the activation of cytoprotective pathways (Cipollina 2015). The pathways in this section describe the biosynthesis of these SPMs.
R-HSA-446193 Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein N-linked glycosylation commences with the 14-step synthesis of a dolichol lipid-linked oligosaccharide (LLO) consisting of 14 sugars (2 core GlcNAcs, 9 mannoses and 3 terminal GlcNAcs). This pathway is highly conserved in eukaryotes, and a closely related pathway is found in many eubacteria and Archaea. Mutations in the genes associated with N-glycan precursor synthesis lead to a diverse group of disorders collectively known as Congenital Disorders of Glycosylation (type I and II) (Sparks et al. 1993). The phenotypes of these disorders reflect the important role that N-glycosylation has during development, controlling the folding and the properties of proteins in the secretory pathway, and proteins that mediate cell-to-cell interactions or timing of development.
R-HSA-196780 Biotin transport and metabolism Biotin (Btn) is an essential cofactor in a variety of carboxylation reactions (Zempleni et al. 2009). Humans cannot synthesize Btn but it is abundant in the human diet and can be taken up from the intestinal lumen by the SLC5A6 transporter. Its uptake, intracellular translocation, covalent conjugation to apoenzymes, and salvage are described here.
R-HSA-9636467 Blockage of phagosome acidification Acidification of the phagosome occurs by insertion of ATPases into the phagosomal membrane in preparation for fusion with lysosomes. The pH of phagosomes containing Mtb never drops below 6.5 due to Mtb interfering with several acidification mechanisms (Queval et al. 2017).
R-HSA-9033658 Blood group systems biosynthesis The association between blood type and disease has been studied since the beginning of the 20th Century (Anstee 2010, Ewald & Sumner 2016). Landsteiner's discovery of blood groups in 1900 was based on agglutination patterns of red blood cells when blood types from different donors were mixed (Landsteiner 1931, Owen 2000, Tan & Graham 2013). His work is the basis of routine compatibility testing and transfusion practices today. The immune system of patients receiving blood transfusions will attack any donor red blood cells that contain antigens that differ from their self-antigens. Therefore, matching blood types is essential for safe blood transfusions. Landsteiner's classification of the ABO blood groups confirmed that antigens were inherited characteristics. In the 1940s, it was established that the specificity of blood group antigens was determined by their unique oligosaccharide structures. Since then, exponential advances in technology have resulted in the identification of over 300 blood group antigens, classified into more than 35 blood group systems by the International Society of Blood Transfusion (ISBT) (Storry et al. 2016).
Blood group antigens comprise either a protein portion or oligosaccharide sequence attached on a glycolipid or glycoprotein. The addition of one or more specific sugar molecules to this oligosaccharide sequence at specific positions by a variety of glycosyltransferases results in the formation of mature blood group antigens. The genes that code for glycosytransferases can contain genetic changes that produce antigenic differences, resulting in new antigens or loss of expression. Blood group antigens are found on red blood cells (RBCs), platelets, leukocytes, and plasma proteins and also exist in soluble form in bodily secretions such as breast milk, seminal fluid, saliva, sweat, gastric secretions and urine. Blood groups are implicated in many diseases such as those related to malignancy (Rummel & Ellsworth 2016), the cardiovascular system (Liumbruno & Franchini 2013), metabolism (Meo et al. 2016, Ewald & Sumner 2016) and infection (Rios & Bianco 2000, McCullough 2014). The most important and best-studied blood groups are the ABO, Lewis and Rhesus systems. The biosynthesis of the antigens in these systems is described in this section.
R-HSA-70895 Branched-chain amino acid catabolism The branched-chain amino acids, leucine, isoleucine, and valine, are all essential amino acids (i.e., ones required in the diet). They are major constituents of muscle protein. The breakdown of these amino acids starts with two common steps catalyzed by enzymes that act on all three amino acids: reversible transamination by branched-chain amino acid aminotransferase, and irreversible oxidative decarboxylation by the branched-chain ketoacid dehydrogenase complex. Isovaleryl-CoA is produced from leucine by these two reactions, alpha-methylbutyryl-CoA from isoleucine, and isobutyryl-CoA from valine. These acyl-CoA's undergo dehydrogenation, catalyzed by three different but related enzymes, and the breakdown pathways then diverge. Leucine is ultimately converted to acetyl-CoA and acetoacetate; isoleucine to acetyl-CoA and succinyl-CoA; and valine to succinyl-CoA. Under fasting conditions, substantial amounts of all three amino acids are generated by protein breakdown. In muscle, the final products of leucine, isoleucine, and valine catabolism can be fully oxidized via the citric acid cycle; in liver they can be directed toward the synthesis of ketone bodies (acetoacetate and acetyl-CoA) and glucose (succinyl-CoA) (Neinast et al. 2019).
R-HSA-9912481 Branched-chain ketoacid dehydrogenase kinase deficiency Branched-chain ketoacid dehydrogenase kinase deficiency (BCKDKD) is a neurological disorder that arises due to mutations in branched-chain ketoacid dehydrogenase kinase (BCKDK) (Joshi et al 2006; Novarino et al, 2012; Garcia-Cazorla et al, 2014; Tangeraas et al, 2023). BCKDK is a negative regulator of the branched-chain ketoacid dehydrogenase complex (BCKDH), the enzyme responsible for oxidative decarboxylation of branched-chain amino acid derivatives. BCKDK-dependent phosphorylation of serine residues in the E1 alpha subunit of the enzyme BCKDHA inactivates the BCKDH (Popov et al, 1992; Li et al, 2004; Wynn et al, 2004).
Inactivating mutations of BCKDK are associated with impaired intellectual development, microencephaly and autism (Joshi et al 2006; Novarino et al, 2012; Garcia-Cazorla et al, 2014; Tangeraas et al, 2023). Consistent with the role of BCKDK in inhibiting BCKDH activity, inactivating mutations in BCKDK result in higher levels of BCKDH activity and reduced BCAAs in plasma, tissues and urine in mouse models, patients and cell lines (Joshi et al, 2006; Novarino et al, 2012). Symptoms of BCKDK deficiency are alleviated in mouse models by dietary supplementation with a BCAA-enriched diet (Joshi et al, 2006; Novarino et al, 2012).
R-HSA-352238 Breakdown of the nuclear lamina Activated caspases cleave nuclear lamins causing the irreversible breakdown of the nuclear lamina.
R-HSA-168302 Budding The process by which influenza virus particles bud from an infected cell is not very well understood. Accumulation of M1 at the inner leaflet of the plasma membrane is thought to be the trigger for the initiation of bud formation. This bud formation continues until the inner core of the virus is completely enveloped. Completion of the budding process requires the membrane at the base of the bud to fuse. Although M1 is thought to be the driving force for bud formation, other viral and cellular proteins have been demonstrated to affect size and shape of the virus particle. Generally, influenza virus particles are either spherical or filamentous and this characteristic morphology is genetically linked to the M segment (Bourmakina, 2003; Roberts, 1998). Host factors such as polarization and the actin cytoskeleton play a critical role in determining the shape of filamentous particles (Roberts, 1998; Simpson-Holley, 2002).
R-HSA-162588 Budding and maturation of HIV virion With the virus components precariously assembled on the inner leaflet of the plasma membrane, the host cell machinery is required for viral budding. The virus takes advantage of the host ESCRT pathway to terminate Gag polymerization and catalyze release. The ESCRT pathway is normally responsible for membrane fission that creates cytoplasm filled vesicular bodies. In this case HIV (and other viruses) take advantage of the ESCRT cellular machinery to facilitate virion budding from the host.
R-HSA-450385 Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA Butyrate Response Factor 1 (BRF1, ZFP36L1, not to be confused with transcription factor IIIB) binds AU-rich elements in the 3' region of mRNAs. After binding, BRF1 recruits exonucleases (XRN1 and the exosome) and decapping enzymes (DCP1a and DCP2) to hydrolyze the RNA. The ability of BRF1 to direct RNA degradation is controlled by phosphorylation of BRF1. Protein kinase B/AKT1 phosphorylates BRF1 at serines 92 and 203. Phosphorylated BRF1 can still bind RNA but is sequestered by binding 14-3-3 protein, preventing BRF1 from destabilizing RNA. BRF1 is also phosphorylated by MK2 at serines 54, 92, 203, and at an unknown site in the C-terminus. It is unknown if this particular phosphorylated form of BRF1 binds 14-3-3.
R-HSA-8851680 Butyrophilin (BTN) family interactions Butyrophilins (BTNs) and butyrophilin like (BTNL) molecules are regulators of immune responses that belong to the immunoglobulin (Ig) superfamily of transmembrane proteins. They are structurally related to the B7 family of co-stimulatory molecules and have similar immunomodulatory functions (Afrache et al. 2012, Arnett & Viney 2014). BTNs are implicated in T cell development, activation and inhibition, as well as in the modulation of the interactions of T cells with antigen presenting cells and epithelial cells. Certain BTNsare genetically associated with autoimmune and inflammatory diseases (Abeler Domer et al. 2014).
The human butyrophilin family includes seven members that are subdivided into three subfamilies: BTN1, BTN2 and BTN3. The BTN1 subfamily contains only the prototypic single copy BTN1A1 gene, whereas the BTN2 and BTN3 subfamilies each contain three genes BTN2A1, BTN2A2 and BTN2A3, and BTN3A1, BTN3A2 and BTN3A3, respectively (note that BTN2A3 is a pseudogene). BTN1A1 has a crucial function in the secretion of lipids into milk (Ogg et al. 2004) and collectively, BTN2 and BTN3 proteins are cell surface transmembrane glycoproteins, that act as regulators of immune responses. BTNL proteins share considerable homology to the BTN family members. The human genome contains four BTNL genes: BTNL2, 3, 8 and 9 (Abeler Domer et al. 2014).
R-HSA-5621481 C-type lectin receptors (CLRs) Pathogen recognition is central to the induction of T cell differentiation. Groups of pathogens share similar structures known as pathogen-associated molecular patterns (PAMPs), which are recognised by pattern recognition receptors (PRRs) expressed on dendritic cells (DCs) to induce cytokine expression. PRRs include archetypical Toll-like receptors (TLRs) and non-TLRs such as retinoic acid-inducible gene I (RIG-I)-like receptors, C-type lectin receptors (CLRs) and intracellular nucleotide-binding domain and leucine-rich-repeat-containing family (NLRs). PRR recognition of PAMPs can lead to the activation of intracellular signalling pathways that elicit innate responses against pathogens and direct the development of adaptive immunity.
CLRs comprises a large family of receptors which bind carbohydrates, through one or more carbohydrate recognition domains (CRDs), or which possess structurally similar C-type lectin-like domains (CTLDs) which do not necessarily recognise carbohydrate ligands. Some CLRs can induce signalling pathways that directly activate nuclear factor-kB (NF-kB), whereas other CLRs affect signalling by Toll-like receptors. These signalling pathways trigger cellular responses, including phagocytosis, DC maturation, chemotaxis, the respiratory burst, inflammasome activation, and cytokine production.
R-HSA-75102 C6 deamination of adenosine Hydrolytic deamination of adenosine leads to inosine. Ammonia is presumed to be released during this reaction.
R-HSA-5218900 CASP8 activity is inhibited Cell death triggered by extrinsic stimuli via death receptors or toll-like receptors (e.g., TLR3, TLR4) may result in either apoptosis or regulated necrosis (necroptosis) (Holler N et al. 2000; Kalai M et al. 2002; Kaiser WJ and Offermann MK 2005; Yang P et al. 2007). Caspase-8 (CASP8) is a cysteine protease, which functions as a key mediator for determining which form of cell death will occur (Kalai M et al. 2002). The proteolytic activity of a fully processed, heterotetrameric form of CASP8 in human and rodent cells is required for proapoptotic signaling and also for a cleavage of kinases RIPK1 and RIPK3, while at the same time preventing RIPK1/RIPK3-dependent regulated necrosis (Juo P et al. 1998; Lin Y et al. 1999; Holler N et al. 2000; Hopkins-Donaldson S et al. 2000). A blockage of CASP8 activity in the presence of caspase inhibitors such as Z-VAD-FMK (pan-caspase inhibitor), endogenous FLIP(S) or viral FLIP-like protein was found to switch signaling to necrotic cell death (Thome M et al. 1997; Kalai M et al. 2002; Feoktistova M et al. 2011; Sawai H 2013).
R-HSA-9662834 CD163 mediating an anti-inflammatory response High expression of the membrane protein CD163 in macrophages is a characteristic of tissues responding to inflammation elicited either by an intracellular pathogen infection (such as Mycobacterium leprae or Leishmania spp.) or due to an acute or chronic inflammatory disorder. The soluble form of this molecule, sCD163, is considered to be a potential inflammation biomarker and a therapeutic target; sCD163 is formed from the increased shedding of CD163 mediated by the tumor necrosis factor-α (TNF-α) cleaving enzyme, ADAM17 (Etzerodt & Moestrup 2013, Silva et al. 2017). The biological function of sCD163 is not yet clear, although several possible functions have been proposed: opsonization of Staphylococcus aureus, inhibition of T-cell proliferation and inhibition of tumor necrosis factor-like weak inducer of apoptosis (TWEAK) (Tran et al. 2005).
R-HSA-5621575 CD209 (DC-SIGN) signaling CD209 (also called as DC-SIGN (DC-specific intracellular adhesion molecule-3-grabbing non-integrin)) is a type II transmembrane C-type lectin receptor preferentially expressed on dendritic cells (DCs). CD209 functions as a pattern recognition receptor (PRR) that recognises several microorganisms and pathogens, contributing to generation of pathogen-tailored immune responses (Gringhuis & Geijtenbeek 2010, den Dunnen et al. 2009, Svajger et al. 2010). CD209 interacts with different mannose-expressing pathogens such as Mycobacterium tuberculosis and HIV-1 (Gringhuis et al. 2007, Geijtenbeek et al. 2000a). It also acts as an adhesion receptor that interacts with ICAM2 (intracellular adhesion molecule-2) on endothelial cells and ICAM3 on T cells (Geijtenbeek et al. 2000b,c). CD209 functions not only as an independent PRR, but is also implicated in the modulation of Toll-like receptor (TLR) signaling at the level of the transcription factor NF-kB (Gringhuis et al. 2009). CLEC7A (Dectin-1) and CD209 (DC-SIGN) signalling modulates Toll-like receptor (TLR) signalling through the kinase RAF1 that is independent of the SYK pathway but integrated with it at the level of NF-kB activation. The activation of RAF1 by CLEC7A or CD209 does not lead to activation of extracellular signal-regulated kinase 1 (ERK1)/2 or Mitogen-activated protein kinase kinase 1 (MEK1)/2 but leads to the phosphorylation and subsequent acetylation of RELA (p65). RELA phosphorylated on S276 not only positively regulates the activity of p65 through acetylation of p65, but also represses RELB activity by sequestering active RELB into inactive p65-RELB dimers that do not bind DNA (Gringhuis et al. 2007, Svajger et al. 2010, Jacque et al. 2005). RAF1-dependent signaling pathway is crucial in dectin-1 mediated immunity as it modulates both the canonical (promoting p65 phosphorylation and acetylation) and non-canonical (forming inactive p65-RELB dimers) NK-kB activation.
R-HSA-5690714 CD22 mediated BCR regulation BCR activation is highly regulated and coreceptors like CD22 (SIGLEC2) set a signalling threshold to prevent aberrant immune response and autoimmune disease (Cyster et al. 1997, Han et al. 2005). CD22 is a glycoprotein found on the surface of B cells during restricted stages of development. CD22 is a member of the receptors of the sialic acid-binding Ig-like lectin (Siglec) family which binds specifically to the terminal sequence N-acetylneuraminic acid alpha(2-6) galactose (NeuAc-alpha(2-6)-Gal) present on many B-cell glycoproteins (Powell et al. 1993, Sgroi et al. 1993). CD22 has seven immunoglobulin (Ig)-like extracellular domains and a cytoplasmic tail containing six tyrosines, three of which belong to the inhibitory immunoreceptor tyrosine-based inhibition motifs (ITIMs) sequences. Upon BCR cross-linking CD22 is rapidly tyrosine phosphorylated by the tyrosine kinase Lyn, thereby recruiting and activating tyrosine phosphatase, SHP-1 and inhibiting calcium signalling.
R-HSA-389357 CD28 dependent PI3K/Akt signaling CD28-mediated PI3K signaling plays a crucial role in augmenting T cell activation and survival. Phosphoinositide 3-kinases (PI3Ks) are lipid kinases that can be activated downstream of various receptors, including the T-cell receptor (TCR), co-stimulatory receptors like CD28, and cytokine or chemokine receptors. The role of PI3K signaling differs depending on the upstream receptor involved. CD28, specifically, contains a YMNM consensus motif in its cytoplasmic tail, which serves as a binding site for the p85 regulatory subunit of PI3K.
When CD28 is engaged, it promotes the recruitment of PI3K, complementing PI3K activation downstream of the TCR. This recruitment triggers the conversion of phosphatidylinositol (4,5)-bisphosphate (PIP2) to phosphatidylinositol (3,4,5)-trisphosphate (PIP3) at the plasma membrane, which serves as a docking site for multiple signaling proteins. Among these, the guanine nucleotide exchange factor VAV and the serine/threonine kinase AKT (also known as protein kinase B, PKB) are key mediators of CD28-induced costimulatory signals. PI3K activation through CD28 promotes cytokine transcription (e.g., IL-2), T cell survival via anti-apoptotic pathways, cell cycle progression, and metabolic changes necessary for T cell growth (Riha and Rudd. 2010, Miller et al. 2009, Han et al. 2012).
R-HSA-389359 CD28 dependent Vav1 pathway CD28 binds to several intracellular signaling proteins, including PI3 kinase, Grb2, Gads, and ITK, which are crucial for amplifying the T cell activation signal initiated by the T-cell receptor (TCR). Grb2, in particular, works in tandem with Vav1 to enhance the activation of NFAT and AP-1 transcription factors, critical regulators of gene expression during T cell activation. CD28 costimulation significantly extends the duration and intensity of Vav1 phosphorylation and its localization at the plasma membrane compared to TCR activation alone, indicating that CD28 provides a sustained signal that enhances T cell responsiveness (Hehner et al. 2000).
Vav1 plays a pivotal role in transducing signals from both TCR and CD28 to multiple downstream pathways, with a direct impact on cytoskeletal rearrangements. Upon activation, Vav1 triggers the small GTPases Rac1 and Cdc42, which lead to the activation of mitogen-activated protein kinases (MAPKs) like JNK and p38. In the context of CD28 signaling, these pathways are essential for regulating the expression of cytokines and promoting T cell proliferation and survival (Laura Inés Salazar-Fontana et al. 2003).
Additionally, Vav1's involvement in CD28 costimulation is critical for several other cellular processes, including calcium flux, ERK MAPK activation, NF-κB signaling, and the inside-out activation of the integrin LFA-1. This enhances T cell adhesion, clustering, and polarization, ultimately contributing to more effective immune responses. Thus, CD28 costimulation ensures that Vav1-mediated signals are robustly sustained, promoting optimal T cell activation and function (Hehner et al. 2000).
R-HSA-9013148 CDC42 GTPase cycle This pathway catalogues CDC42 guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs), GDP dissociation inhibitors (GDIs) and CDC42 effectors. CDC42 is one of the three best characterized RHO GTPases, the other two being RHOA and RAC1. By regulating the cytoskeleton, CDC42 regulates cell polarity across different species, from yeast to humans (Pichaud et al. 2019, Woods and Lew 2019). CDC42 is an essential regulator of polarized morphogenesis in epithelial cells, where it coordinates formation of the apical membrane and lumen formation, as well as junction maturation (Pichaud et al. 2019). CDC42 plays a role in cell-to-cell adhesion and cell cycle regulation (Xiao et al. 2018). CDC42 takes part in the regulation of membrane trafficking. Dysfunction of several CDC42-specific GEFs has been shown to impair intracellular trafficking (Egorov and Polishchuk 2017). CDC42 participates in insulin synthesis and secretion and contributes to the pathogenesis of insulin resistance and diabetic nephropathy (Huang et al. 2019). CDC42 is often dysregulated in cancer because a number of GEFs and GEF activators that act upstream of RAC1 and CDC42 are known oncogenes (Aguilar et al. 2017; Maldonado et al. 2018; Zhang et al. 2019; Maldonado et al. 2020). CDC4 promotes cancer cell proliferation, survival, invasion, migration and metastasis (Xiao et al. 2018), especially under hyperglycemia (Huang et al. 2019).
R-HSA-68689 CDC6 association with the ORC:origin complex Cdc6 is a regulator of DNA replication initiation in both yeasts and human cells (Mendez and Stillman 2000), but its mechanism of action differs between the two systems. Genetic studies in budding yeast (S. cerevisiae) and fission yeast (S. pombe) indicate that the normal function of Cdc6 protein is required to restrict DNA replication to once per cell cycle. Specifically, Cdc6 may function as an ATPase switch linked to Mcm2-7:Cdt1 association with the Cdc6:ORC:origin complex (Lee and Bell 2000). In S. cerevisiae, Cdc6 protein is expressed late in the M phase of the cell cycle and, in cells with a prolonged G1 phase, late in G1. This protein has a short half-life, and is destroyed by ubiquitin-mediated proteolysis, mediated by the SCF complex (Piatti et al. 1995, Drury et al. 1997, Drury et al. 2000, Perkins et al. 2001). Human Cdc6 protein levels are reduced early in G1 but otherwise are constant throughout the cell cycle (Petersen et al. 2000). Some reports have suggested that after cells enter S phase, Cdc6 is phosphorylated, excluded from the nucleus and subject to ubiquitination and degradation (Saha et al. 1998, Jiang et al. 1999, Petersen et al. 1999). Replenishing Cdc6 protein levels during G1 appears to be regulated by E2F transcription factors (Yan et al. 1998).
R-HSA-9833576 CDH11 homotypic and heterotypic interactions Based on surface plasmon resonance experiments, CDH11 forms a specificity subgroup with CDH8 and, probably, CDH24. CDH11 forms homotypic trans dimers (Patel et al. 2006, Brasch et al. 2018), and heterotypic trans dimers with CDH8 (Brasch et al. 2018) and, based on sequence similarity, probably with CDH24 (Brasch et al. 2018).
R-HSA-69017 CDK-mediated phosphorylation and removal of Cdc6 As cells enter S phase, HsCdc6p is phosphorylated by CDK promoting its export from the nucleus (see Bell and Dutta 2002).
R-HSA-447041 CHL1 interactions Close homolog of L1 (CHL1) is a member of the L1 family of cell adhesion molecules expressed by subpopulations of neurons and glia in the central and peripheral nervous system. CHL1 like L1 promotes neuron survival and neurite outgrowth. CHL1 shares the basic structural arrangement of L1 family members yet in contrast to all the members it is not capable of forming homophilic adhesion. The second Ig-like domain of CHL1 contains the integrin interaction motif RGD rather than with in the sixth Ig-like domain as in L1, however the sixth Ig-like domain of CHL1 has another potential integrin binding motif DGEA. CHL1 binds NP-1 via the Ig1 sequence FASNRL to mdediate repulsive axon guidance to Sema3A. CHL1 is the only L1 family member with an altered sequence (FIGAY) in the ankyrin-binding domain, and it lacks the sorting/endocytosis RSLE motif, which is characteristic of other L1 family members.
R-HSA-5607763 CLEC7A (Dectin-1) induces NFAT activation CLEC7A (Dectin-1) signals through the classic calcineurin/NFAT pathway through Syk activation phospholipase C-gamma 2 (PLCG2) leading to increased soluble IP3 (inositol trisphosphate). IP3 is able to bind endoplasmic Ca2+ channels, resulting in an influx of Ca2+ into the cytoplasm. This increase in calcium concentration induces calcineurin activation and consequently, dephosphorylation of NFAT and its translocation into the nucleus, triggering gene transcription and extracellular release of Interleukin-2 (Plato et al. 2013, Goodridge et al. 2007, Mourao-Sa et al. 2011).
R-HSA-5607764 CLEC7A (Dectin-1) signaling CLEC7A (also known as Dectin-1) is a pattern-recognition receptor (PRR) expressed by myeloid cells (macrophages, dendritic cells and neutrophils) that detects pathogens by binding to beta-1,3-glucans in fungal cell walls and triggers direct innate immune responses to fungal and bacterial infections. CLEC7A belongs to thetype-II C-type lectin receptor (CLR) family that can mediate its own intracellular signaling. Upon binding particulate beta-1,3-glucans, CLEC7A mediates intracellular signalling through its cytoplasmic immunoreceptor tyrosine-based activation motif (ITAM)-like motif (Brown 2006). CLEC7A signaling can induce the production of various cytokines and chemokines, including tumour-necrosis factor (TNF), CXC-chemokine ligand 2 (CXCL2, also known as MIP2), interleukin-1beta (IL-1b), IL-2, IL-10 and IL-12 (Brown et al. 2003), it also triggers phagocytosis and stimulates the production of reactive oxygen species (ROS), thus contributing to microbial killing (Gantner et al. 2003, Herre et al. 2004, Underhill et al. 2005, Goodridge at al. 2011, Reid et al. 2009). These cellular responses mediated by CLEC7A rely on both Syk-dependent and Syk-independent signaling cascades. The pathways leading to the Syk-dependent activation of NF-kB can be categorised into both canonical and non-canonical routes (Gringhuis et al. 2009). Activation of the canonical NF-kB pathway is essential for innate immunity, whereas activation of the non-canonical pathway is involved in lymphoid organ development and adaptive immunity (Plato et al. 2013).
R-HSA-5660668 CLEC7A/inflammasome pathway Antifungal immunity through the induction of T-helper 17 cells (TH17) responses requires the production of mature, active interleukin-1beta (IL1B). CLEC7A (dectin-1) through the SYK route induces activation of NF-kB and transcription of the gene encoding pro-IL1B via the CARD9-BCL10-MALT1 complex as well as the formation and activation of a MALT1-caspase-8-ASC complex that mediated the processing of pro-IL1B. The inactive precursor pro-IL1B has to be processed into mature bioactive form of IL1B and is usually mediated by inflammatory cysteine protease caspase-1. Gringhuis et al. showed that CLEC7A mediated processing of IL1B occurs through two distinct mechanisms: CLEC7A triggering induced a primary noncanonical caspase-8 inflammasome for pro-IL1B processing that was independent of caspase-1 activity, whereas some fungi triggered a second additional mechanism that required activation of the NLRP3/caspase 1 inflammasome. Unlike the canonical caspase-1 inflammasome, CLEC7A mediated noncanonical caspase-8-dependent inflammasome is independent of pathogen internalization. CLEC7A/inflammasome pathway enables the host immune system to mount a protective TH17 response against fungi and bacterial infection (Gringhuis et al. 2012, Cheng et al. 2011).
R-HSA-6811434 COPI-dependent Golgi-to-ER retrograde traffic Retrograde traffic from the cis-Golgi to the ERGIC or the ER is mediated in part by microtubule-directed COPI-coated vesicles (Letourneur et al, 1994; Shima et al, 1999; Spang et al, 1998; reviewed in Lord et al, 2013; Spang et al, 2013). These assemble at the cis side of the Golgi in a GBF-dependent fashion and are tethered at the ER by the ER-specific SNAREs and by the conserved NRZ multisubunit tethering complex, known as DSL in yeast (reviewed in Tagaya et al, 2014; Hong and Lev, 2014). Typical cargo of these retrograde vesicles includes 'escaped' ER chaperone proteins, which are recycled back to the ER for reuse by virtue of their interaction with the Golgi localized KDEL receptors (reviewed in Capitani and Sallese, 2009; Cancino et al, 2013).
R-HSA-6811436 COPI-independent Golgi-to-ER retrograde traffic In addition to the better characterized COPI-dependent retrograde Golgi-to-ER pathway, a second COPI-independent pathway has also been identified. This pathway is RAB6 dependent and transports cargo such as glycosylation enzymes and Shiga and Shiga-like toxin through tubular carriers rather than vesicles (White et al, 1999; Girod et al, 1999; reviewed in Heffernan and Simpson, 2014). In the absence of a COPI coat, the membrane curvature necessary to initiate tubulation may be provided through the action of phospholipase A, which hydrolyzes phospholipids at the sn2 position to yield lysophospholipids. This activity is countered by lysophospholipid acyltransferases, and the balance of these may influence whether transport tubules or transport vesicles form (de Figuiredo et al, 1998; reviewed in Bechler et al, 2012). RAB6-dependent tubules also depend on the dynein-dynactin motor complex and the hoomodimeric Bicaudal proteins (Matanis et al, 2002; Yamada et al, 2013; reviewed in Heffernan and Simpson, 2014).
R-HSA-6807878 COPI-mediated anterograde transport The ERGIC (ER-to-Golgi intermediate compartment, also known as vesicular-tubular clusters, VTCs) is a stable, biochemically distinct compartment located adjacent to ER exit sites (Ben-Tekaya et al, 2005; reviewed in Szul and Sztul, 2011). The ERGIC concentrates COPII-derived cargo from the ER for further anterograde transport to the cis-Golgi and also recycles resident ER proteins back to the ER through retrograde traffic. Both of these pathways appear to make use of microtubule-directed COPI-coated vesicles (Pepperkok et al, 1993; Presley et al, 1997; Scales et al, 1997; Stephens and Pepperkok, 2002; Stephens et al, 2000; reviewed in Lord et al, 2001; Spang et al, 2013).
R-HSA-204005 COPII-mediated vesicle transport COPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the ER-Golgi intermediate compartment (ERGIC). COPII-coated vesicles were originally discovered in the yeast Saccharomyces cerevisiae using genetic approaches coupled with a cell-free assay. The mammalian counterpart of this pathway is represented here. Newly synthesized proteins destined for secretion are sorted into COPII-coated vesicles at specialized regions of the ER. These vesicles leave the ER, become uncoated and subsequently fuse with the ERGIC membrane.
R-HSA-140180 COX reactions Arachidonic acid (AA) is a 20 carbon unsaturated fatty acid which is present in the lipid bilayer of all mammalian cells. AA is released from the membrane by phospholipases, thus making it available for conversion to bioactive lipids. The cyclooxygenase pathway is one of three pathways (the others being lipoxygenase and P450 monooxygenase pathways) that perform this conversion.\n\nThe enzyme that acts in the cyclooxygenase pathway is called cyclooxygenase (COX) or prostaglandin H synthase (PGHS). PGHS exhibits a dual catalytic activity, a cyclooxygenase and a peroxidase. The cyclooxygenase catalyzes the initial conversion of AA to an intermediate, prostaglandin G2 (PGG2) whilst the peroxidase converts PGG2 to prostaglandin H2 (PGH2) via a two-electron reduction. PGH2 is the intermediate for products that play critical roles in immune function regulation, kidney development and mucosal integrity of the GI tract.\n\nPGHS exists in two isoforms, 1 and 2 and both forms can perform the above reactions. Form 1 is constitutively expressed in most tissues and is involved in performing normal physiological functions. Form 2, in contrast, is inducible and is involved in critical steps of rheumatic disease, inflammation and tumorigenesis.
R-HSA-199920 CREB phosphorylation Nerve growth factor (NGF) activates multiple signalling pathways that mediate the phosphorylation of CREB at the critical regulatory site, serine 133. CREB phosphorylation at serine 133 is a crucial event in neurotrophin signalling, being mediated by ERK/RSK, ERK/MSK1 and p38/MAPKAPK2 pathways. Several kinases, such as MSK1, RSK1/2/3 (MAPKAPK1A/B/C), and MAPKAPK2, are able to directly phosphorylate CREB at S133. MSK1 is also able to activate ATF (Cyclic-AMP-dependent transcription factor). However, the NGF-induced CREB phosphorylation appears to correlate better with activation of MSK1 rather than RSK1/2/3, or MAPKAPK2. In retrograde signalling, activation of CREB occurs within 20 minutes after neurotrophin stimulation of distal axons.
R-HSA-442742 CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling Ca2+ influx through the NMDA receptor activates RAS guanyl nucleotide exchange factor RasGRF, which promotes formation of active RAS:GTP complexes (Anborgh et al. 1999, Krapivinsky et al. 2003). CaMKII, also activated by NMDA receptor-mediated Ca2+ influx, can contribute to activation of RAS/RAF/MAPK signaling by phosphorylation of RAF1 (Salzano et al. 2012). ERKs (MAPK1 and MAPK3), activated downstream of RAS signaling, phosphorylate ribosomal protein S6 kinases (RSKs), initiating activation of RSKs (reviewed by Anjum and Blenis 2012). Activated RSKs phosphorylate the transcription factor CREB1 at serine residue S133, thus stimulating CREB1-mediated transcription (De Cesare et al. 1998, Harum et al. 2001, Schinelli et al. 2001, Song et al. 2003).
R-HSA-442720 CREB1 phosphorylation through the activation of Adenylate Cyclase Ca2+ influx through activated NMDA receptors in the post synaptic neurons activates adenylate cyclase-mediated signal transduction, leading to the activation of PKA and phosphorylation and activation of CREB1 induced transcription (Masada et al. 2012, Chetkovich et al. 1991, Chetkovich and Sweatt 1993
R-HSA-442729 CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde In addition to inducing long-term potentiation (LTP), NMDA receptor-mediated activation of CaMKII leads to transcriptional changes that are implicated in LTP maintenance (reviewed by Miyamoto 2006). CaMKII-gamma (CAMK2G) isoform is involved in nuclear shuttling of the calcium/calmodulin complex (CALM1:4xCa2+), which enables CaMKK-mediated activation of the nuclear calcium/calmodulin dependent kinase CaMKIV (CAMK4). Activated CaMKIV phosphorylates the transcription factor CREB1 and activates CREB1-mediated transcription (Ma et al. 2014, Cohen et al. 2018).
R-HSA-8874211 CREB3 factors activate genes Members of the CREB3 family (also known as the OASIS family) are tissue-specific proteins that each contain a transcription activation domain, a basic leucine zipper (bZIP) domain that promotes dimerization and DNA binding, and a transmembrane domain that anchors the protein to the membrane of the endoplasmic reticulum (ER) (reviewed in Asada et al. 2011, Chan et al. 2011, Kondo et al. 2011, Fox and Andrew 2015). The family includes CREB3 (LUMAN), CREB3L1 (OASIS), CREB3L2 (BBF2H7, Tisp40), CREB3L3 (CREB-H), and CREB3L4 (CREB4). Activation of the proteins occurs when they transit from the ER to the Golgi and are cleaved sequentially by the Golgi resident proteases MBTPS1 (S1P) and MBTPS2 (S2P), a process known as regulated intramembrane proteolysis that releases the cytoplasmic region of the protein containing the transcription activation domain and the bZIP domain. This protein fragment then transits from the cytosol to the nucleus where it activates transcription of target genes. CREB3L1, CREB3L2, and CREB3L3 are activated by ER stress, although the mechanisms that cause the transit of the CREB3 proteins are not fully characterized. Unlike the ATF6 factors, CREB3 proteins do not appear to interact with HSPA5 (BiP) and therefore do not appear to sense unfolded proteins by dissociation of HSPA5 when HSPA5 binds the unfolded proteins.
R-HSA-399956 CRMPs in Sema3A signaling CRMPs are a small family of plexinA-interacting cytosolic phosphoproteins identified as mediators of Sema3A signaling and neuronal differentiation. After Sema3A activation Plexin-A bound CRMP's undergo phosphorylation by Cdk5, GSK3beta and Fes kinases. Phosphorylation of CRMPs by these kinases blocks the ability of CRMP to bind to tubulin dimers, subsequently induces depolymerization of F-actin, and ultimately leads to growth cone collapse.
R-HSA-2024101 CS/DS degradation Lysosomal degradation of glycoproteins is part of the cellular homeostasis of glycosylation (Winchester 2005). The steps outlined below describe the degradation of chondroitin sulfate and dermatan sulfate. Complete degradation of glycoproteins is required to avoid build up of glycosaminoglycan fragments which can cause lysosomal storage diseases. Complete degradation steps are not shown as they are repetitions of the main ones described here. The proteolysis of the core protein of the glycoprotein is not shown here.
R-HSA-5358747 CTNNB1 S33 mutants aren't phosphorylated S33 mutations of beta-catenin interfere with GSK3 phosphorylation and result in stabilization and nuclear localization of the protein and enhanced WNT signaling (Groen et al, 2008; Nhieu et al, 1999; Clements et al, 2002; reviewed in Polakis, 2000). S33 mutations have been identified in cancers of the central nervous system, liver, endometrium and stomach, among others (reviewed in Polakis, 2000).
R-HSA-5358749 CTNNB1 S37 mutants aren't phosphorylated S37 mutations of beta-catenin interfere with GSK3 phosphorylation and stabilize the protein, resulting in enhanced WNT pathway signaling (Nhieu et al, 1999; Clements et al, 2002; reviewed in Polakis, 2000). S37 mutations have been identified in cancers of the brain, liver, ovary and large intestine, among others (reviewed in Polakis, 2000).
R-HSA-5358751 CTNNB1 S45 mutants aren't phosphorylated S45 mutants of beta-catenin have been identified in colorectal and hepatocellular carcinomas, soft tissue cancer and Wilms Tumors, among others (reviewed in Polakis, 2000). These mutations abolish the CK1alpha phosphorylation site of beta-catenin which acts as a critical priming site for GSK3 phosphorylation of T41( and subsequently S37 and S33) thus preventing its ubiquitin-mediated degradation (Morin et al, 1997; Amit et al, 2002).
R-HSA-5358752 CTNNB1 T41 mutants aren't phosphorylated T41 mutations of beta-catenin interfere with GSK3 phosphorylation and result in stabilization and nuclear accumulation of the protein (Moreno-Bueno et al, 2002; Taniguchi et al, 2002; reviewed in Polakis, 2012). T41 mutations have been identified in cancers of the liver and brain, as well as in the pituitary, endometrium, large intestine and skin, among others (reviewed in Polakis, 2000; Saito-Diaz et al, 2013).
R-HSA-211999 CYP2E1 reactions CYP2E1 can metabolize and activate a large number of solvents and industrial monomers as well as drugs. This quality of CYP2E1 may make it an important determinant of human susceptibility to the toxic effects of industrial and environmental chemicals. Typical CYP2E1 substrates include acetaminophen, benzene, CCl4, halothane, ethanol and vinyl chloride. CYP2E1 contributes to oxidative stress by producing oxidising species called reactive oxygen species (ROS) which can lead to damage to mitochondria, DNA and initiate lipid peroxidation or even cell death.
R-HSA-111996 Ca-dependent events Calcium, as the ion Ca2+, is essential in many biological processes. The majority of Ca2+ in many organisms is bound to phosphates which form skeletal structures and also buffer Ca2+ levels in extracellular fluids (typically 1 millimolar). Intracellular free Ca2+, by contrast, is 10,000 times lower than the outside of the cell (typically 10 micromolar). This concentration gradient is used to import Ca2+ into cells where it acts as a second messenger.
R-HSA-1296052 Ca2+ activated K+ channels Ca2+ activated potassium channels are expressed in neuronal and non-neuronal tissue such as smooth muscle, epithelial cell and sensory cells. Ca2+ activated potassium channels are activated when the Ca2+ ion concentration increased, The efflux of K+ via these channels leads to repolarization/hyperpolarization of the membrane potential which limits the Ca2+ influx though voltage activated Ca2+ channels (VGCC) thereby regulating the influx of Ca2+ flow via VGCC.
R-HSA-4086398 Ca2+ pathway A number of so called non-canonical WNT ligands have been shown to promote intracellular calcium release upon FZD binding. This beta-catenin-independent WNT pathway acts through heterotrimeric G proteins and promotes calcium release through phophoinositol signaling and activation of phosphodiesterase (PDE). Downstream effectors include the calcium/calmodulin-dependent kinase II (CaMK2) and PKC (reviewed in De, 2011). The WNT Ca2+ pathway is important in dorsoventral polarity, convergent extension and organ formation in vertebrates and also has roles in negatively regulating 'canonical' beta-catenin-dependent transcription. Non-canonical WNT Ca2+ signaling is also implicated in inflammatory response and cancer (reviewed in Kohn and Moon, 2005; Sugimura and Li, 2010).
R-HSA-111997 CaM pathway Calmodulin (CaM) is a small acidic protein that contains four EF-hand motifs, each of which can bind a calcium ion, therefore it can bind up to four calcium ions. The protein has two approximately symmetrical domains, separated by a flexible hinge region. Calmodulin is the prototypical example of the EF-hand family of Ca2+-sensing proteins. Changes in intracellular Ca2+ concentration regulate calmodulin in three distinct ways. First, by directing its subcellular distribution. Second, by promoting association with different target proteins. Third, by directing a variety of conformational states in calmodulin that result in target-specific activation. Calmodulin binds and activates several effector protein (e.g. the CaM-dependent adenylyl cyclases, phosphodiesterases, protein kinases and the protein phosphatase calcineurin).
R-HSA-111932 CaMK IV-mediated phosphorylation of CREB The Ca2+-calmodulin-dependent protein kinase (CaM kinase) cascade includes three kinases: CaM-kinase kinase (CaMKK); and the CaM kinases CaMKI and CaMKIV, which are phosphorylated and activated by CaMKK. Members of this cascade respond to elevation of intracellular Ca2+ levels. CaMKK and CaMKIV localize both to the nucleus and to the cytoplasm, whereas CaMKI is only cytosolic. Nuclear CaMKIV regulates transcription through phosphorylation of several transcription factors, including CREB. In the cytoplasm, there is extensive cross-talk between CaMKK, CaMKIV and other signaling cascades, including those that involve the cAMP-dependent kinase (PKA), MAP kinases and protein kinase B (PKB/Akt).
R-HSA-2025928 Calcineurin activates NFAT Signaling by the B cell receptor and the T cell receptor stimulate transcription by NFAT factors via calcium (reviewed in Gwack et al. 2007). Cytosolic calcium from intracellular stores and extracellular sources binds calmodulin and activates the protein phosphatase calcineurin. Activated calcineurin dephosphorylates NFATs in the cytosol, exposing nuclear localization sequences on the NFATs and causing the NFATs to be imported into the nucleus where they regulate transcription of target genes in complexes with other transcription factors such as AP-1 and JUN. Calcineurin in the target of the immunosuppressive drugs cyclosporin A and FK-506 (reviewed in Lee and Park 2006).
R-HSA-419812 Calcitonin-like ligand receptors The calcitonin peptide family comprises calcitonin, amylin, calcitonin gene-related peptide (CGRP), adrenomedullin (AM) and intermedin (AM2). Calcitonin is a 32 amino acid peptide, involved in bone homeostasis (Sexton PM et al, 1999). Amylin is a product of the islet beta-cell (Cooper GJ et al, 1987), along with insulin and probably has a hormonal role in the regulation of nutrient intake (Young A and Denaro M, 1998). Adrenomedullin (AM) is a ubiquitously expressed peptide initially isolated from phaechromocytoma (a tumour of the adrenal medulla) (Kitamura K et al, 1993). Both AM and AM2 (Takei Y et al, 2004) belong to a family of calcitonin-related peptide hormones important for regulating diverse physiologic functions and the chemical composition of fluids and tissues.
The receptor family for these peptides consists of two class B GPCRs, the calcitonin receptor (CT) and calcitonin receptor-like receptor (CL) (Poyner DR er al, 2002). Whilst the receptor for calcitonin is a conventional class B GPCR, the receptors for CGRP, AM and amylin require additional proteins, called the receptor activity modifying proteins (RAMPs). There are three RAMPs in mammals; they interact with the CT receptor to convert it to receptors for amylin. For CGRP and AM, the related CL interacts with RAMP1 to give a CGRP receptor and RAMP2 or 3 to give AM receptors. CL by itself will bind no known endogenous ligand.
R-HSA-111933 Calmodulin induced events One important physiological role for Calmodulin is the regulation of adenylylcyclases. Four of the nine known adenylylcyclases are calcium sensitive, in particular type 8 (AC8).
R-HSA-901042 Calnexin/calreticulin cycle The unfolded protein is recognized by a chaperon protein (calnexin or calreticulin) and the folding process starts. The binding of these protein requires a mono-glucosylated glycan (Caramelo JJ and Parodi AJ, 2008) and lectin-based interaction with client proteins is the predominant contributor to chaperone activity of calreticulin (inferred from the mouse homolog in Lum et al. 2016).
R-HSA-111957 Cam-PDE 1 activation Human Ca2+/calmodulin-dependent phosphodiesterase PDE1 is activated by the binding of calmodulin in the presence of Ca(2+). PDE1 has three subtypes PDE1A, PDE1B and PDE1C and their role is to hydrolyze both cGMP and cAMP. Their role is to antagonize the increased concentration of the intracellular second messengers determined by the synthetic activity of the adenylate cyclase enzymes thus governing intracellular cAMP dynamics in response to changes in the cytosolic Ca2+ concentration. PDE1 are mainly cytosolic but different isoforms are expressed in different tissues.
R-HSA-72737 Cap-dependent Translation Initiation Translation initiation is a complex process in which the Met-tRNAi initiator, 40S, and 60S ribosomal subunits are assembled by eukaryotic initiation factors (eIFs) into an 80S ribosome at the start codon of an mRNA. The basic mechanism for this process can be described as a series of five steps: 1) formation of a pool of free 40S subunits, 2) formation of the ternary complex (Met-tRNAi/eIF2/GTP), and subsequently, the 43S complex (comprising the 40S subunit, Met-tRNAi/eIF2/GTP, eIF3 and eIF1A), 3) activation of the mRNA upon binding of the cap-binding complex eIF4F, and factors eIF4A, eIF4B and eIF4H, with subsequent binding to the 43S complex, 4) ribosomal scanning and start codon recognition, and 5) GTP hydrolysis and joining of the 60S ribosomal subunit.
R-HSA-8955332 Carboxyterminal post-translational modifications of tubulin Tubulins fold into compact globular domains with less structured carboxyterminal tails. These tails vary in sequence between tubulin isoforms and are exposed on the surfaces of microtubules. They can undergo a variety of posttranslational modifications, including the attachment and removal of polyglutamate chains and in the case of alpha-tunulins the loss and reattachment of a terminal tyrosine (Tyr) residue. These modifications are associated with changes in the rigidity and stability of microtubules (Song & Brady 2015; Yu et al. 2015).
Mutations affecting these modification processes can have severe effects on phenotype (e.g., Ikegami et al. 2007). Nevertheless, the precise molecular mechanisms by which these changes in tubulin structure modulate its functions remain unclear, so these modification processes are simply annotated here as a series of chemical transformations of tubulins.
R-HSA-5576891 Cardiac conduction The normal sequence of contraction of atria and ventricles of the heart require activation of groups of cardiac cells. The mechanism must elicit rapid changes in heart rate and respond to changes in autonomic tone. The cardiac action potential controls these functions. Action potentials are generated by the movement of ions through transmembrane ion channels in cardiac cells. Like skeletal myocytes (and axons), in the resting state, a given cardiac myocyte has a negative membrane potential. In both muscle types, after a delay (the absolute refractory period), K+ channels reopen and the resulting flow of K+ out of the cell causes repolarisation. The voltage-gated Ca2+ channels on the cardiac sarcolemma membrane are generally triggered by an influx of Na+ during phase 0 of the action potential. Cardiac muscle cells are so tightly bound that when one of these cells is excited the action potential spreads to all of them. The standard model used to understand the cardiac action potential is the action potential of the ventricular myocyte (Park & Fishman 2011, Grant 2009).
The action potential has 5 phases (numbered 0-4). Phase 4 describes the membrane potential when a cell is not being stimulated. The normal resting potential in the ventricular myocardium is between -85 to -95 mV. The K+ gradient across the cell membrane is the key determinant in the normal resting potential. Phase 0 is the rapid depolarisation phase in which electrical stimulation of a cell opens the closed, fast Na+ channels, causing a large influx of Na+ creating a Na+ current (INa+). This causes depolarisation of the cell. The slope of phase 0 represents the maximum rate of potential change and differs in contractile and pacemaker cells. Phase 1 is the inactivation of the fast Na+ channels. The transient net outward current causing the small downward deflection (the "notch" of the action potetial) is due to the movement of K+ and Cl- ions. In pacemaker cells, this phase is due to rapid K+ efflux and closure of L-type Ca2+ channels. Phase 2 is the plateau phase which is sustained by a balance of Ca2+ influx and K+ efflux. This phase sustains muscle contraction. Phase 3 of the action potential is where a concerted action of two outward delayed currents brings about repolarisation back down to the resting potential (Bartos et al. 2015).
R-HSA-9733709 Cardiogenesis Gradients of Bone Morphogenetic Protein (BMP), Wingless-related integration site (WNT), and NODAL promote the formation of cardiac progenitors anteriolateral to the primitive streak during gastrulation (reviewed in Munoz-Chapuli and Perez-Pomares 2010, Cui et al. 2018, Prummel et al. 2020, Witman et al. 2019, Miyamoto e al. 2021). Eomesodermin (EOMES) and TBXT (T, Brachyury) expressed in the cardiac mesoderm activate expression of MESP1, a master regulator of cardiogenesis and the first observed marker of cardiac progenitors. MESP1-expressing cells migrate anteriorly towards the midline to form the cardiac crescent posterior to the head folds at about 2 weeks of gestation in humans (E7.5 in mice).
Within the cardiac crescent, two populations of cells can be identified based on gene expression and timing of contribution to the developing heart: the first heart field (FHF) forms the initial heart tube and contributes to the systemic ventricle (the left ventricle in crocodilians, birds, and mammals), the septum, and, to a lesser extent, the atria; the second heart field (SHF) extends the poles of the heart and contributes to the atria, the outflow tract, the septum, and the right ventricle, which is responsible for pulmonary circulation and distinguishes crocodilians, birds, and mammals (reviewed in Meilhac and Buckingham 2018).
At about 3 weeks gestation in humans (E8 in mice), FHF cells migrate axially to the midline and fuse to form the heart tube. Elongation of the heart tube leads to rightward looping and eventual formation of atria and ventricles (reviewed in Desgrange et al. 2018). FHF cells do not proliferate as much as SHF cells and mostly differentiate into cardiomyocytes due to the actions of myocardial differentiation factors such as NKX2-5, GATA4, TBX5, and HAND1. SHF cells are initially located in the posterior region of the cardiac crescent then, during formation of the heart tube, become located at the arterial and venous poles of the heart tube. SHF cells proliferate more than FHF cells and can differentiate to form cardiomyocytes, endothelial cells, smooth muscle cells, and fibroblasts. A reservoir of SHF progenitors located at the core of the pharyngeal mesoderm continuously contributes to the developing heart. Proliferating SHF cells express FGF8 and FGF10 driven by ISL1 and TBX1.
Cardiac progenitors are regulated by a distinct set of transcription factors and mutations in these factors and other factors involved in gene expression are responsible for congenital heart defects (reviewed in Diab et al. 2021, Houyel and Meilhac 2021, Kodo et al. 2021, Miyamoto et al. 2021, Lescroart and Zaffran 2022, Wang et al. 2022). Additionally, combinations of these transcription factors are now being used to reprogram fibroblasts and other cell types into cardiomyocytes for repairing damaged hearts (reviewed in Adams et al. 2021, Garry et al. 2021, Kim et al. 2022, Thomas et al. 2022, Zhu et al. 2022). TBXT (T, Brachyury) is expressed early in developing mesoderm and is activated by WNT signaling, which maintains proliferation and is subsequently downregulated during differentiation. Activation of MESP1 expression by TBXT and EOMES occurs early in gastrulation. MESP1 is expressed in both the FHF and the SHF. MESP1, in turn, directly activates two key regulators of cardiac development: GATA4 and NKX2-5 (NKX2.5, the ortholog of Tinman in Drosophila). Bone Morphogenetic Protein (BMP) signaling originating from BMPs secreted by underlying endoderm also enhances expression of GATA4 and NKX2-5, apparently through binding of SMAD proteins to the promoters of GATA4 and NKX2-5. GATA4 and NKX2-5 proteins, in turn, regulate each other's expression and directly interact to regulate downstream target genes. NKX2-5 directly activates GATA6 throughout the cardiac mesoderm.
The FHF is characterized by expression of TBX5 and HCN4; the SHF is characterized by transient expression of TBX1, ISL1, FGF8, FGF10, and SIX2. In the FHF, NKX2-5 binds the promoter of the TBX5 gene and activates transcription. TBX5, in turn, directly activates expression of SRF. TBX5 protein interacts directly with NKX2-5 and GATA4 proteins to activate further downstream targets. Sonic hedgehog (SHH) from the pharyngeal endoderm and WNT signaling maintain proliferation of SHF cells, In the SHF, TBX1, GATA4 and LEF1:CTNN1 (LEF1:Beta-catenin from Wnt signaling) directly activate ISL1, characteristic of SHF cells, and ISL1 then activates expression of HAND2 (dHAND), also characteristic of SHF cells.
R-HSA-5694530 Cargo concentration in the ER Computational analysis suggests that ~25% of the proteome may be exported from the ER in human cells (Kanapin et al, 2003). These cargo need to be recognized and concentrated into COPII vesicles, which range in size from 60-90 nm, and which move cargo from the ER to the ERGIC in mammalian cells (reviewed in Lord et al, 2013; Szul and Sztul, 2011). Recognition of transmembrane cargo is mediated by interaction with one of the 4 isoforms of SEC24, a component of the inner COPII coat (Miller et al, 2002; Miller et al, 2003; Mossessova et al, 2003; Mancias and Goldberg, 2008). Soluble cargo in the ER lumen is concentrated into COPII vesicles through interaction with a receptor of the ERGIC-53 family, the p24 family or the ERV family. Each of these families of transmembrane receptors interact with cargo through their lumenal domains and with components of the COPII coat with their cytoplasmic domains and are packaged into the COPII vesicle along with the cargo. The receptors are subsequently recycled to the ER in COPI vesicles through retrograde traffic (reviewed in Dancourt and Barlowe, 2010). Packaging of large cargo such as fibrillar collagen depends on the transmembrane accessory factors MIA3 (also known as TANGO1) and CTAGE5. Like the ERGIC, p24 and ERV cargo receptors, MIA3 and MIA2 (also known as CTAGE5) interact both with the collagen cargo and with components of the COPII coat. Unlike the other cargo receptors, however, MIA3 and MIA2 are not loaded into the vesicle but remain in the ER membrane (reviewed in Malhotra and Erlmann, 2011; Malhotra et al, 2015).
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis Recruitment of plasma membrane-localized cargo into clathrin-coated endocytic vesicles is mediated by interaction with a variety of clathrin-interacting proteins collectively called CLASPs (clathrin-associated sorting proteins). CLASP proteins, which may be monomeric or tetrameric, are recruited to the plasma membrane through interaction with phosphoinsitides and recognize linear or conformational sequences or post-translational modifications in the cytoplasmic tails of the cargo protein. Through bivalent interactions with clathrin and/or other CLASP proteins, they bridge the recruitment of the cargo to the emerging clathrin coated pit (reviewed in Traub and Bonifacino, 2013). The tetrameric AP-2 complex, first identified in early studies of clathrin-mediated endocytosis, was at one time thought to be the primary CLASP protein involved in cargo recognition at the plasma membrane, and indeed plays a key role in the endocytosis of cargo carrying dileucine- or tyrosine-based motifs.
A number of studies have been performed to test whether AP-2 is essential for all forms of clathrin-mediated endocytosis (Keyel et al, 2006; Motely et al, 2003; Huang et al, 2004; Boucrot et al, 2010; Henne et al, 2010; Johannessen et al, 2006; Gu et al, 2013; reviewed in Traub, 2009; McMahon and Boucrot, 2011). Although depletion of AP-2 differentially affects the endocytosis of different cargo, extensive depletion of AP-2 through RNAi reduces clathrin-coated pit formation by 80-90%, and the CCPs that do form still contain AP-2, highlighting the critcical role of this complex in CME (Johannessen et al, 2006; Boucrot et al, 2010; Henne et al, 2010).
In addition to AP-2, a wide range of other CLASPs including proteins of the beta-arrestin, stonin and epsin families, engage sorting motifs in other cargo and interact either with clathrin, AP-2 or each other to facilitate assembly of a clathin-coated pit (reviewed in Traub and Bonifacino, 2013).
R-HSA-5620920 Cargo trafficking to the periciliary membrane Proteomic studies suggest that the cilium is home to approximately a thousand proteins, and has a unique protein and lipid make up relative to the bulk cytoplasm and plasma membrane (Pazour et al, 2005; Ishikawa et al, 2012; Ostrowoski et al, 2002; reviewed in Emmer et al, 2010; Rohatgi and Snell, 2010). In addition, the cilium is a dynamic structure, and the axoneme is continually being remodeled by addition and removal of tubulin at the distal tip (Marshall and Rosenbaum, 2001; Stephens, 1997; Song et al, 2001). As a result, the function and structure of this organelle relies on the directed trafficking of protein and vesicles to the cilium. Small GTPases of the RAS, RAB, ARF and ARL families are involved in cytoskeletal organization and membrane traffic and are required to regulate the traffic from the Golgi and the trans-Golgi network to the cilium (reviewed in Deretic, 2013; Li et al, 2012). ARF4 is a Golgi-resident GTPase that acts in conjunction with a ciliary-targeting complex consisting of the ARF-GAP ASAP1, RAB11A, the RAB11 effector FIP3 and the RAB8A guanine nucleotide exchange factor RAB3IP/RABIN8 to target cargo bearing a putative C-terminal VxPx targeting motif to the cilium. A well-studied example of this system involves the trafficking of rhodopsin to the retinal rod photoreceptors, a specialized form of the cilium (reviewed in Deretic, 2013). ARL3, ARL13B and ARL6 are all small ARF-like GTPases with assorted roles in ciliary trafficking and maintenance. Studies in C. elegans suggest that ARL3 and ARL13B have opposing roles in maintaining the stability of the anterograde IFT trains in the cilium (Li et al, 2010). In addition, both ARL3 and ARL13B have roles in facilitating the traffic of subsets of ciliary cargo to the cilium. Myristoylated cargo such as peripheral membrane protein Nephrocystin-3 (NPHP3) is targeted to the cilium in a UNC119- and ARL3-dependent manner, while ARL13B is required for the PDE6-dependent ciliary localization of INPP5E (Wright et al, 2011; Humbert et al, 2012; reviewed in Li et al, 2012). ARL6 was also identified as BBS3, a gene that when mutated gives rise to the ciliopathy Bardet-Biedl syndrome (BBS). ARL6 acts upstream of a complex of 8 other BBS-associated proteins known as the BBSome. ARL6 and the BBSome are required for the ciliary targeting of proteins including the melanin concentrating hormone receptor (MCHR) and the somatostatin receptor (SSTR3), among others (Nachury et al, 2007; Loktev et al, 2008; Jin et al, 2010; Zhang et al, 2011). Both the BBSome and ARL6 may continue to be associated with cargo inside the cilium, as they are observed to undergo typical IFT movements along the axoneme (Fan et al, 2004; Lechtreck et al, 2009; reviewed in Li et al, 2012).
R-HSA-200425 Carnitine shuttle The mitochondrial carnitine system catalyzes the transport of long-chain fatty acids into the mitochondrial matrix where they undergo beta oxidation. This transport system consists of the malonyl-CoA sensitive carnitine palmitoyltransferase I (CPT-I) localized in the mitochondrial outer membrane, the carnitine:acylcarnitine translocase, an integral inner membrane protein, and carnitine palmitoyltransferase II localized on the matrix side of the inner membrane. (Kerner & Hoppel, 2000; Ramsay et al. 2001). Additional reactions annotated here enable the uptake of carnitine and the regulation of fatty acid biosynthesis at the level of ACACA and ACACB to minimize simultaeous mitochondrial catabolism and cytosolic biosynthesis of long-chain fatty acids.
R-HSA-71262 Carnitine synthesis Carnitine is required for the shuttling of fatty acids into the mitochondrial matrix and its deficiency is associated with metabolic diseases. It is abundant in a typical Western diet but can also be synthesized in four steps from trimethyllysine (generated in turn by the S-adenosyl-methionine-mediated methylation of lysine residues in proteins, followed by protein hydrolysis). The enzymes that catalyze the first three steps of carnitine synthesis, converting trimethyllysine to gamma-butyrobetaine, are widely distributed in human tissues. The enzyme that catalyzes the last reaction, converting gamma-butyrobetaine to carnitine, is found only in liver and kidney cells, and at very low levels in brain tissues. Other tissues that require carnitine, such as muscle, are dependent on transport systems that mediate its export from the liver and uptake by other tissues (Bremer 1983; Kerner & Hoppel 1998; Rebouche & Engel 1980; Vaz & Wanders 2002).
R-HSA-140534 Caspase activation via Death Receptors in the presence of ligand Caspase-8 is synthesized as zymogen (procaspase-8) and is formed from procaspase-8 as a cleavage product. However, the cleavage itself appears not to be sufficient for the formation of an active caspase-8. Only the coordinated dimerization and cleavage of the zymogen produce efficient activation in vitro and apoptosis in cellular systems [Boatright KM and Salvesen GS 2003; Keller N et al 2010; Oberst A et al 2010].
The caspase-8 zymogens are present in the cells as inactive monomers, which are recruited to the death-inducing signaling complex (DISC) by homophilic interactions with the DED domain of FADD. The monomeric zymogens undergo dimerization and the subsequent conformational changes at the receptor complex, which results in the formation of catalytically active form of procaspase-8.[Boatright KM et al 2003; Donepudi M et al 2003; Keller N et al 2010; Oberst A et al 2010]. R-HSA-418889 Caspase activation via Dependence Receptors in the absence of ligand In the presence of Netrin1, DCC and UNC5 generate attractive and repulsive signals to growing axons. In the absence of Netrin-1, DCC induces cell death signaling initiated via caspase cleavage of DCC and the interaction of caspase-9. Recent reports have shown that UNC5 receptors similarly induce apoptosis in the absence of Netrin-1. These reactions proceed without a requirement for cytochrome c release from mitochondria or interaction with apoptotic protease activating factor 1 (APAF1). DCC thus regulates an apoptosome-independent pathway for caspase activation. DCC and UNC-5 are hence defined as dependence receptors. Dependence receptors exhibit dual functions depending on the availability of ligand. They create cellular states of dependence on their respective ligands by either inducing apoptosis when unoccupied by the ligand, or inhibiting apoptosis in the presence of the ligand. R-HSA-5357769 Caspase activation via extrinsic apoptotic signalling pathway Caspases, a family of cysteine proteases, execute apoptotic cell death. Caspases exist as inactive zymogens in cells and undergo a cascade of catalytic activation at the onset of apoptosis. Initiation of apoptosis occurs through either a cell-intrinsic or cell-extrinsic pathway. Extrinsic pathway cell death signals originate at the plasma membrane where:
A family of protein serine/threonine kinases known as the cyclin-dependent kinases (CDKs) controls progression through the cell cycle. As the name suggests, the activity of the catalytic subunit is dependent on binding to a cyclin partner. The human genome encodes several cyclins and several CDKs, with their names largely derived from the order in which they were identified. The oscillation of cyclin abundance is one important mechanism by which these enzymes phosphorylate key substrates to promote events at the relevant time and place. Additional post-translational modifications and interactions with regulatory proteins ensure that CDK activity is precisely regulated, frequently confined to a narrow window of activity.
In addition, genome integrity in the cell cycle is maintained by the action of a number of signal transduction pathways, known as cell cycle checkpoints, which monitor the accuracy and completeness of DNA replication during S phase and the orderly chromosomal condensation, pairing and partition into daughter cells during mitosis.
Replication of telomeric DNA at the ends of human chromosomes and packaging of their centromeres into chromatin are two aspects of chromosome maintenance that are integral parts of the cell cycle.
Meiosis is the specialized form of cell division that generates haploid gametes from diploid germ cells, associated with recombination (exchange of genetic material between chromosomal homologs). R-HSA-69620 Cell Cycle Checkpoints A hallmark of the human cell cycle in normal somatic cells is its precision. This remarkable fidelity is achieved by a number of signal transduction pathways, known as checkpoints, which monitor cell cycle progression ensuring an interdependency of S-phase and mitosis, the integrity of the genome and the fidelity of chromosome segregation.
Checkpoints are layers of control that act to delay CDK activation when defects in the division program occur. As the CDKs functioning at different points in the cell cycle are regulated by different means, the various checkpoints differ in the biochemical mechanisms by which they elicit their effect. However, all checkpoints share a common hierarchy of a sensor, signal transducers, and effectors that interact with the CDKs.
The stability of the genome in somatic cells contrasts to the almost universal genomic instability of tumor cells. There are a number of documented genetic lesions in checkpoint genes, or in cell cycle genes themselves, which result either directly in cancer or in a predisposition to certain cancer types. Indeed, restraint over cell cycle progression and failure to monitor genome integrity are likely prerequisites for the molecular evolution required for the development of a tumor. Perhaps most notable amongst these is the p53 tumor suppressor gene, which is mutated in >50% of human tumors. Thus, the importance of the checkpoint pathways to human biology is clear. R-HSA-69278 Cell Cycle, Mitotic The events of replication of the genome and the subsequent segregation of chromosomes into daughter cells make up the cell cycle. DNA replication is carried out during a discrete temporal period known as the S (synthesis)-phase, and chromosome segregation occurs during a massive reorganization of cellular architecture at mitosis. Two gap-phases separate these cell cycle events: G1 between mitosis and S-phase, and G2 between S-phase and mitosis. Cells can exit the cell cycle for a period and enter a quiescent state known as G0, or terminally differentiate into cells that will not divide again, but undergo morphological development to carry out the wide variety of specialized functions of individual tissues.
A family of protein serine/threonine kinases known as the cyclin-dependent kinases (CDKs) controls progression through the cell cycle. As the name suggests, the kinase activity of the catalytic subunits is dependent on binding to cyclin partners, and control of cyclin abundance is one of several mechanisms by which CDK activity is regulated throughout the cell cycle.
A complex network of regulatory processes determines whether a quiescent cell (in G0 or early G1) will leave this state and initiate the processes to replicate its chromosomal DNA and divide. This regulation, during the Mitotic G1-G1/S phases of the cell cycle, centers on transcriptional regulation by the DREAM complex, with major roles for D and E type cyclin proteins.
Chromosomal DNA synthesis occurs in the S phase, or the synthesis phase, of the cell cycle. The cell duplicates its hereditary material, and two copies of each chromosome are formed. A key aspect of the regulation of DNA replication is the assembly and modification of a pre-replication complex assembled on ORC proteins.
Mitotic G2-G2/M phases encompass the interval between the completion of DNA synthesis and the beginning of mitosis. During G2, the cytoplasmic content of the cell increases. At G2/M transition, duplicated centrosomes mature and separate and CDK1:cyclin B complexes become active, setting the stage for spindle assembly and chromosome condensation at the start of mitotic M phase. Mitosis, or M phase, results in the generation of two daughter cells each with a complete diploid set of chromosomes. Events of the M/G1 transition, progression out of mitosis and division of the cell into two daughters (cytokinesis) are regulated by the Anaphase Promoting Complex.
The Anaphase Promoting Complex or Cyclosome (APC/C) plays additional roles in regulation of the mitotic cell cycle, insuring the appropriate length of the G1 phase. The APC/C itself is regulated by phosphorylation and interactions with checkpoint proteins. R-HSA-204998 Cell death signalling via NRAGE, NRIF and NADE p75NTR is a key regulator of neuronal apoptosis, both during development and after injury. Apoptosis is triggered by binding of either mature neurotrophin or proneurotrophin (proNGF, proBDNF). ProNGF is at least 10 times more potent than mature NGF in inducing apoptosis. TRKA signalling protects neurons from apoptosis. The molecular mechanisms involved in p75NTR-apoptosis are not well understood. The death signalling requires activation of c-JUN N-terminal Kinase (JNK), as well as transcriptional events. JNK activation appears to involve the receptor interacting proteins TRAF6, NRAGE, and Rac. The transcription events are thought to be regulated by another p75-interacting protein, NRIF. Two other p75-interacting proteins, NADE and Necdin, have been implicated in apoptosis, but their role is less clear. R-HSA-446728 Cell junction organization Cell junction organization in Reactome currently covers aspects of cell-cell junction organization, cell-extracellular matrix interactions, and Type I hemidesmosome assembly. R-HSA-9664424 Cell recruitment (pro-inflammatory response) Migration of immune cells is orchestrated by a fine balance of cytokine and chemokine responses. During Leishmania macrophage interaction, either pro inflammatory or anti-inflammatory cytokines are produced, having an impact in the establishment of infection and further clinical outcome (Navas et al. 2014). Toll like receptors, GPCRs such as the purinergic receptors P2YRs, complement receptor 3A and interleukin receptor 15 amongst others, have been associated with the production of pro inflammatory cytokines (Lai and Gallo 2012 & Cekic et al. 2016). A strong pro inflammatory response in the acute phase of the infection helps to control the parasite load when the recruited cells enhance microbiocidal mechanisms. However, alterations in the chemokine network may contribute to uncontrolled immune responses that can modulate parasite survival and promote or mitigate the associated immunopathology, thereby influencing the outcome of infection (Navas et al. 2014). R-HSA-1222541 Cell redox homeostasis The most important response of Mtb to oxidative stress is provided by catalase and peroxiredoxins, both of which get their reducing equivalents through a network of disulfide proteins and, finally, from NAD(P)H. Multiple redundancies make choosing a good drug target difficult (Koul et al. 2011). Optimum efficacy can only be expected from inhibitors of the most upstream components of the redox cascades, i.e. the NAD(P)H-dependent reductases TrxB and Lpd (Jaeger & Flohe 2006). R-HSA-202733 Cell surface interactions at the vascular wall Leukocyte extravasation is a rigorously controlled process that guides white cell movement from the vascular lumen to sites of tissue inflammation. The powerful adhesive interactions that are required for leukocytes to withstand local flow at the vessel wall is a multistep process mediated by different adhesion molecules. Platelets adhered to injured vessel walls form strong adhesive substrates for leukocytes. For instance, the initial tethering and rolling of leukocytes over the site of injury are mediated by reversible binding of selectins to their cognate cell-surface glycoconjugates.
Endothelial cells are tightly connected through various proteins, which regulate the organization of the junctional complex and bind to cytoskeletal proteins or cytoplasmic interaction partners that allow the transfer of intracellular signals. An important role for these junctional proteins in governing the transendothelial migration of leukocytes under normal or inflammatory conditions has been established.
This pathway describes some of the key interactions that assist in the process of platelet and leukocyte interaction with the endothelium, in response to injury. R-HSA-1500931 Cell-Cell communication Cell-to-Cell communication is crucial for multicellular organisms because it allows organisms to coordinate the activity of their cells. Some cell-to-cell communication requires direct cell-cell contacts mediated by receptors on their cell surfaces. Members of the immunoglobulin superfamily (IgSF) proteins are some of the cell surface receptors involved in cell-cell recognition, communication and many aspects of the axon guidance and synapse formation-the crucial processes during embryonal development (Rougon & Hobert 2003).
Processes annotated here as aspects of cell junction organization mediate the formation and maintenance of adherens junctions, tight junctions, and gap junctions, as well as aspects of cellular interactions with extracellular matrix and hemidesmosome assembly. Nephrin protein family interactions are central to the formation of the slit diaphragm, a modified adherens junction. Interactions among members of the signal regulatory protein family are important for the regulation of migration and phagocytosis by myeloid cells.
R-HSA-421270 Cell-cell junction organization Epithelial cell-cell contacts consist of three major adhesion systems: adherens junctions (AJs), tight junctions (TJs), and desmosomes. These adhesion systems differ in their function and composition. AJs play a critical role in initiating cell-cell contacts and promoting the maturation and maintenance of the contacts (reviewed in Ebnet, 2008; Hartsock and Nelson, 2008). TJs form physical barriers in various tissues and regulate paracellular transport of water, ions, and small water soluble molecules (reviewed in Rudini and Dejana, 2008; Ebnet, 2008; Aijaz et al., 2006; Furuse and Tsukit, 2006). Desmosomes mediate strong cell adhesion linking the intermediate filament cytoskeletons between cells and playing roles in wound repair, tissue morphogenesis, and cell signaling (reviewed in Holthofer et al., 2007).
R-HSA-446353 Cell-extracellular matrix interactions Cell-extracellular matrix (ECM) interactions play a critical role in regulating a variety of cellular processes in multicellular organisms including motility, shape change, survival, proliferation and differentiation. Cell-ECM contact is mediated by transmembrane cell adhesion receptors, such as integrins, that interact with extracellular matrix proteins as well as a number of cytoplasmic adaptor proteins. Many of these adaptor proteins physically interact with the actin cytoskeleton or function in signal transduction.
Several protein complexes interact with the cytoplasmic tail of integrins and function in transducing bi-directional signals between the ECM and intracellular signaling pathways (reviewed in Sepulveda et al., 2005).
Early events that are triggered by interactions with ECM, such as formation/turnover of Focal Adhesions, regulation of actin dynamics and protrusion of lamellipodia to promote cellular spreading and motility are modulated by PINCH- ILK- parvin complexes (see Sepulveda et al., 2005). A number of partners of the PINCH-ILK-parvin complex components have been identified that regulate and/or mediate the functions of these complexes (reviewed in Wu, 2004). Interactions with some of these partners modulate cytoskeletal remodeling and cell spreading.
R-HSA-2559583 Cellular Senescence Cellular senescence involves irreversible growth arrest accompanied by phenotypic changes such as enlarged morphology, reorganization of chromatin through formation of senescence-associated heterochromatic foci (SAHF), and changes in gene expression that result in secretion of a number of proteins that alter local tissue environment, known as senescence-associated secretory phenotype (SASP).
Senescence is considered to be a cancer protective mechanism and is also involved in aging. Senescent cells accumulate in aged tissues (reviewed by Campisi 1997 and Lopez-Otin 2013), which may be due to an increased senescence rate and/or decrease in the rate of clearance of senescent cells. In a mouse model of accelerated aging, clearance of senescent cells delays the onset of age-related phenotypes (Baker et al. 2011).
Cellular senescence can be triggered by the aberrant activation of oncogenes or loss-of-function of tumor suppressor genes, and this type of senescence is known as the oncogene-induced senescence, with RAS signaling-induced senescence being the best studied. Oxidative stress, which may or may not be caused by oncogenic RAS signaling, can also trigger senescence. Finally, the cellular senescence program can be initiated by DNA damage, which may be caused by reactive oxygen species (ROS) during oxidative stress, and by telomere shortening caused by replicative exhaustion which may be due to oncogenic signaling. The senescent phenotype was first reported by Hayflick and Moorhead in 1961, when they proposed replicative senescence as a mechanism responsible for the cessation of mitotic activity and morphological changes that occur in human somatic diploid cell strains as a consequence of serial passaging, preventing the continuous culture of untransformed cells-the Hayflick limit (Hayflick and Moorhead 1961).
Secreted proteins that constitute the senescence-associated secretory phenotype (SASP), also known as the senescence messaging secretome (SMS), include inflammatory and immune-modulatory cytokines, growth factors, shed cell surface molecules and survival factors. The SASP profile is not significantly affected by the type of senescence trigger or the cell type (Coppe et al. 2008), but the persistent DNA damage may be a deciding SASP initiator (Rodier et al. 2009). SASP components function in an autocrine manner, reinforcing the senescent phenotype (Kuilman et al. 2008, Acosta et al. 2008), and in the paracrine manner, where they may promote epithelial-to-mesenchymal transition (EMT) and malignancy in the nearby premalignant or malignant cells (Coppe et al. 2008).
Senescent cells may remain viable for years, such as senescent melanocytes of moles and nevi, or they can be removed by phagocytic cells. The standard marker for immunohistochemical detection of senescent cells is senescence-associated beta-galactosidase (SA-beta-Gal), a lysosomal enzyme that is not required for senescence.
For reviews of this topic, please refer to Collado et al. 2007, Adams 2009, Kuilman et al. 2010. For a review of differential gene expression between senescent and immortalized cells, please refer to Fridman and Tainsky 2008. R-HSA-189200 Cellular hexose transport Two gene families are responsible for glucose transport in humans. SLC2 (encoding GLUTs) and SLC5 (encoding SGLTs) families mediate glucose absorption in the small intestine, glucose reabsorption in the kidney, glucose uptake by the brain across the blood-brain barrier and glucose release by all cells in the body. Glucose is taken up from interstitial fluid by a passive, facilitative transport driven by the diffusion gradient of glucose (and other sugars) across the plasma membrane. This process is mediated by a family of Na+-independent, facilitative glucose transporters (GLUTs) encoded by the SLC2A gene family (Zhao & Keating 2007; Wood & Trayhurn 2003). There are 14 members belonging to this family (GLUT1-12, 14 and HMIT (H+/myo-inositol symporter)). The GLUT family can be subdivided into three subclasses (I-III) based on sequence similarity and characteristic sequence motifs (Joost & Thorens 2001).
Hexoses, notably fructose, glucose, and galactose, generated in the lumen of the small intestine by breakdown of dietary carbohydrate are taken up by enterocytes lining the microvilli of the small intestine and released from them into the blood. Uptake into enterocytes is mediated by two transporters localized on the lumenal surfaces of the cells, SGLT1 (glucose and galactose, together with sodium ions) and GLUT5 (fructose). GLUT2, localized on the basolateral surfaces of enterocytes, mediates the release of these hexoses into the blood (Wright et al. 2004). GLUT2 may also play a role in hexose uptake from the gut lumen into enterocytes when the lumenal content of monosaccharides is very high (Kellet & Brot-Laroche 2005) and GLUT5 mediates fructose uptake from the blood into cells of the body, notably hepatocytes.
Cells take up glucose by facilitated diffusion, via glucose transporters (GLUTs) associated with the plasma membrane, a reversible reaction. Four tissue-specific GLUT isoforms are known. Glucose in the cytosol is phosphorylated by tissue-specific kinases to yield glucose 6-phosphate, which cannot cross the plasma membrane because of its negative charge. In the liver, this reaction is catalyzed by glucokinase which has a low affinity for glucose (Km about 10 mM) but is not inhibited by glucose 6-phosphate. In other tissues, this reaction is catalyzed by isoforms of hexokinase. Hexokinases are feedback-inhibited by glucose 6-phosphate and have a high affinity for glucose (Km about 0.1 mM). Liver cells can thus accumulate large amounts of glucose 6-phosphate but only when blood glucose concentrations are high, while most other tissues can take up glucose even when blood glucose concentrations are low but cannot accumulate much intracellular glucose 6-phosphate. These differences are consistent with the view that that the liver functions to buffer blood glucose concentrations, while most other tissues take up glucose to meet immediate metabolic needs.
Glucose 6-phosphatase, expressed in liver and kidney, allows glucose 6-phosphate generated by gluconeogenesis (both tissues) and glycogen breakdown (liver) to leave the cell. The absence of glucose 6-phosphatase from other tissues makes glucose uptake by these tissues essentially irreversible, consistent with the view that cells in these tissues take up glucose for local metabolic use.
Class II facilitative transporters consist of GLUT5, 7, 9 and 11 (Zhao & Keating 2007, Wood & Trayhurn 2003).
R-HSA-9711123 Cellular response to chemical stress Cells are equipped with versatile physiological stress responses to prevent hazardous consequences resulting from exposure to chemical insults of endogenous and exogenous origin. Even at equitoxic doses, different stressors induce distinctive and complex signaling cascades. The responses typically follow cell perturbations at the subcellular organelle level.
Expression of heme oxygenase 1 (HMOX1) is regulated by various indicators of cell stress. Cytoprotection by HMOX1 is exerted directly by HMOX1 and by the antioxidant metabolites it produces through the degradation of heme (Origassa et al, 2013; Ryter et al, 2006).
Reactive oxygen and nitrogen species (RONS) are important mediators of chemical stress, as they are produced endogenously in mitochondria, and also result from redox activities of many toxins and heavy metal cations. The points of RONS action in the cell are plasma and ER membrane lipids, as well as DNA, both acting as sensors for the cellular response. On the other hand, chemotherapeutic agents exert their action via generation of RONS and induction of cancer cell apoptosis, while drug resistance associates with RONS-induced cancer cell survival (Sampadi et al, 2020; Moldogazieva et al, 2018).
R-HSA-3371556 Cellular response to heat stress In response to exposure to elevated temperature and certain other proteotoxic stimuli (e.g., hypoxia, free radicals) cells activate a number of cytoprotective mechanisms known collectively as "heat shock response". Major aspects of the heat shock response (HSR) are evolutionarily conserved events that allow cells to recover from protein damage induced by stress (Liu XD et al. 1997; Voellmy R & Boellmann F 2007; Shamovsky I & Nudler E 2008; Anckar J & Sistonen L 2011). The main hallmark of HSR is the dramatic alteration of the gene expression pattern. A diverse group of protein genes is induced by the exposure to temperatures 3-5 degrees higher than physiological. Functionally, most of these genes are molecular chaperones that ensure proper protein folding and quality control to maintain cell proteostasis.
At the same time, heat shock-induced phosphorylation of translation initiation factor eIF2alpha leads to the shutdown of the nascent polypeptide synthesis reducing the burden on the chaperone system that has to deal with the increased amount of misfolded and thermally denatured proteins (Duncan RF & Hershey JWB 1989; Sarkar A et al. 2002; Spriggs KA et al. 2010).
The induction of HS gene expression primarily occurs at the level of transcription and is mediated by heat shock transcription factor HSF1(Sarge KD et al. 1993; Baler R et al. 1993). Human cells express five members of HSF protein family: HSF1, HSF2, HSF4, HSFX and HSFY. HSF1 is the master regulator of the heat inducible gene expression (Zuo J et al. 1995; Akerfelt M et al. 2010). HSF2 is activated in response to certain developmental stimuli in addition to being co-activated with HSF1 to provide promoter-specific fine-tuning of the HS response by forming heterotrimers with HSF1 (Ostling P et al. 2007; Sandqvist A et al. 2009). HSF4 lacks the transcription activation domain and acts as a repressor of certain genes during HS (Nakai A et al. 1997; Tanabe M et al. 1999; Kim SA et al. 2012). Two additional family members HSFX and HSFY, which are located on the X and Y chromosomes respectively, remain to be characterized (Bhowmick BK et al. 2006; Shinka T et al. 2004; Kichine E et al. 2012).
Under normal conditions HSF1 is present in both cytoplasm and nucleus in the form of an inactive monomer. The monomeric state of HSF1 is maintained by an intricate network of protein-protein interactions that include the association with HSP90 multichaperone complex, HSP70/HSP40 chaperone machinery, as well as intramolecular interaction of two conserved hydrophobic repeat regions. Monomeric HSF1 is constitutively phosphorylated on Ser303 and Ser 307 by (Zou J et al. 1998; Knauf U et al. 1996; Kline MP & Moromoto RI 1997; Guettouche T et al. 2005). This phosphorylation plays an essential role in ensuring cytoplasmic localization of at least a subpopulation of HSF1 molecules under normal conditions (Wang X et al. 2004).
Exposure to heat and other proteotoxic stimuli results in the release of HSF1 from the inhibitory complex with chaperones and its subsequent trimerization, which is promoted by its interaction with translation elongation factor eEF1A1 (Baler R et al. 1993; Shamovsky I et al. 2006; Herbomel G et al 2013). The trimerization is believed to involve intermolecular interaction between hydrophobic repeats 1-3 leading to the formation of a triple coil structure. Additional stabilization of the HSF1 trimer is provided by the formation of intermolecular S-S bonds between Cys residues in the DNA binding domain (Lu M et al.2008). Trimeric HSF1 is predominantly localized in the nucleus where it binds the specific sequence in the promoter of hsp genes (Sarge KD et al. 1993; Wang Y and Morgan WD 1994). The binding sequence for HSF1 (HSE, heat shock element) contains series of inverted repeats nGAAn in head-to-tail orientation, with at least three elements being required for the high affinity binding. Binding of the HSF1 trimer to the promoter is not sufficient to induce transcription of the gene (Cotto J et al. 1996). In order to do so, HSF1 needs to undergo inducible phosphorylation on specific Ser residues such as Ser230, Ser326. This phosphorylated form of HSF1 trimer is capable of increasing the promoter initiation rate. HSF1 bound to DNA promotes recruiting components of the transcription mediator complex and relieving promoter-proximal pause of RNA polymerase II through its interaction with TFIIH transcription factor (Yuan CX & Gurley WB 2000).
HSF1 activation is regulated in a precise and tight manner at multiple levels (Zuo J et al. 1995; Cotto J et al. 1996). This allows fast and robust activation of HS response to minimize proteotoxic effects of the stress. The exact set of HSF1 inducible genes is probably cell type specific. Moreover, cells in different pathophysiological states will display different but overlapping profile of HS inducible genes. R-HSA-1234174 Cellular response to hypoxia Oxygen plays a central role in the functioning of human cells: it is both essential for normal metabolism and toxic. Here we have annotated one aspect of cellular responses to oxygen, the role of hypoxia-inducible factor in regulating cellular transcriptional responses to changes in oxygen availability.
In the presence of oxygen members of the transcription factor family HIF-alpha, comprising HIF1A, HIF2A (EPAS1), and HIF3A, are hydroxylated on proline residues by PHD1 (EGLN2), PHD2 (EGLN1), and PHD3 (EGLN3) and on asparagine residues by HIF1AN (FIH) (reviewed in Pouyssegur et al. 2006, Semenza 2007, Kaelin and Ratcliffe 2008, Nizet and Johnson 2009, Brahimi-Horn and Pouyssegur 2009, Majmundar et al. 2010, Loenarz and Schofield 2011). Both types of reaction require molecular oxygen as a substrate and it is probable that at least some HIF-alpha molecules carry both hydroxylated asparagine and hydroxylated proline (Tian et al. 2011).
Hydroxylated asparagine interferes with the ability of HIF-alpha to interact with p300 and CBP while hydroxylated proline facilitates the interaction of HIF-alpha with the E3 ubiquitin ligase VHL, causing ubiquitination and proteolysis of HIF-alpha. Hypoxia inhibits both types of hydroxylation, resulting in the stabilization of HIF-alpha, which then enters the nucleus, binds HIF-beta, and recruits p300 and CBP to activate target genes such as EPO and VEGF.
R-HSA-9840373 Cellular response to mitochondrial stress Mitochondrial stress caused by depolarization of the mitochondrial inner membrane, inhibition of proton flux across the mitochondrial inner membrane, or insufficient protein import capacity caused by inhibition of ATP synthase or iron deficiency is communicated to the cytosol and nucleus, resulting in decreased protein production and increased transcription of chaperones and metabolic genes among others. This pathway is known as the mitochondrial stress response and is a part of mitochondrial signaling and the integrated stress response (Reviewed in Eckl et al. 2021, Picard and Shirihai 2022, Lu et al. 2022, Liu and Birsoy 2023). The mitochondrial stress response participates in adapting cells to harsher environments and, hence, plays a role in tumor progression and metastasis (reviewed in Lee et al. 2022).
In unstressed mitochondria, DELE1 is constitutively imported into the mitochondrial matrix and degraded by the LONP1 ATP-dependent protease (Fessler et al. 2022, Sekine et al. 2023). Mitochondrial stress inhibits the complete transit of DELE1 into the matrix and activates the inner membrane protease OMA1 by self-cleavage (Fessler et al. 2022, Sekine et al. 2023, inferred from the mouse Oma1 homolog in Baker et al. 2014, Zhang et al. 2014). Activated OMA1 cleaves the N-terminal region of DELE1 on the outer face of the inner membrane as DELE1 is unable to fully cross the inner membrane (Fessler et al. 2020, Guo et al. 2020, Fessler et al. 2022). The resulting C-terminal fragment of DELE1 egresses from the intermembrane space to the cytosol where it oligomerizes to form an octamer (Yang et al. 2023) which binds and activates EIF2AK1, a constituent kinase of the integrated stress response that phosphorylates EIF2S1, the alpha subunit of the eukaryotic translation initiation factor 2 (eIF2) (Fessler et al. 2020, Guo et al. 2020, Cheng et al. 2022). Phosphorylation of EIF2S1 inhibits general translation but increases translation of specific mRNAs that possess upstream open reading frames (reviewed in Wek 2018). Among these mRNAs are the transcription factors DDIT3 (CHOP), ATF4, and ATF5, which activate expression of chaperone genes among others.
R-HSA-9711097 Cellular response to starvation Deprivation of nutrients triggers diverse short- and long terms adaptations in cells. Here we have annotated two aspects of cellular responses to amino acid deprivation, ones mediated by EIF2AK4 and ones mediated by mTORC.
EIF2AK4 (GCN2) senses amino acid deficiency by binding uncharged tRNAs near the ribosome, and phosphorylating EIF2S1 (reviewed in Chaveroux et al. 2010, Castilho et al. 2014, Gallinetti et al. 2013, Bröer and Bröer 2017, Wek 2018). This reduces translation of most mRNAs but increases translation of mRNAs, notably ATF4, that mediate stress responses (reviewed in Kilberg et al. 2012, Wortel et al. 2017; Dever and Hinnebusch 2005).
The mTORC1 complex acts as an integrator that regulates translation, lipid synthesis, autophagy, and cell growth in response to multiple inputs, notably glucose, oxygen, amino acids, and growth factors such as insulin (reviewed in Sabatini 2017, Meng et al. 2018, Kim and Guan 2019).
MTOR, the kinase subunit of mTORC1, is activated by interaction with RHEB:GTP at the cytosolic face of lysosomal membrane (Long et al. 2005, Tee et al. 2005, Long et al. 2007, Yang et al. 2017). This process is regulated by various individual amino acids (reviewed in Zhuang et al. 2019, Wolfson and Sabatini 2017, Yao et al. 2017) and is reversed in response to the removal of amino acids, through the action of TSC1 (Demetriades et al. 2014).
R-HSA-9855142 Cellular responses to mechanical stimuli Molecular mechanosensors are biomolecules that convert a physical force into an intracellular chemical signal (reviewed in Martino et al. 2018, Li et al. 2022). One of the most common types of mechanosensor is the mechanically gated ion channel such as PIEZO1 (reviewed in Fang et al. 2021). Other mechanosensors include integrins (reviewed in Hirata et al. 2015) and receptors such as AGTR1 and GPR68 (reviewed in Xiao et al. 2023). After activation by force, mechanosensors then activate mechanotransducers such as kinases and channels to amplify and transfer the signal to chemical processes that produce downstream effects such as changes in gene expression, cell growth, and behavior (reviewed in Martino et al. 2018).
Mechanosensors and mechanotransducers enable endothelial cells to respond to laminar and turbulent blood flow (reviewed in Davis et al. 2023, Rahaman et al. 2023, Lim and Harraz 2024), osteocytes to respond to mechanical load and fluid flow (reviewed in Qin et al. 2021, Moharrer and Boerckel 2022, Wang et al. 2023), and specialized cellular structures such as Merkel cells and Pacinian corpuscles to respond to touch (reviewed in Handler and Ginty 2021, Logan et al. 2024).
R-HSA-8953897 Cellular responses to stimuli Individual cells detect and respond to diverse external molecular and physical signals. Appropriate responses to these signals are essential for normal development, maintenance of homeostasis in mature tissues, and effective defensive responses to potentially noxious agents (Kultz 2005). It is convenient, if somewhat arbitrary, to distinguish responses to signals involved in development and homeostasis from ones involved in stress responses, and that classification is followed here, with macroautophagy and responses to metal ions classified as responses to normal external stimuli, while responses to hypoxia, reactive oxygen species, and heat, and the process of cellular senescence are classified as stress responses. Signaling cascades are integral components of all of these response mechanisms but because of their number and diversity, they are grouped in a separate signal transduction superpathway in Reactome.
R-HSA-2262752 Cellular responses to stress Cells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. Cells are also subject to internal molecular stresses such as production of reactive metabolic byproducts. The ability of cells and tissues to modulate molecular processes in response to such stresses is essential to the maintenance of tissue homeostasis (Kultz 2005). Specific stress-related processes annotated here are cellular response to hypoxia, cellular response to heat stress, cellular senescence, HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand, response of EIF2AK1 (HRI) to heme deficiency, heme signaling, cellular response to chemical stress, cellular response to starvation, and unfolded protein response.
R-HSA-380287 Centrosome maturation The centrosome is the primary microtubule organizing center (MTOC) in vertebrate cells and plays an important role in orchestrating the formation of the mitotic spindle. Centrosome maturation is an early event in this process and involves a major reorganization of centrosomal material at the G2/M transition. During maturation, centrosomes undergo a dramatic increase in size and microtubule nucleating capacity. As part of this process, a number of proteins and complexes, including some that are required for microtubule nucleation and anchoring, are recruited to the centrosome while others that are required for organization of interphase microtubules and centrosome cohesion are lost (reviewed in Schatten, 2008; Raynaud-Messina and Merdes 2007).
R-HSA-193681 Ceramide signalling In certain cell types, ligand binding to p75NTR leads to ceramide production, which can mediate either cell survival (e.g. in noecotical subplate neurons) or apoptosis (e.g. in oligodendrocytes). Low levels of ceramide are also able to stimulate axonal outgrowth in hippocampal neurons.
R-HSA-163765 ChREBP activates metabolic gene expression ChREBP (Carbohydrate Response Element Binding Protein) is a large multidomain protein containing a nuclear localization signal near its amino terminus, polyproline domains, a basic helix-loop-helix-leucine zipper domain, and a leucine-zipper-like domain (Uyeda et al., 2002). Its dephosphorylation in response to molecular signals associated with the well-fed state allows it to enter the nucleus, interact with MLX protein, and bind to ChRE DNA sequence motifs near Acetyl-CoA carboxylase, Fatty acid synthase, and Pyruvate kinase (L isoform) genes (Ishi et al.2004). This sequence of events is outlined schematically in the picture below (adapted from Kawaguchi et al. (2001) - copyright (2001) National Academy of Sciences, U.S.A.).
R-HSA-9613829 Chaperone Mediated Autophagy In contrary to the vesicle-mediated macroautophagy, the chaperone mediated mechanism of autophagy selectively targets individual proteins to the lysosome for degradation. Chaperones bind intracellular proteins based on recognition motifs and transports them from the cytosol to the lysosomal membrane. Subsequently, the protein is translocated into the lumen for digestion (Cuervo A M et al. 2014, Kaushik S et al. 2018).
R-HSA-390466 Chaperonin-mediated protein folding The eukaryotic chaperonin TCP-1 ring complex (TRiC/ CCT) plays an essential role in the folding of a subset of proteins prominent among which are the actins and tubulins (reviewed in Altschuler and Willison, 2008). CCT/TRiC is an example of a type II chaperonin, defined (in contrast to type I) as functioning in the absence of a cochaperonin. TriC/CCT is a multisubunit toroidal complex that forms a cylinder containing two back-to-back stacked rings enclosing a cavity where substrate folding occurs in an ATP dependent process (reviewed in Altschuler and Willison, 2008 ). CCT/TriC contains eight paralogous subunits that are conserved throughout eukaryotic organisms (Leroux and Hartl 2000; Archibald et al. 2001; Valpuesta et al. 2002). CCT-mediated folding of non-native substrate protein involves capture through hydrophobic contacts with multiple chaperonin subunits followed by transfer of the protein into the central ring cavity where it folds. Although folding is initiated within this central cavity, only 5%-20% of proteins that are released have partitioned to the native state. The remaining portion is then recaptured by other chaperonin molecules (Cowan and Lewis 2001). This cycling process may be repeated multiple times before a target protein partitions to the native state. In the cell, binding to CCT occurs via presentation of target protein bound to upstream chaperones. During translation, the emerging polypeptide chain may be transferred from the ribosome to CCT via the chaperone Prefoldin (Vainberg et al., 1998) or the Hsp70 chaperone machinery (Melville et al., 2003). While the majority of CCT substrates ultimately partition to the native state as soluble, monomeric proteins, alpha and beta tubulin are unusual in that they require additional cofactors that are required to assemble the tubulin heterodimer (Cowan and Lewis 2001).
R-HSA-380108 Chemokine receptors bind chemokines Chemokine receptors are cytokine receptors found on the surface of certain cells, which interact with a type of cytokine called a chemokine. Following interaction, these receptors trigger a flux of intracellular calcium which leads to chemotaxis. Chemokine receptors are divided into different families, CXC chemokine receptors, CC chemokine receptors, CX3C chemokine receptors and XC chemokine receptors that correspond to the 4 distinct subfamilies of chemokines they bind.
R-HSA-75035 Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex DNA damage induced activation of the checkpoint kinases Chk1/Chk2(Cds1) results in the conversion and/or maintenance of CyclinB:Cdc2 complex in its Tyrosine 15 phosphorylated (inactive) state. Cdc2 activity is regulated by a balance between the phosphorylation and dephosphorylation by the Wee1/Myt1 kinase and Cdc25 phosphatase. Inactivation of the Cyclin B:Cdc2 complex likely involves both inactivation of Cdc25 and/or stimulation of Wee1/Myt1 kinase activity.
R-HSA-191273 Cholesterol biosynthesis Cholesterol is synthesized de novo from acetyl CoA. The overall synthetic process is outlined in the attached illustration. Enzymes whose regulation plays a major role in determining the rate of cholesterol synthesis in the body are highlighted in red, and connections to other metabolic processes are indicated. The transformation of zymosterol into cholesterol can follow either of routes, one in which reduction of the double bond in the isooctyl side chain is the final step (cholesterol synthesis via desmosterol, also known as the Bloch pathway) and one in which this reduction is the first step (cholesterol biosynthesis via lathosterol, also known as the Kandutsch-Russell pathway). The former pathway is prominent in the liver and many other tissues while the latter is prominent in skin, where it may serve as the source of the 7-dehydrocholesterol that is the starting point for the synthesis of D vitamins. Defects in several of the enzymes involved in this process are associated with human disease and have provided useful insights into the regulatory roles of cholesterol and its synthetic intermediates in human development (Gaylor 2002; Herman 2003; Kandutsch & Russell 1960; Mitsche et al. 2015; Song et al. 2005).
R-HSA-6807047 Cholesterol biosynthesis via desmosterol The transformation of zymosterol into cholesterol can follow either of routes, one in which reduction of the double bond in the isooctyl side chain is the final step (cholesterol synthesis via desmosterol, also known as the Bloch pathway) and one in which this reduction is the first step (cholesterol biosynthesis via lathosterol, also known as the Kandutsch-Russell pathway). The former pathway is prominent in the liver and many other tissues while the latter is prominent in skin, where it may serve as the source of the 7-dehydrocholesterol that is the starting point for the synthesis of D vitamins (Mitsche et al. 2015).
R-HSA-6807062 Cholesterol biosynthesis via lathosterol The transformation of zymosterol into cholesterol can follow either of routes, one in which reduction of the double bond in the isooctyl side chain is the final step (cholesterol synthesis via desmosterol, also known as the Bloch pathway) and one in which this reduction is the first step (cholesterol biosynthesis via lathosterol, also known as the Kandutsch-Russell pathway). The former pathway is prominent in the liver and many other tissues while the latter is prominent in skin, where it may serve as the source of the 7-dehydrocholesterol that is the starting point for the synthesis of D vitamins (Kandutsch & Russell 1960; Mitsche et al. 2015).
R-HSA-6798163 Choline catabolism Choline is an essential water-soluble nutrient in humans, serving as a precursor of phospholipids and the neurotransmitter acetylcholine. It is often associated with B vitamins based on its chemical structure but it isn't an official B vitamin. Its oxidation to betaine provides a link to folate-dependent, one-carbon metabolism where betaine is a methyl donor in the methionine cycle. Betaine is further metabolised to dimethylglycine which is cleared by the kidney (Ueland 2011, Hollenbeck 2012).
R-HSA-2022870 Chondroitin sulfate biosynthesis Chondroitin sulfate (CS) glycosaminoglycan consists of N-acetylgalactosamine (GalNAc) residues alternating in glycosidic linkages with glucuronic acid (GlcA). GalNAc residues are sulfated to varying degrees on 4- and/or 6- positions. The steps below describe the biosynthesis of a simple CS molecule (Pavao et al. 2006, Silbert & Sugumaran 2002).
R-HSA-1793185 Chondroitin sulfate/dermatan sulfate metabolism Chondroitin sulfate (CS) is a sulfated glycosaminoglycan (GAG). CS chains are unbranched polysaccharides of varying length containing two alternating monosaccharides: D-glucuronic acid (GlcA) and N-acetyl-D-galactosamine (GalNAc). The chains are usually attached to proteins forming a proteoglycan. CS is an important structural component of cartilage due to it's ability to withstand compression. It is also a widely used dietary supplement for osteoarthritis. When some of the GlcA residues are epimerized into L-iduronic acid (IdoA) the resulting disaccharide is then referred to as dermatan sulfate (DS) (Silbert & Sugumaran 2002). DS is the most predominant GAG in skin but is also found in blood vessels, heart valves, tendons, and the lungs. It may play roles in cardiovascular disease, tumorigenesis, infection, wound repair and fibrosis (Trowbridge & Gallo 2002).
R-HSA-9821002 Chromatin modifications during the maternal to zygotic transition (MZT) Chromatin in the zygotic pronuclei transitions to a more open and accessible conformation by DNA demethylation and changes to histone modifications. As development proceeds through the cleavage stages to the blastocyst, chromatin continues to become more accessible until DNA methylation and a more restrictive chromatin conformation are re-established after implantation of the embryo in the uterus.
In the oocyte, H3K9me2 produced by EHMT2 (G9a, KMT1C) and H3K9me3 produced by SETDB1 (KMT1E) are transmitted to the female pronucleus of the zygote and protect maternal DNA from active demethylation (inferred from mouse zygotes in Zeng et al. 2019, reviewed in de Macedo et al. 2021). DPPA3 binds H3K9me2, preventing the 5-methylcytosine oxidase TET3 from being recruited to chromatin (inferred from mouse homologs in Nakamura et al. 2007, Wossidlo et al. 2011, Nakamura et al. 2012). DPPA3 also displaces UHRF1 from chromatin, preventing the maintenance DNA methylase DNMT1 from being recruited to chromatin and thus allowing passive DNA demethylation to occur in the female genome (inferred from mouse homologs in Funaki et al. 2014, Li et al. 2018, Du et al. 2019, Mulholland et al. 2020).
In the male pronucleus of the zygote, AICDA (AID) deaminates cytosine residues and long patch repair replaces the mismatches and adjacent 5-methylcytidine residues with cytidine (Santos et al. 2013, Franchini et al. 2014). After this initial demethylation, TET3 is recruited to chromatin by METTL23 and STGP4 (GSE) (inferred from mouse homologs in Hatanaka et al. 2017) where it oxidizes remaining 5-methylcytidine to 5-hydroxymethylcytidine, which is removed by base excision repair and replaced with cytidine (inferred from mouse homologs in Gu et al. 2011, Iqbal et al. 2011, Wossidlo et al. 2011, Santos et al. 2013, Amouroux et al. 2016, Hatanaka et al. 2017).
The repressive mark H3K27me3 decreases in 2-cell embryos near developmentally related genes (Xia et al. 2019). The H3K27me3 demethylases KDM6B (inferred from bovine embryos in Chung et al. 2017, Canovas et al. 2012) and KDM6A (inferred from mouse embryos in Bai et al. 2019) appear to play a role in the decrease of H3K27me3, as downregulation of them impairs H3K27me3 loss, zygotic genome activation, and embryonic development. Embryonic development also requires H3K36me3, a permissive mark located in transcribed gene bodies that is produced in the oocyte by SETD2 (inferred from mouse embryos in Xu et al. 2019).
In mouse oocytes, H3K4me3 occurs in unusually broad regions that span genes Dahl et al. 2016, Zhang et al. 2016). These broad regions persist in the zygote and into the 2-cell stage. In the late 2-cell stage the more usual patterns of H3K4me3 are established as sharp peaks of H3K4me3 near the transcription start sites and stop sites of genes. The histone methyltransferase KMT2B is at least partly responsible for establishing the broad regions of H3K4me3 in the oocyte and the histone demethylases KDM5B and KDM5A remove the broad H3K4me3 in the late 2-cell stage embryo (inferred from mouse homologs in Dahl et al. 2016, reviewed in Eckerseley-Maslin et al. 2018).
In human oocytes and zygotes, however, broad regions of H3K4me3 are not observed across genes but are located across distal, CpG-rich domains which have partial DNA methylation (Xia et al. 2019). At the 8-cell stage, expression of KDM5B increases and the H3K4me3 at the distal domains is lost as zygotic genome activation occurs, suggesting a role for KDM5B in loss of H3K4me3 (Xia et al. 2019).
R-HSA-3247509 Chromatin modifying enzymes Eukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect it from damage. Access to DNA is achieved by highly regulated local chromatin decondensation.
The 'building block' of chromatin is the nucleosome. This contains ~150 bp of DNA wrapped around a histone octamer which consists of two each of the core histones H2A, H2B, H3 and H4 in a 1.65 left-handed superhelical turn (Luger et al. 1997, Andrews & Luger 2011).
Most organisms have multiple genes encoding the major histone proteins. The replication-dependent genes for the five histone proteins are clustered together in the genome in all metazoans. Human replication-dependent histones occur in a large cluster on chromosome 6 termed HIST1, a smaller cluster HIST2 on chromosome 1q21, and a third small cluster HIST3 on chromosome 1q42 (Marzluff et al. 2002). Histone genes are named systematically according to their cluster and location within the cluster.
The 'major' histone genes are expressed primarily during the S phase of the cell cycle and code for the bulk of cellular histones. Histone variants are usually present as single-copy genes that are not restricted in their expression to S phase, contain introns and are often polyadenylated (Old & Woodland 1984). Some variants have significant differences in primary sequence and distinct biophysical characteristics that are thought to alter the properties of nucleosomes. Others localize to specific regions of the genome. Some variants can exchange with pre-existing major histones during development and differentiation, referred to as replacement histones (Kamakaka & Biggins 2005). These variants can become the predominant species in differentiated cells (Pina & Suau 1987, Wunsch et al. 1991). Histone variants may have specialized functions in regulating chromatin dynamics.
The H2A histone family has the highest sequence divergence and largest number of variants. H2A.Z and H2A.XH2A are considered 'universal variants', found in almost all organisms (Talbert & Henikoff 2010). Variants differ mostly in the C-terminus, including the docking domain, implicated in interactions with the (H3-H4)x2 tetramer within the nucleosome, and in the L1 loop, which is the interaction interface of H2A-H2B dimers (Bonisch & Hake 2012). Canonical H2A proteins are expressed almost exclusively during S-phase. There are several nearly identical variants (Marzluff et al. 2002). No functional specialization of these canonical H2A isoforms has been demonstrated (Bonisch & Hake 2012). Reversible histone modifications such as acetylation and methylation regulate transcription from genomic DNA, defining the 'readability' of genes in specific tissues (Kouzarides 2007, Marmorstein & Trievel 2009, Butler et al. 2012).
N.B. The coordinates of post-translational modifications represented here follow Reactome standardized naming, which includes the UniProt standard practice whereby coordinates refer to the translated protein before any further processing. Histone literature typically refers to coordinates of the protein after the initiating methionine has been removed; therefore the coordinates of post-translated histone residues described here are frequently +1 when compared with the literature. For more information on Reactome's standards for naming pathway events, the molecules that participate in them and representation of post-translational modifications, please refer to Naming Conventions on the Reactome Wiki or Jupe et al. 2014.
R-HSA-4839726 Chromatin organization Chromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance of the physical structure of eukaryotic chromatin. These processes include histone modification, DNA modification, and transcription. The modifications are bound by specific proteins that alter the conformation of chromatin.
R-HSA-73886 Chromosome Maintenance Maintenance of chromosomal organization is critical for stable chromosome function. Two aspects of maintenance annotated in Reactome are centromeric chromatin assembly outside the context of DNA replication, involving nucleosome assembly with the histone H3 variant CenH3 (also called CENP-A), and the maintenance of telomeres, protein-DNA complexes at the ends of linear chromosomes that are important for genome stability.
R-HSA-8963888 Chylomicron assembly Chylomicrons transport triacylglycerol, phospholipid, and cholesterol derived from dietary lipid from the small intestine to other tissues of the body. Each chylomicron assembles around a single molecule of apolipoprotein B-48 (Phillips et al. 1997) which at the time the particle leaves the intestine and enters the lymphatic circulation is complexed with >200,000 molecules of triacylglycerol (TG), ~35,000 of phospholipid, ~11,000 of cholesterol ester, ~8,000 of free cholesterol, ~60 copies of apolipoprotein A-I, ~15 copies of apolipoprotein A-IV, and copies of apolipoprotein A-II (Bhattacharya and Redgrave 1981).
R-HSA-8964026 Chylomicron clearance Circulating chylomicrons acquire molecules of apolipoproteins C and E and through interaction with endothelial lipases lose a large fraction of their triacylglycerol. These changes convert them to chylomicron remnants which bind to LDL receptors, primarily on the surfaces of liver cells, clearing them from the circulation.
This binding and clearance process involves several steps and requires the presence of heparan sulfate proteoglycan (HSPG)-associated hepatic lipase (HL). The molecular details of LDLR binding, and of the following steps of remnant endocytosis, are inferred from those of the coorresponding step of LDLR-mediated low-density lipoprotein (LDL) endocytosis (Redgrave 2004).
R-HSA-8963901 Chylomicron remodeling As chylomicrons circulate in the body, they acquire molecules of apolipoproteins C and E, and through interaction with endothelial lipases can lose a large fraction of their triacylglycerol. These changes convert them to chylomicron remnants which bind to LDL receptors, primarily on the surfaces of liver cells, clearing them from the circulation. This whole sequence of events is rapid: the normal lifespan of a chylomicron is 30 - 60 minutes (Redgrave 2004).
R-HSA-5617833 Cilium Assembly Cilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguished by the structure of their microtubule-based axonemes. The axoneme consists of nine peripheral doublet microtubules, and in the case of many motile cilia, may also contain a pair of central single microtubules. These are referred to as 9+0 or 9+2 axonemes, respectively. Relative to their non-motile counterparts, motile cilia also contain additional structures that contribute to motion, including inner and outer dynein arms, radial spokes and nexin links. Four main types of cilia have been identified in humans: 9+2 motile (such as respiratory cilia), 9+0 motile (nodal cilia), 9+2 non-motile (kinocilium of hair cells) and 9+0 non-motile (primary cilium and photoreceptor cells) (reviewed in Fliegauf et al, 2007). This pathway describes cilia formation, with an emphasis on the primary cilium. The primary cilium is a sensory organelle that is required for the transduction of numerous external signals such as growth factors, hormones and morphogens, and an intact primary cilium is needed for signaling pathways mediated by Hh, WNT, calcium, G-protein coupled receptors and receptor tyrosine kinases, among others (reviewed in Goetz and Anderson, 2010; Berbari et al, 2009; Nachury, 2014). Unlike the motile cilia, which are generally present in large numbers on epithelial cells and are responsible for sensory function as well as wave-like beating motions, the primary cilium is a non-motile sensory organelle that is present in a single copy at the apical surface of most quiescent cells (reviewed in Hsiao et al, 2012). Cilium biogenesis involves the anchoring of the basal body, a centriole-derived organelle, near the plasma membrane and the subsequent polymerization of the microtubule-based axoneme and extension of the plasma membrane (reviewed in Ishikawa and Marshall, 2011; Reiter et al, 2012). Although the ciliary membrane is continuous with the plasma membrane, the protein and lipid content of the cilium and the ciliary membrane are distinct from those of the bulk cytoplasm and plasma membrane (reviewed in Emmer et al, 2010; Rohatgi and Snell, 2010). This specialized compartment is established and maintained during cilium biogenesis by the formation of a ciliary transition zone, a proteinaceous structure that, with the transition fibres, anchors the basal body to the plasma membrane and acts as a ciliary pore to limit free diffusion from the cytosol to the cilium (reviewed in Nachury et al, 2010; Reiter et al, 2012). Ciliary components are targeted from the secretory system to the ciliary base and subsequently transported to the ciliary tip, where extension of the axoneme occurs, by a motor-driven process called intraflagellar transport (IFT). Anterograde transport of cargo from the ciliary base to the tip of the cilium requires kinesin-2 type motors, while the dynein-2 motor is required for retrograde transport back to the ciliary base. In addition, both anterograde and retrograde transport depend on the IFT complex, a multiprotein assembly consisting of two subcomplexes, IFT A and IFT B. The primary cilium is a dynamic structure that undergoes continuous steady-state turnover of tubulin at the tip; as a consequence, the IFT machinery is required for cilium maintenance as well as biogenesis (reviewed in Bhogaraju et al, 2013; Hsiao et al, 2012; Li et al, 2012; Taschner et al, 2012; Sung and Leroux, 2013). The importance of the cilium in signaling and cell biology is highlighted by the wide range of defects and disorders, collectively known as ciliopathies, that arise as the result of mutations in genes encoding components of the ciliary machinery (reviewed in Goetz and Anderson, 2010; Madhivanan and Aguilar, 2014).
R-HSA-9793528 Ciprofloxacin ADME Ciprofloxacin (Cipro) is a widely used broad spectrum bacterial antibiotic. Due to its association with disabling and potentially persistent adverse reactions and current high levels of resistance its use is now recommended in patients who have no alternative treatment option for respiratory and urinary tract infections, skin and soft tissue infections, bone and joint infections, infectious diarrhea, typhoid fever and gonorrhea with susceptible strains. Adverse reactions include tendinitis, tendon rupture, peripheral neuropathy, and CNS effects. The usual dosages are 250 mg and 500 mg (FDA, 2016; Bayer Inc, 2020).
Cipro is highly soluble in aqeuous media below pH 5 and above pH 10. About 60 to 80 percent are taken up by the body. The main absorption site of ciprofloxacin is the upper GI tract, up to the jejunum (Harder et al, 1990; summarized in Olivera et al, 2011). In the context of the Biopharmaceutics Classification System (BCS) Cipro is "not highly soluble", and "not highly permeable". It is classified as BCS class 2, 3, and 4, and uptake and efflux transporters have a big effect on its absorption and excretion. BCS class 4 drugs are primarily excreted unchanged via the biliary or renal routes (Wu and Benet, 2005).
Very high concentrations of Cipro with respect to plasma concentrations are seen in kidney and gall bladder; high concentrations are also found in liver, prostatic tissue, and lung. The main excretion routes for unchanged Cipro are renal (about 65% of plasma amount) and intestinal (about 10%) (Rohwedder et al, 1990; Viell et al, 1992; reviewed by Sörgel, 1989). The intestinal figure includes excretion through epithelial GI cells, and through hepatic cells and the bile duct. The rest of plasma Cipro (10 to 20%) is metabolised, with the major species recovered from urine being oxociprofloxacin and, in faeces, sulfociprofloxacin. Both account for about five per cent each of total excretion (reviewed by Campoli-Richards et al, 1988).
R-HSA-400253 Circadian Clock At the center of the mammalian circadian clock is a negative transcription/translation-based feedback loop: The BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) heterodimer transactivates CRY and PER genes by binding E-box elements in their promoters; the CRY and PER proteins then inhibit transactivation by BMAL1:CLOCK/NPAS2. BMAL1:CLOCK/NPAS2 activates transcription of CRY, PER, and several other genes in the morning. Levels of PER and CRY proteins rise during the day and inhibit expression of CRY, PER, and other BMAL1:CLOCK/NPAS2-activated genes in the afternoon and evening. During the night CRY and PER proteins are targeted for degradation by phosphorylation and polyubiquitination, allowing the cycle to commence again in the morning.
Transcription of the BMAL1 (ARNTL) gene is controlled by ROR-alpha and REV-ERBA (NR1D1), both of which are targets of BMAL1:CLOCK/NPAS2 in mice and both of which compete for the same element (RORE) in the BMAL1 promoter. ROR-alpha (RORA) activates transcription of BMAL1; REV-ERBA represses transcription of BMAL1. This mutual control forms a secondary, reinforcing loop of the circadian clock. REV-ERBA shows strong circadian rhythmicity and confers circadian expression on BMAL1.
BMAL1 can form heterodimers with either CLOCK or NPAS2, which act redundantly but show different tissue specificity. The BMAL1:CLOCK and BMAL1:NPAS2 heterodimers activate a set of genes that possess E-box elements (consensus CACGTG) in their promoters. This confers circadian expression on the genes. The PER genes (PER1, PER2, PER3) and CRY genes (CRY1, CRY2) are among those activated by BMAL1:CLOCK and BMAL1:NPAS2. PER and CRY mRNA accumulates during the morning and the proteins accumulate during the afternoon. PER and CRY proteins form complexes in the cytosol and these are bound by either CSNK1D or CSNK1E kinases which phosphorylate PER and CRY. The phosphorylated PER:CRY:kinase complex is translocated into the nucleus due to the nuclear localization signal of PER and CRY. Within the nucleus the PER:CRY complexes bind BMAL1:CLOCK and BMAL1:NPAS2, inhibiting their transactivation activity and their phosphorylation. This reduces expression of the target genes of BMAL1:CLOCK and BMAL1:NPAS2 during the afternoon and evening.
PER:CRY complexes also traffic out of the nucleus into the cytosol due to the nuclear export signal of PER. During the night PER:CRY complexes are polyubiquitinated and degraded, allowing the cycle to begin again. Phosphorylated PER is bound by Beta-TrCP1, a cytosolic F-box type component of some SCF E3 ubiquitin ligases. CRY is bound by FBXL3, a nucleoplasmic F-box type component of some SCF E3 ubiquitin ligases. Phosphorylation of CRY1 by Adenosine monophosphate-activated kinase (AMPK) enhances degradation of CRY1. PER and CRY are subsequently polyubiquitinated and proteolyzed by the 26S proteasome.
The circadian clock is cell-autonomous and some, but not all cells of the body exhibit circadian rhythms in metabolism, cell division, and gene transcription. The suprachiasmatic nucleus (SCN) in the hypothalamus is the major clock in the body and receives its major input from light (via retinal neurons) and a minor input from nutrient intake. The SCN and other brain tissues determine waking and feeding cycles and influence the clocks in other tissues by hormone secretion and nervous stimulation. Independently of the SCN, other tissues such as liver receive inputs from signals from the brain and from nutrients.
R-HSA-71403 Citric acid cycle (TCA cycle) In the citric acid or tricarboxylic acid (TCA) cycle, the acetyl group of acetyl CoA (derived primarily from oxidative decarboxylation of pyruvate, beta-oxidation of long-chain fatty acids, and catabolism of ketone bodies and several amino acids) can be completely oxidized to CO2 in reactions that also yield one high-energy phosphate bond (as GTP or ATP) and four reducing equivalents (three NADH + H+, and one FADH2). Then, the electron transport chain oxidizes NADH and FADH2 to yield nine more high-energy phosphate bonds (as ATP). All reactions of the citric acid cycle take place in the mitochondrion.
Eight canonical reactions mediate the synthesis of citrate from acetyl-CoA and oxaloacetate and the metabolism of citrate to re-form oxaloacetate. Three reactions are reversible: the interconversions of citrate and isocitrate, of fumarate and malate, and of malate and oxaloacetate. The reverse reactions are irrelevant under normal physiological conditions but appear to have a role in glucose- and glutamine-stimulated insulin secretion (Zhang et al., 2020) and cancer metabolism (e.g., Jiang et al., 2016). Succinate synthesis from succinyl-CoA can be coupled to the phosphorylation of either GDP (the canonical reaction) or ADP; we annotate both reactions. Two mitochondrial isocitrate dehydrogenase isozymes catalyze the oxidative decarboxylation of isocitrate to form alpha-ketoglutarate (2-oxoglutarate): IDH3 catalyzes the canonical reaction coupled to the reduction of NAD+, while IDH2 catalyzes the same reaction coupled to the reduction of NADP+, a reaction whose normal physiological function is unclear. Both reactions are annotated.
The cyclical nature of the reactions responsible for the oxidation of acetate was first suggested by Hans Krebs from biochemical studies of pigeon breast muscle (Krebs et al., 1938; Krebs and Eggleston, 1940). Ochoa and colleagues studied many molecular details of individual reactions, mainly by studying enzymes purified from pig hearts (Ochoa, 1980). While the human homologs of these enzymes have all been identified, their biochemical characterization has, in general, been limited, and many molecular details of the human reactions are inferred from those worked out in studies of the model systems. Studies examining the impact of elevated citric acid cycle intermediates such as succinate and fumarate led to the recognition of the role of metabolites in driving cancer progression ('oncometabolites') (Pollard et al., 2005; reviewed in Hayashi et al., 2018). The role of TCA enzymes in disease was reviewed by Kang et al., 2021.
R-HSA-373076 Class A/1 (Rhodopsin-like receptors) Rhodopsin-like receptors (class A/1) are the largest group of GPCRs and are the best studied group from a functional and structural point of view. They show great diversity at the sequence level and thus, can be subdivided into 19 subfamilies (Subfamily A1-19) based on a phylogenetic analysis (Joost P and Methner A, 2002). They represent members which include hormone, light and neurotransmitter receptors and encompass a wide range of functions including many autocrine, paracrine and endocrine processes.
R-HSA-373080 Class B/2 (Secretin family receptors) This family is known as Family B (secretin-receptor family, family 2) G-protein-coupled receptors. Family B GPCRs include secretin, calcitonin, parathyroid hormone/parathyroid hormone-related peptides and vasoactive intestinal peptide receptors; all of which activate adenylyl cyclase and the phosphatidyl-inositol-calcium pathway (Harmar AJ, 2001).
R-HSA-420499 Class C/3 (Metabotropic glutamate/pheromone receptors) The class C G-protein-coupled receptors are a class of G-protein coupled receptors that include the metabotropic glutamate receptors and several additional receptors (Brauner-Osborne H et al, 2007). Family C GPCRs have a large extracellular N-terminus which binds the orthosteric (endogenous) ligand. The shape of this domain is often likened to a clam. Several allosteric ligands to these receptors have been identified and these bind within the seven transmembrane region.
R-HSA-983169 Class I MHC mediated antigen processing & presentation Major histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular bacteria or tumor-associated antigens. They bind peptide fragments of these proteins and presenting them to CD8+ T cells at the cell surface. This enables cytotoxic T cells to identify and eliminate cells that are synthesizing abnormal or foreign proteins. MHC class I is a trimeric complex composed of a polymorphic heavy chain (HC or alpha chain) and an invariable light chain, known as beta2-microglobulin (B2M) plus an 8-10 residue peptide ligand. Represented here are the events in the biosynthesis of MHC class I molecules, including generation of antigenic peptides by the ubiquitin/26S-proteasome system, delivery of these peptides to the endoplasmic reticulum (ER), loading of peptides to MHC class I molecules and display of MHC class I complexes on the cell surface.
R-HSA-9603798 Class I peroxisomal membrane protein import Most peroxisomal membrane proteins (PMPs) are inserted into the peroxisomal membrane by the receptor-chaperone PEX19 and the docking receptor PEX3 (Soukupova et al. 1999, Muntau et al. 2003, Fang et al. 2004, Fujiki et al. 2006, Matsuzono and Fujiki 2006, Matsuzono et al. 2006, Pinto et al. 2006, Sato et al. 2008, Sato et al. 2010, Schmidt et al. 2010, Hattula et al. 2014, reviewed in Fujiki et al. 2014, Mayerhofer 2016). PEX19 binds the PMP as it is translated in the cytosol. Recognition of the PMP by PEX 19 appears to depend on positively charged residues in the transmembrane domain of the PMP (Costello et al. 2017). The PEX19:PMP complex then interacts with PEX3 located in the peroxisomal membrane. Through a mechanism that is not yet clear, the PMP is inserted into the peroxisomal membrane and PEX19 dissociates from PEX3. A current model involves transfer of the PMP from PEX19 to a hydrophobic region of PEX3 followed by insertion of the PMP into the membrane (Chen et al. 2014, reviewed by Giannopoulou et al. 2016). The process does not appear to require hydrolysis of ATP or GTP (Pinto et al. 2006).
Unlike other PMPs, PEX3 is inserted into the peroxisomal membrane by binding PEX19 and then docking with PEX16 (Matsuzaki and Fujiki 2008). Both PEX3 and PEX16 can also be co-translationally inserted into the endoplasmic reticulum membrane (Kim et al. 2006, Yonekawa et al. 2011, Aranovich et al. 2014, Hua et al. 2015, Mayerhofer et al. 2016). This region of the ER membrane then buds to contribute to new peroxisomes. PEX3 is also observed to insert into the mitochondrial outer membrane (Sugiura et al. 2017). Regions of the ER membrane and mitochondrial outer membrane are then released to form pre-peroxisomal vesicles which fuse to form new peroxisomes (Sugiura et al. 2017). Peroxisomes therefore appear to arise from fission of existing peroxisomes and production of new peroxisomes from precursors derived from mitochondria and the ER (Sugiura et al. 2017, reviewed in Fujiki et al. 2014, Hua and Kim 2016).
R-HSA-1296053 Classical Kir channels Classical Kir channels are inwardly rectifying K+ channels with strong inwardly rectifying currents that contribute to highly negative resting membrane potential, prolonged action potential plateau and rapid repolarization in the final stage of action potential. Classical Kir channels are found in various cells such as cardiac myocytes, purkinje fibers, atrial and ventricular tissues. Rectification is caused by intracellular Mg2+ ions and polyamines.
R-HSA-173623 Classical antibody-mediated complement activation C1, the first component of complement is a complex containing three protein species, C1q, C1r, and C1s. C1q is assembled from six identical subunits each of which consists of three homologous chains (A, B, and C). These chains form a globular domain at the C-terminus, followed by the "neck" and a coil in the "stalk." The six subunits are held together by the collagenous stalk parts (giving rise to the comparison of C1q with a "bunch of six tulips"). The stalks also interact with the [C1s:C1r:C1r:C1s] tetramer assembled in a linear chain. Binding of an antigen to an antibody of the IgM or IgG class induces a conformational change in the Fc domain of the antibody that allows it to bind to the C1q component of C1. C1 activation requires interaction with two separate Fc domains, so pentavalent IgM antibody is far more efficient at complement activation than IgG antibody. Antibody binding results in a conformational change in the C1r component of the C1 complex and a proteolytic cleavage of C1r, activating it. Active C1r then cleaves and activates the C1s component of the C1 complex (Muller-Eberhard 1988).
R-HSA-8856828 Clathrin-mediated endocytosis Clathrin-mediated endocytosis (CME) is one of a number of process that control the uptake of material from the plasma membrane, and leads to the formation of clathrin-coated vesicles (Pearse et al, 1975; reviewed in Robinson, 2015; McMahon and Boucrot, 2011; Kirchhausen et al, 2014). CME contributes to signal transduction by regulating the cell surface expression and signaling of receptor tyrosine kinases (RTKs) and G-protein coupled receptors (GPCRs). Most RTKs exhibit a robust increase in internalization rate after binding specific ligands; however, some RTKs may also exhibit significant ligand-independent internalization (reviewed in Goh and Sorkin, 2013). CME controls RTK and GPCR signaling by organizing signaling both within the plasma membrane and on endosomes (reviewed in Eichel et al, 2016; Garay et al, 2015; Vieira et al, 1996; Sorkin and von Zastrow, 2014; Di Fiori and von Zastrow, 2014; Barbieri et al, 2016). CME also contributes to the uptake of material such as metabolites, hormones and other proteins from the extracellular space, and regulates membrane composition by recycling membrane components and/or targeting them for degradation.
Clathrin-mediated endocytosis involves initiation of clathrin-coated pit (CCP) formation, cargo selection, coat assembly and stabilization, membrane scission and vesicle uncoating. Although for simplicity in this pathway, the steps leading to a mature CCP are represented in a linear and temporally distinct fashion, the formation of a clathrin-coated vesicle is a highly heterogeneous process and clear temporal boundaries between these processes may not exist (see for instance Taylor et al, 2011; Antonescu et al, 2011; reviewed in Kirchhausen et al, 2014). Cargo selection in particular is a critical aspect of the formation of a mature and stable CCP, and many of the proteins involved in the initiation and maturation of a CCP contribute to cargo selection and are themselves stabilized upon incorporation of cargo into the nascent vesicle (reviewed in Kirchhausen et al, 2014; McMahon and Boucrot, 2011).
Although the clathrin triskelion was identified early as a major component of the coated vesicles, clathrin does not bind directly to membranes or to the endocytosed cargo. Vesicle formation instead relies on many proteins and adaptors that can bind the plasma membrane and interact with cargo molecules. Cargo selection depends on the recognition of endocytic signals in cytoplasmic tails of the cargo proteins by adaptors that interact with components of the vesicle's inner coat. The classic adaptor for clathrin-coated vesicles is the tetrameric AP-2 complex, which along with clathrin was identified early as a major component of the coat. Some cargo indeed bind directly to AP-2, but subsequent work has revealed a large family of proteins collectively known as CLASPs (clathrin- associated sorting proteins) that mediate the recruitment of diverse cargo into the emerging clathrin-coated vesicles (reviewed in Traub and Bonifacino, 2013). Many of these CLASP proteins themselves interact with AP-2 and clathrin, coordinating cargo recruitment with coat formation (Schmid et al, 2006; Edeling et al, 2006; reviewed in Traub and Bonifacino, 2013; Kirchhausen et al, 2014).
Initiation of CCP formation is also influenced by lipid composition, regulated by clathrin-associated phosphatases and kinases (reviewed in Picas et al, 2016). The plasma membrane is enriched in PI(4,5)P2. Many of the proteins involved in initiating clathrin-coated pit formation bind to PI(4,5)P2 and induce membrane curvature through their BAR domains (reviewed in McMahon and Boucrot, 2011; Daumke et al, 2014). Epsin also contributes to early membrane curvature through its Epsin N-terminal homology (ENTH) domain, which promotes membrane curvature by inserting into the lipid bilayer (Ford et al, 2002).
Following initiation, some CCPs progress to formation of vesicles, while others undergo disassembly at the cell surface without producing vesicles (Ehrlich et al, 2004; Loerke et al, 2009; Loerke et al, 2011; Aguet et al, 2013; Taylor et al, 2011). The assembly and stabilization of nascent CCPs is regulated by several proteins and lipids (Mettlen et al, 2009; Antonescu et al, 2011).
Maturation of the emerging clathrin-coated vesicle is accompanied by further changes in the lipid composition of the membrane and increased membrane curvature, promoted by the recruitment of N-BAR domain containing proteins (reviewed in Daumke et al, 2014; Ferguson and De Camilli, 2012; Picas et al, 2016). Some N-BAR domain containing proteins also contribute to the recruitment of the large GTPase dynamin, which is responsible for scission of the mature vesicle from the plasma membrane (Koh et al, 2007; Lundmark and Carlsson, 2003; Soulet et al, 2005; David et al, 1996; Owen et al, 1998; Shupliakov et al, 1997; Taylor et al, 2011; Ferguson et al, 2009; Aguet et al, 2013; Posor et al, 2013; Chappie et al, 2010; Shnyrova et al, 2013; reviewed in Mettlen et al, 2009; Daumke et al, 2014). After vesicle scission, the clathrin coat is dissociated from the new vesicle by the ATPase HSPA8 (also known as HSC70) and its DNAJ cofactor auxilin, priming the vesicle for fusion with a subsequent endocytic compartment and releasing clathrin for reuse (reviewed in McMahon and Boucrot, 2011; Sousa and Laufer, 2015).
R-HSA-110331 Cleavage of the damaged purine Damaged purines are cleaved from the sugar-phosphate backbone by purine-specific glycosylases (Saparbaev and Laval 1994, Lindahl and Wood 1999).
R-HSA-110329 Cleavage of the damaged pyrimidine Damaged pyrimidines are cleaved by pyrimide-specific glycosylases (Lindahl and Wood 1999).
R-HSA-9927353 Co-inhibition by BTLA BTLA (B and T Lymphocyte Attenuator) is a co-inhibitory receptor that plays a crucial role in regulating immune responses, maintaining immune homeostasis, and preventing autoimmunity. BTLA interacts with its ligand, HVEM (Herpesvirus Entry Mediator), a member of the tumor necrosis factor receptor (TNFR) family. Upon engagement with HVEM, BTLA recruits the Src homology region 2 domain-containing phosphatases SHP-1 and SHP-2 to its cytoplasmic tail. These phosphatases dephosphorylate key signaling molecules downstream of the T cell receptor (TCR), effectively dampening TCR-mediated signaling and inhibiting T cell activation.
This signaling pathway is essential for modulating the immune response, particularly in maintaining peripheral tolerance and preventing the overactivation of T cells that can lead to autoimmune diseases. BTLA is expressed on various immune cells, including T cells, B cells, and dendritic cells, and it functions similarly to other immune checkpoint molecules like CTLA-4 and PD-1, but it has unique structural and functional properties.
BTLA's interaction with HVEM also influences the function of other immune cells. For instance, HVEM is expressed on many cell types, including T cells, B cells, and myeloid cells, and its interaction with BTLA can modulate the immune response in a context-dependent manner. This complex interplay is crucial for fine-tuning immune responses and ensuring that immune activation is appropriately regulated.
R-HSA-389513 Co-inhibition by CTLA4 Cytotoxic T lymphocyte antigen-4 (CTLA-4) is an immune checkpoint molecule predominantly expressed on the surface of activated T cells and regulatory T (Treg) cells. It plays a critical role in inhibiting T-cell activation and maintaining immune homeostasis (Alegre et al. 2001). After acctivation of T lymphocytes through their antigen receptor (TCR) induces the upregulation of CTLA-4 expression. CTLA-4 engagement alongside TCR activation inhibits T cell responses through two primary mechanisms: competing with CD28 for B7 binding to reduce costimulation, and delivering a negative signal directly into the T cells. It has been reported that phosphotyrosine-dependent recruitment of the SHP-2 phosphatase to CTLA-4 inhibits T cell activation and expansion by dephosphorylation of CD3/TCR chains.
CTLA-4 inhibits T cell activation through several mechanisms, including the reduction of IL-2 production and expression, as well as by arresting T cells in the G1 phase of the cell cycle (Greenwald et al. 2002). This checkpoint molecule not only impacts the T cells that express it but also exerts a dominant regulatory influence on the proliferation of other T cells. This ability to limit the proliferation of surrounding T cells is crucial in preventing autoreactivity and maintaining immune tolerance, ensuring that the immune system does not inadvertently target the body's own tissues.
Due to its ability to modulate immune responses, CTLA-4 has emerged as a significant therapeutic target for managing conditions such as cancer, autoimmune diseases, and transplant rejection (Tivol et al. 1995, Chambers et al. 1997, Rudd and Schneider 2003).
R-HSA-389948 Co-inhibition by PD-1 Programmed cell death protein 1 (PD-1) is a crucial inhibitory receptor that regulates T cell receptor (TCR) signaling and plays a vital role in maintaining immune homeostasis. PD-1 exerts its suppressive effects both directly, by inhibiting early activation events that are otherwise enhanced by co-stimulatory signals like CD28, and indirectly, by reducing interleukin-2 (IL-2) production, which is essential for T cell proliferation and survival. Upon ligation, PD-1 inhibits the expression of key survival and differentiation factors, such as Bcl-xL, and downregulates transcription factors that are central to effector T cell function, including GATA-3, T-bet, and Eomes. Mechanistically, PD-1 recruits the tyrosine phosphatases SHP-1 and SHP-2 to the immune synapse, leading to the dephosphorylation of critical signaling molecules like the CD3-zeta chain, PI3K, and AKT, thereby attenuating TCR signaling and inhibiting T cell activation and function (Keir et al. 2008).
R-HSA-389356 Co-stimulation by CD28 CD28 signaling plays a critical role in shaping immune responses by ensuring effective T-cell activation and enhancing T-cell survival and proliferation. When CD28 engages its ligands, B7-1 (CD80) and B7-2 (CD86), on antigen-presenting cells, it provides an essential secondary signal that complements T-cell receptor (TCR) activation. This costimulatory signal leads to the production of interleukin-2 (IL-2), which supports the clonal expansion of T cells, promoting both their proliferation and survival by initiating anti-apoptotic pathways (Ribot et al. 2012, Alegre et al. 2001).
The cytoplasmic tail of CD28, upon ligand binding, undergoes phosphorylation by Src family kinases like LCK and FYN, triggering downstream signaling pathways involving PI3K, VAV-1, Tec family kinases, AKT, and other adaptor proteins (Sharpe & Freeman 2002; Chen & Flies 2013).
R-HSA-9927354 Co-stimulation by ICOS ICOS (Inducible T-cell COStimulator) is a critical costimulatory receptor that enhances T cell responses following initial activation. Unlike CD28, which is constitutively expressed on naive T cells, ICOS expression is induced upon T cell activation. Both ICOS and CD28 engage class IA phosphatidylinositol 3-kinase (PI3K), leading to the production of phosphatidylinositol 3,4,5-trisphosphate (PIP3) and activation of downstream signaling pathways, including AKT. However, ICOS signaling is distinguished by a stronger induction of PIP3 production and more robust AKT phosphorylation compared to CD28 signaling (Fos et al. 2008). This enhanced signaling through ICOS contributes to its unique role in promoting T cell survival, cytokine production, and differentiation, particularly in the context of T follicular helper (Tfh) cell development and function (Dong et al. 2001). Despite these similarities, detailed knowledge about ICOS-specific downstream signaling pathways remains limited, highlighting a key area for further research to fully understand its distinct and overlapping roles with CD28 in T cell immunity (Wikenheiser & Stumhofer 2016).
R-HSA-9759218 Cobalamin (Cbl) metabolism The reactions by which adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl) cofactors are synthesized and regenerated are annotated here (Banerjee et al. 2021).
R-HSA-196741 Cobalamin (Cbl, vitamin B12) transport and metabolism Vitamin B12 (cobalamin) is a water soluble vitamin, consisting of a planar corrin ring coordinating with a cobalt atom through four nitrogen atoms. A 5,6 dimethylbenzamidizole base coordinates with the cobalt atom in the lower axial position. Groups that can coordinate with the cobalt atom in the upper axial position include methyl (methylcobalamin, MetCbl), adenosyl (adenosylcobalamin, AdoCbl) and cyano (cyanocobalamin (CNCbl)). Only bacteria and archaea synthesise cobalamin so humans need a dietary intake to prevent deficiency. Food derived from animals provides cobalamins (RCbl) including MeCbl and AdoCbl. CNCbl, a semi synthetic form of the vitamin produced from bacterial hydroxocobalamin is provided by many pharmaceuticals, supplements, and food additives.
Cbl derivatives function as cofactors in two reactions, AdoCbl in the conversion of homocysteine to methionine and MetCbl in the conversion of L-methylmalonyl CoA to succinyl CoA. Both reactions are essential for normal human function, however, and defects in the steps by which Cbl or CNCbl is taken up from the diet, transported to metabolically active cells, and transformed to AdoCbl and MeCbl are associated with severe defects in blood formation and neural function (Banerjee et al. 2021, Froese & Gravel 2010, Green 2010, Nielsen et al. 2012, Quadros 2010; Seetharam 1999).
The overall process of Cbl utilization is presented here in three parts: its uptake from the diet into gut enterocytes, its release into the blood, circulation within the body (including renal re-uptake), and delivery to the cells where it is used, and its metabolism in those cells to generate AdoCbl and MeCbl.
R-HSA-196783 Coenzyme A biosynthesis Coenzyme A (CoA) is a ubiquitous cofactor that functions as an acyl group carrier in diverse processes including fatty acid metabolism and the TCA cycle (Lipmann 1953). It is synthesized from the vitamin pantothenate in a sequence of five reactions (Daugherty et al. 2002; Leonardi et al. 2005; Robishaw and Neely 1985). These reactions all occur in the cytosol or the mitochondrial intermembrane space (Leonardi et al. 2005). A recently described transport protein appears to mediate the uptake of Coenzyme A into the mitochondrial matrix (Prohl et al. 2001).
R-HSA-2470946 Cohesin Loading onto Chromatin In mitotic telophase, as chromosomes decondense, cohesin complex associated with PDS5 (PDS5A and PDS5B) and WAPAL (WAPL) proteins is loaded onto chromatin (Shintomi and Hirano, 2009, Kueng et al. 2006, Gandhi et al. 2006, Chan et al. 2012). Cohesin loading is facilitated by the complex of NIPBL (SCC2) and MAU2 (SCC4) proteins, which constitute an evolutionarily conserved cohesin loading complex. MAU2 depletion in HeLa cells results in 2-3-fold reduction in the amount of cohesin in the chromatin fraction (Watrin et al. 2006). NIPBL mutations are the cause of the Cornelia de Lange syndrome, a dominantly inherited disorder characterized by facial malformations, limb defects, and growth and cognitive retardation (Tonkin et al. 2004). Cornelia de Lange syndrome can also be caused by mutations in cohesin subunits SMC1A (Musio et al. 2006, Borck et al. 2007, Deardorff et al. 2007, Pie et al. 2010) and SMC3 (Deardorff et al. 2007).
R-HSA-1650814 Collagen biosynthesis and modifying enzymes The biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proline and lysine residues may be hydroxylated by prolyl 3-, prolyl 4- and lysyl hydroxylases. 4-hydroxyproline is essential for intramolecular hydrogen bonding and stability of the triple helical collagenous domain. In fibril forming collagens approximately 50% of prolines are 4-hydroxylated; the extent of this and of 3-hydroxyproline and lysine hydroxylation varies between tissues and collagen types (Kivirikko et al. 1972, 1992). Hydroxylysine molecules can form cross-links between collagen molecules in fibrils, and are sites for glycosyl- and galactosylation. Collagen peptides all have non-collagenous domains; collagens within the subclasses have common chain structures. These non-collagenous domains have regulatory functions; some are biologically active when cleaved from the main peptide chain. Fibrillar collagens all have a large triple helical domain (COL1) bordered by N and C terminal extensions, called the N and C propeptides, which are cleaved prior to formation of the collagen fibril. The C propeptide, also called the NC1 domain, is highly conserved. It directs chain association during intracellular assembly of the procollagen molecule from three collagen propeptide alpha chains (Hulmes 2002). The N-propeptide has a short linker (NC2) connecting the main triple helix to a short minor one (COL2) and a globular N-terminal region NC3. NC3 domains are variable both in size and the domains they contain.
Collagen propeptides typically undergo a number of post-translational modifications. Proline and lysine residues are hydroxylated by prolyl 3-, prolyl 4- and lysyl hydroxylases. 4-hydroxyproline is essential for intramolecular hydrogen bonding and stability of the triple helical collagenous domain. Prolyl 4-hydroxylase may also have a role in alpha chain association as no association of the C-propeptides of type XII collagen was seen in the presence of prolyl 4-hydroxylase inhibitors (Mazzorana et al. 1993, 1996). In fibril forming collagens approximately 50% of prolines are 4-hydroxylated; the extent of this is species dependent, lower hydroxylation correlating with lower ambient temperature and thermal stability (Cohen-Solal et al. 1986, Notbohm et al. 1992). Similarly the extent of 3-hydroxyproline and lysine hydroxylation varies between tissues and collagen types (Kivirikko et al. 1992). Hydroxylysine molecules can form cross-links between collagen molecules in fibrils, and are sites for glycosyl- and galactosylation.
Collagen molecules fold and assemble through a series of distinct intermediates (Bulleid 1996). Individual collagen polypeptide chains are translocated co-translationally across the membrane of the endoplasmic reticulum (ER). Intra-chain disulfide bonds are formed within the N-propeptide, and hydroxylation of proline and lysine residues occurs within the triple helical domain (Kivirikko et al. 1992). When the peptide chain is fully translocated into the ER lumen the C-propeptide folds, the conformation being stabilized by intra-chain disulfide bonds (Doege and Fessler 1986). Pro alpha-chains associate via the C-propeptides (Byers et al. 1975, Bachinger et al. 1978), or NC2 domains for FACIT family collagens (Boudko et al. 2008) to form an initial trimer which can be stabilized by the formation of inter-chain disulfide bonds (Schofield et al. 1974, Olsen et al. 1976), though these are not a prerequisite for further folding (Bulleid et al. 1996). The triple helix then nucleates and folds in a C- to N- direction. The association of the individual chains and subsequent triple helix formation are distinct steps (Bachinger et al. 1980). The N-propeptides associate and in some cases form inter-chain disulfide bonds (Bruckner et al., 1978). Procollagen is released via carriers into the exracellular space (Canty & Kadler 2005). Fibrillar procollagens undergo removal of the C- and N-propeptides by procollagen C and N proteinases respectively, both Zn2+ dependent metalloproteinases. Propeptide processing is a required step for normal collagen I and III fibril formation, but collagens can retain some or all of their non-collagenous propeptides. Retained collagen type V and XI N-propeptides contribute to the control of fibril growth by sterically limiting lateral molecule addition (Fichard et al. 1995). Processed fibrillar procollagen is termed tropocollagen, which is considered to be the unit of higher order fibrils and fibres. Tropocollagens of the fibril forming collagens I, II, III, V and XI sponteneously aggregate in vitro in a manner that has been compared with crystallization, commencing with a nucleation event followed by subsequent organized aggregation (Silver et al. 1992, Prockop & Fertala 1998). Fibril formation is stabilized by lysyl oxidase catalyzed crosslinks between adjacent molecules (Siegel & Fu 1976).
R-HSA-8948216 Collagen chain trimerization The C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the composition of the trimer, brings the individual chains into the correct register and initiates formation of the triple helix at the C-terminus, which then proceeds towards the N-terminus in a zipper-like fashion (Engel & Prockop 1991). Most early refolding studies were performed with collagen type III, which contains a disulfide linkage at the C-terminus of its triple helix (Bächinger et al. 1978, Bruckner et al. 1978) that acts as a permanent linker even after removal of the non-collagenous domains.
Mutations within the C-propeptides further suggest that they are crucial for the correct interaction of the three polypeptide chains and for subsequent correct folding (refs. in Boudko et al. 2011).
R-HSA-1442490 Collagen degradation Collagen fibril diameter and spatial organisation are dependent on the species, tissue type and stage of development (Parry 1988). The lengths of collagen fibrils in mature tissues are largely unknown but in tendon can be measured in millimetres (Craig et al. 1989). Collagen fibrils isolated from adult bovine corneal stroma had ~350 collagen molecules in transverse section, tapering down to three molecules at the growing tip (Holmes & Kadler 2005).
The classical view of collagenases is that they actively unwind the triple helical chain, a process termed molecular tectonics (Overall 2002, Bode & Maskos 2003), before preferentially cleaving the alpha2 chain followed by the remaining chains (Chung et al. 2004). More recently it has been suggested that collagen fibrils exist in an equilibrium between protected and vulnerable states (Stultz 2002, Nerenberg & Stultz 2008). The prototypical triple-helical structure of collagen does not fit into the active site of collagenase MMPs. In addition the scissile bonds are not solvent-exposed and are therefore inaccessible to the collagenase active site (Chung et al. 2004, Stultz 2002). It was realized that collagen must locally unfold into non-triple helical regions to allow collagenolysis. Observations using circular dichroism and differential scanning calorimetry confirm that there is considerable heterogeneity along collagen fibres (Makareeva et al. 2008) allowing access for MMPs at physiological temperatures (Salsas-Escat et al. 2010).
Collagen fibrils with cut chains are unstable and accessible to proteinases that cannot cleave intact collagen strands (Woessner & Nagase 2000, Somerville et al. 2003). Continued degradation leads to the formation of gelatin (Lovejoy et al. 1999). Degradation of collagen types other than I-III is less well characterized but believed to occur in a similar manner.
Metalloproteinases (MMPs) play a major part in the degradation of several extracellular macromolecules including collagens. MMP1 (Welgus et al. 1981), MMP8 (Hasty et al. 1987), and MMP13 (Knauper et al. 1996), sometimes referred to as collagenases I, II and III respectively, are able to initiate the intrahelical cleavage of the major fibril forming collagens I, II and III at neutral pH, and thus thought to define the rate-limiting step in normal tissue remodeling events. All can cleave additional substrates including other collagen subtypes. Collagenases cut collagen alpha chains at a single conserved Gly-Ile/Leu site approximately 3/4 of the molecule's length from the N-terminus (Fields 1991, Chung et al. 2004). The cleavage site is characterised by the motif G(I/L)(A/L); the G-I/L bond is cleaved. In collagen type I this corresponds to G953-I954 in the Uniprot canonical alpha chain sequences (often given as G775-I776 in literature). It is not clear why only this bond is cleaved, as the motif occurs at several other places in the chain. MMP14, a membrane-associated MMP also known as Membrane-type matrix metalloproteinase 1 (MT-MMP1), is able to cleave collagen types I, II and III (Ohuchi et al. 1997).
R-HSA-1474290 Collagen formation Collagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in mammals making up about 25% to 35% of whole-body protein content. A defining feature of collagens is the formation of trimeric left-handed polyproline II-type helical collagenous regions. The packing within these regions is made possible by the presence of the smallest amino acid, glycine, at every third residue, resulting in a repeating motif Gly-X-Y where X is often proline (Pro) and Y often 4-hydroxyproline (4Hyp). Gly-Pro-Hyp is the most common triplet in collagen (Ramshaw et al. 1998). Collagen peptide chains also have non-collagenous domains, with collagen subclasses having common chain structures. Collagen fibrils are mostly found in fibrous tissues such as tendon, ligament and skin. Other forms of collagen are abundant in cornea, cartilage, bone, blood vessels, the gut, and intervertebral disc. In muscle tissue, collagen is a major component of the endomysium, constituting up to 6% of muscle mass. Gelatin, used in food and industry, is collagen that has been irreversibly hydrolyzed. On the basis of their fibre architecture in tissues, the genetically distinct collagens have been divided into subgroups. Group 1 collagens have uninterrupted triple-helical domains of about 300 nm, forming large extracellular fibrils. They are referred to as the fibril-forming collagens, consisting of collagens types I, II, III, V, XI, XXIV and XXVII. Group 2 collagens are types IV and VII, which have extended triple helices (>350 nm) with imperfections in the Gly-X-Y repeat sequences. Group 3 are the short-chain collagens. These have two subgroups. Group 3A have continuous triple-helical domains (type VI, VIII and X). Group 3B have interrupted triple-helical domains, referred to as the fibril-associated collagens with interrupted triple helices (FACIT collagens, Shaw & Olsen 1991). FACITs include collagen IX, XII, XIV, XVI, XIX, XX, XXI, XXII and XXVI plus the transmembrane collagens (XIII, XVII, XXIII and XXV) and the multiple triple helix domains and interruptions (Multiplexin) collagens XV and XVIII (Myllyharju & Kivirikko 2004). The non-collagenous domains of collagens have regulatory functions; several are biologically active when cleaved from the main peptide chain. Fibrillar collagen peptides all have a large triple helical domain (COL1) bordered by N and C terminal extensions, called the N- and C-propeptides, which are cleaved prior to formation of the collagen fibril. The intact form is referred to as a collagen propeptide, not procollagen, which is used to refer to the trimeric triple-helical precursor of collagen before the propeptides are removed. The C-propeptide, also called the NC1 domain, directs chain association during assembly of the procollagen molecule from its three constituent alpha chains (Hulmes 2002).
Fibril forming collagens are the most familiar and best studied subgroup. Collagen fibres are aggregates or bundles of collagen fibrils, which are themselves polymers of tropocollagen complexes, each consisting of three polypeptide chains known as alpha chains. Tropocollagens are considered the subunit of larger collagen structures. They are approximately 300 nm long and 1.5 nm in diameter, with a left-handed triple-helical structure, which becomes twisted into a right-handed coiled-coil 'super helix' in the collagen fibril. Tropocollagens in the extracellular space polymerize spontaneously with regularly staggered ends (Hulmes 2002). In fibrillar collagens the molecules are staggered by about 67 nm, a unit known as D that changes depending upon the hydration state. Each D-period contains slightly more than four collagen molecules so that every D-period repeat of the microfibril has a region containing five molecules in cross-section, called the 'overlap', and a region containing only four molecules, called the 'gap'. The triple-helices are arranged in a hexagonal or quasi-hexagonal array in cross-section, in both the gap and overlap regions (Orgel et al. 2006). Collagen molecules cross-link covalently to each other via lysine and hydroxylysine side chains. These cross-links are unusual, occuring only in collagen and elastin, a related protein.
The macromolecular structures of collagen are diverse. Several group 3 collagens associate with larger collagen fibers, serving as molecular bridges which stabilize the organization of the extracellular matrix. Type IV collagen is arranged in an interlacing network within the dermal-epidermal junction and vascular basement membranes. Type VI collagen forms distinct microfibrils called beaded filaments. Type VII collagen forms anchoring fibrils. Type VIII and X collagens form hexagonal networks. Type XVII collagen is a component of hemidesmosomes where it is complexed wtih alpha6Beta4 integrin, plectin, and laminin-332 (de Pereda et al. 2009). Type XXIX collagen has been recently reported to be a putative epidermal collagen with highest expression in suprabasal layers (Soderhall et al. 2007). Collagen fibrils/aggregates arranged in varying combinations and concentrations in different tissues provide specific tissue properties. In bone, collagen triple helices lie in a parallel, staggered array with 40 nm gaps between the ends of the tropocollagen subunits, which probably serve as nucleation sites for the deposition of crystals of the mineral component, hydroxyapatite (Ca10(PO4)6(OH)2) with some phosphate. Collagen structure affects cell-cell and cell-matrix communication, tissue construction in growth and repair, and is changed in development and disease (Sweeney et al. 2006, Twardowski et al. 2007). A single collagen fibril can be heterogeneous along its axis, with significantly different mechanical properties in the gap and overlap regions, correlating with the different molecular organizations in these regions (Minary-Jolandan & Yu 2009).
R-HSA-140875 Common Pathway of Fibrin Clot Formation The common pathway consists of the cascade of activation events leading from the formation of activated factor X to the formation of active thrombin, the cleavage of fibrinogen by thrombin, and the formation of cleaved fibrin into a stable multimeric, cross-linked complex. Thrombin also efficiently catalyzes the activation of several factors required earlier in the clotting cascade, thus acting in effect as a positive regulator of clotting. At the same time, thrombin activates protein C, which in turn catalyzes the inactivation of several of these upstream factors, thereby limiting the clotting process. Thrombin can be trapped in stable, inactive complexes with: antithrombin-III (SERPINC1), a circulating blood protein; heparin cofactor II (SERPIND1) which inhibits thrombin in a dermatan sulfate–dependent manner in the arterial vasculature; protein C inhibitor (SERPINA5) that inhibits thrombin in complex with thrombomodulin; and Protease nexin-1 (SERPINE2) that inhibits thrombin at the vessel wall and platelet surface. The quantitative interplay among these positive and negative modulators is critical to the normal regulation of clotting, facilitating the rapid formation of a protective clot at the site of injury, while limiting and physically confining the process.
These events are outlined in the drawing: black arrows connect the substrates (inputs) and products (outputs) of individual reactions, and blue lines connect output activated enzymes to the other reactions that they catalyze.
R-HSA-8948700 Competing endogenous RNAs (ceRNAs) regulate PTEN translation Coding and non-coding RNAs can prevent microRNAs from binding to PTEN mRNA. These RNAs are termed competing endogenous RNAs or ceRNAs. Transcripts of the pseudogene PTENP1 and mRNAs transcribed from SERINC1, VAPA and CNOT6L genes exhibit this activity (Poliseno et al. 2010, Tay et al. 2011, Tay et al. 2014). SERINC1 mRNA will be annotated in this context when additional experimental details become available.
R-HSA-166658 Complement cascade In the complement cascade, a panel of soluble molecules rapidly and effectively senses a danger or damage and triggers reactions to provide a response that discriminates among foreign intruders, cellular debris, healthy and altered host cells (Ricklin D et al. 2010). Complement proteins circulate in the blood stream in functionally inactive states. When triggered the complement cascade generates enzymatically active molecules (such as C3/C5 convertases) and biological effectors: opsonins (C3b, C3d and C4b), anaphylatoxins (C3a and C5a), and C5b, which initiates assembly of the lytic membrane attack complex (MAC). Three branches lead to complement activation: the classical, lectin and alternative pathways (Kang YH et al. 2009; Ricklin D et al. 2010). The classical pathway is initiated by C1 complex binding to immune complexes, pentraxins or other targets such as apoptotic cells leading to cleavage of C4 and C2 components and formation of the classical C3 convertase, C4bC2a. The lectin pathway is activated by binding of mannan-binding lectin (MBL) to repetitive carbohydrate residues, or by binding of ficolins to carbohydrate or acetylated groups on target surfaces. MBL and ficolins interact with MBL-associated serine proteases (MASP) leading to cleavage of C4 and C2 and formation of the classical C3 convertase, C4bC2a. The alternative pathway is spontaneously activated by the hydrolysis of the internal thioester group of C3 to give C3(H2O). Alternative pathway activation involves interaction of C3(H2O) and/or previously generated C3b with factor B, which is cleaved by factor D to generate the alternative C3 convertases C3(H2O)Bb and/or C3bBb. All three pathways merge at the proteolytic cleavage of component C3 by C3 convertases to form opsonin C3b and anaphylatoxin C3a. C3b covalently binds to glycoproteins scattered across the target cell surface. This is followed by an amplification reaction that generates additional C3 convertases and deposits more C3b at the local site. C3b can also bind to C3 convertases switching them to C5 convertases, which mediate C5 cleavage leading to MAC formation. Thus, the activation of the complement system leads to several important outcomes: opsonization of target cells to enhance phagocytosis, lysis of target cells via membrane attack complex (MAC) assembly on the cell surface, production of anaphylatoxins C3a/C5a involved in the host inflammatory response, C5a-mediated leukocyte chemotaxis, and clearance of antibody-antigen complexes. The complement system is able to distinguish between pathological and physiological challenges, i.e. the outcomes of complement activation are predetermined by the trigger and are tightly tuned by a combination of initiation events with several regulatory mechanisms. These regulatory mechanisms use soluble (e.g., C4BP, CFI and CFH) and membrane-bound regulators (e.g., CR1, CD46(MCP), CD55(DAF) and CD59) and are coordinated by complement receptors such as CR1, CR2, etc. In response to microbial infection complement activation results in flagging microorganisms with opsonins for facilitated phagocytosis, formation of MAC on cells such as Gram-negative bacteria leading to cell lysis, and release of C3a and C5a to stimulate downstream immune responses and to attract leukocytes. Most pathogens can be eliminated by these complement-mediated host responses, though some pathogenic microorganisms have developed ways of avoiding complement recognition or blocking host complement attack resulting in greater virulence (Lambris JD et al. 2008; Serruto D et al. 2010). All three complement pathways (classical, lectin and alternative) have been implicated in clearance of dying cells (Mevorach D et al. 1998; Ogden CA et al. 2001; Gullstrand B et al.2009; Kemper C et al. 2008). Altered surfaces of apoptotic cells are recognized by complement proteins leading to opsonization and subsequent phagocytosis. In contrast to pathogens, apoptotic cells are believed to induce only a limited complement activation by allowing opsonization of altered surfaces but restricting the terminal pathway of MAC formation (Gershov D et al. 2000; Braunschweig A and Jozsi M 2011). Thus, opsonization facilitates clearance of dying cells and cell debris without triggering danger signals and further inflammatory responses (Fraser DA et al. 2007, 2009; Benoit ME et al. 2012). C1q-mediated complement activation by apoptotic cells has been shown in a variety of human cells: keratinocytes, human umbilical vein endothelial cells (HUVEC), Jurkat T lymphoblastoid cells, lung adenocarcinoma cells (Korb LC and Ahearn JM 1997; Mold C and Morris CA 2001; Navratil JS et al. 2001; Nauta AJ et al. 2004). In addition to C1q the opsonization of apoptotic Jurkat T cells with MBL also facilitated clearance of these cells by both dendritic cells (DC) and macrophages (Nauta AJ et al. 2004). Also C3b, iC3b and C4b deposition on apoptotic cells as a consequence of activation of the complement cascade may promote complement-mediated phagocytosis. C1q, MBL and cleavage fragments of C3/C4 can bind to several receptors expressed on macrophages (e.g. cC1qR (calreticulin), CR1, CR3, CR4) suggesting a potential clearance mechanism through this interaction (Mevorach D et al. 1998; Ogden CA et al. 2001). Apoptosis is also associated with an altered expression of complement regulators on the surface of apoptotic cells. CD46 (MCP) bound to the plasma membrane of a healthy cell protects it from complement-mediated attack by preventing deposition of C3b and C4b, and reduced expression of CD46 on dying cells may lead to enhanced opsonization (Elward K et al. 2005). Upregulation of CD55 (DAF) and CD59 on apoptotic cell surfaces may protect damaged cells against complement mediated lysis (Pedersen ED et al. 2007; Iborra A et al. 2003; Hensel F et al. 2001). In addition, fluid-phase complement regulators such as C4BP, CFH may also inhibit lysis of apoptotic cells by limiting complement activation (Trouw LA et al 2007; Braunschweig A and Jozsi M. 2011). Complement facilitates the clearance of immune complexes (IC) from the circulation (Chevalier J and Kazatchkine MD 1989; Nielsen CH et al. 1997). Erythrocytes bear clusters of complement receptor 1 (CR1 or CD35), which serves as an immune adherence receptor for C3 and/or C4 fragments deposited on IC that are shuttled to liver and spleen, where IC are transferred and processed by tissue macrophages through an Fc receptor-mediated process. Complement proteins are always present in the blood and a small percentage spontaneously activate. Inappropriate activation leads to host cell damage, so on healthy human cells any complement activation or amplification is strictly regulated by surface-bound regulators that accelerate decay of the convertases (CR1, CD55), act as a cofactor for the factor I (CFI)-mediated degradation of C3b and C4b (CR1, CD46), or prevent the formation of MAC (CD59). Soluble regulators such as C4BP, CFH and FHL1 recognize self surface pattern-like glycosaminoglycans and further impair activation. Complement components interact with other biological systems. Upon microbial infection complement acts in cooperation with Toll-like receptors (TLRs) to amplify innate host defense. Anaphylatoxin C5a binds C5a receptor (C5aR) resulting in a synergistic enhancement of the TLR and C5aR-mediated proinflammatory cytokine response to infection. This interplay is negatively modulated by co-ligation of TLR and the second C5a receptor, C5L2, suggesting the existence of complex immunomodulatory interactions (Kohl J 2006; Hajishengallis G and Lambris JD 2010). In addition to C5aR and C5L2, complement receptor 3 (CR3) facilitates TLR2 or TLR4 signaling pathways by promoting a recruitment of their sorting adaptor TIRAP (MAL) to the receptor complex (van Bruggen R et al. 2007; Kagan JC and Medzhitov R 2006). Complement may activate platelets or facilitate biochemical and morphological changes in the endothelium potentiating coagulation and contributing to homeostasis in response to injury (Oikonomopoulou K et al. 2012). The interplay of complement and coagulation also involves cleavage of C3 and C5 convertases by coagulation proteases, generating biologically active anaphylatoxins (Amara U et al. 2010). Complement is believed to link the innate response to both humoral and cell-mediated immunity (Toapanta FR and Ross TM 2006; Mongini PK et al. 1997). The majority of published data is based on experiments using mouse as a model organism. Further characterization of the influence of complement on B or T cell activation is required for the human system, since differences between murine models and the human system are not yet fully determined. Complement is also involved in regulation of mobilization and homing of hematopoietic stem/progenitor cells (HSPCs) from bone marrow to the circulation and peripheral tissue in order to accommodate blood cell replenishment (Reca R et al. 2006). Thus, the complement system orchestrates the host defense by sensing a danger signal and transmitting it into specific cellular responses while extensively communicating with associated biological pathways ranging from immunity and inflammation to homeostasis and development. Originally the larger fragment of Complement Factor 2 (C2) was designated C2a. However, complement scientists decided that the smaller of all C fragments should be designated with an 'a', the larger with a 'b', changing the nomenclature for C2. Recent literature may use the updated nomenclature and refer to the larger C2 fragment as C2b, and refer to the classical C3 convertase as C4bC2b. Throughout this pathway Reactome adheres to the original convention to agree with the current (Sep 2013) Uniprot names for C2 fragments. The complement cascade pathway is organised into the following sections: initial triggering, activation of C3 and C5, terminal pathway and regulation.
R-HSA-6799198 Complex I biogenesis Complex I (NADH:ubiquinone oxidoreductase or NADH dehydrogenase) utilises NADH formed from glycolysis and the TCA cycle to pump protons out of the mitochondrial matrix. It is the largest enzyme complex in the electron transport chain, containing 11 core and 34 accessory subunits. Seven subunits (ND1-6, ND4L) are encoded by mitochondrial DNA, the remainder are encoded in the nucleus. The enzyme has a FMN prosthetic group and 8 Iron-Sulfur (Fe-S) clusters. The subunits are assembled together in a coordinated manner via preassembled subcomplexes to form the mature holoenzyme. At least 24 so-called "assembly factor" proteins, acting intrinsically or transiently, are required for constructing complex I although their exact roles in the biogenesis are not fully understood (Fernandez-Vizarra et al. 2009, Mckenzie & Ryan 2010, Mimaki et al. 2012, Andrews et al. 2013; reviewed by Laube et al., 2024).
R-HSA-9865881 Complex III assembly Assembly of the cytochrome c (cytochrome bc1) reductase (Complex III) was mainly investigated in yeast. The process in humans is considered to recapitulate the process in the yeast system based on the high similarity in structure and composition of the yeast and human complexes. Human Complex III probably consists of two identical sub-complexes, each containing at least 11 subunits: the catalytic core containing cytochrome b (MT-CYTB), cytochrome c1 (CYC1), and the Rieske protein (UQCRFS1), as well as the additional subunits UQCRC1, UQCRC2, UQCRC10, UQCRC11, UQCRCB, UQCRCH, UQCRCQ (Guo et al., 2017; Dennerlein et al., 2021; reviewed in Ndi et al., 2018; Signes & Fernandez-Vizarra, 2018). While complex I, III, and IV form a supercomplex, there is no evidence of any physiological advantage of this configuration (reviewed in Kohler et al., 2023; Brischigliaro et al., 2023). Mutations in nuclear genes coding for subunits of Complex III, as well as assembly factors, can cause complex III deficiency (MC3D; reviewed in Fernández-Vizarra & Zeviani, 2015).
R-HSA-9864848 Complex IV assembly At least 30 proteins are required to form the functional human complex IV, 14 of which are complex subunits. The complex contains the cofactors heme a, heme a3, and one mononuclear copper (CuB) center in the COX1 subunit, and a binuclear copper (CuA) in COX2, as well as several lipid molecules (phosphatidylethanolamine, PE, cardiolipin, CL) in different subunits (PDB 5Z62; Zong et al., 2018). The insertion of these cofactors is an intricate process requiring many assembly factors (Nývltová et al, 2022; reviewed in Mick et al., 2011; Timón-Gómez et al., 2018; Watson & McStay, 2020; Dennerlein et al., 2023).
Mutations in any complex IV subunits or assembly factors lead to different types of complex IV deficiency, usually manifesting as Leigh syndrome (MIM:220110; reviewed in Pecina et al., 2004; Čunátová et al., 2020)
R-HSA-2514853 Condensation of Prometaphase Chromosomes The condensin I complex is evolutionarily conserved and consists of five subunits: two SMC (structural maintenance of chromosomes) family subunits, SMC2 and SMC4, and three non-SMC subunits, NCAPD2, NCAPH and NCAPG. The stoichiometry of the complex is 1:1:1:1:1 (Hirano and Mitchinson 1994, Hirano et al. 1997, Kimura et al. 2001). SMC2 and SMC4 subunits, shared between condensin I and condensin II, are DNA-dependent ATPases, and condensins are able to introduce positive supercoils into DNA in an ATP-dependent manner (Kimura and Hirano 1997).
Protein levels of condensin subunits are constant during the cell cycle, however condensins are enriched on mitotic chromosomes. Four of the five subunits, SMC4, NCAPD2, NCAPG and NCAPH, are phosphorylated in both mitotic and interphase HeLa cells, but on different sites (Takemoto et al. 2004). CDK1 (CDC2) in complex with CCNB (cyclin B) phosphorylates NCAPD2, NCAPG and NCAPH in mitosis (Kimura et al. 1998, Kimura et al. 2001, Takemoto et al. 2006, Murphy et al. 2008), but other mitotic kinases, such as PLK1 (St-Pierre et al. 2009), and other post-translational modifications, such as acetylation, may also be involved (reviewed by Bazile et al. 2010). Global proteomic analysis of human cell lines has identified N6-acetylation of lysine residues in condensin subunits SMC2, SMC4 and NCAPH (Choudhary et al. 2009). Another high throughput proteomic study showed that condensin I subunits NCAPD2 and NCAPH are phosphorylated upon DNA damage, probably by ATM or ATR kinase (Matsuoka et al. 2007).
As condensin I is cytosolic, it gains access to chromosomes only after the nuclear envelope breakdown at the start of prometaphase (Ono et al. 2004). Condensin I, activated by CDK1-mediated phosphorylation, promotes hypercondensation of chromosomes that were condensed in prophase through the action of condensin II (Hirota et al. 2004). AURKB may also regulate association of condensin I complex with chromatin (Lipp et al. 2007). Protein phosphatase PP2A acts independently of its catalytic activity to target condensin II complex to chromatin, but does not interact with condensin I (Takemoto et al. 2009). Full activation of condensin I requires dephosphorylation of sites modified by CK2 during interphase (Takemoto et al. 2006). Besides being essential for chromosome condensation in mitosis, condensin I may also contribute to cohesin removal from chromosome arms in prometaphase, but the exact mechanism is not known (Hirota et al. 2004).
R-HSA-2299718 Condensation of Prophase Chromosomes In mitotic prophase, the action of the condensin II complex enables initial chromosome condensation.
The condensin II complex subunit NCAPD3 binds monomethylated histone H4 (H4K20me1), thereby associating with chromatin (Liu et al. 2010). Binding of the condensin II complex to chromatin is partially controlled by the presence of RB1 (Longworth et al. 2008).
Two mechanisms contribute to the accumulation of H4K20me1 at mitotic entry. First, the activity of SETD8 histone methyltransferase peaks at G2/M transition (Nishioka et al. 2002, Rice et al. 2002, Wu et al. 2010). Second, the complex of CDK1 and cyclin B1 (CDK1:CCNB1) phosphorylates PHF8 histone demethylase at the start of mitosis, removing it from chromatin (Liu et al. 2010).
Condensin II complex needs to be phosphorylated by the CDK1:CCNB1 complex, and then phosphorylated by PLK1, in order to efficiently condense prophase chromosomes (Abe et al. 2011).
R-HSA-177135 Conjugation of benzoate with glycine Benzoic acid, widely used as a food preservative, is converted to hippuric acid by activation and conjugation with glycine. This was one of the first detoxification pathways discovered, and was formerly exploited clinically as an alternative means of nitrogen excretion in patients with urea cycle defects (Brusilow and Horwich 2001).
R-HSA-159424 Conjugation of carboxylic acids Xenobiotics and endogenous compounds containing carboxylate groups can be activated with coenzyme A to produce acyl-CoA thioesters and then conjugated with the amino groups of glycine or glutamine to form amide-linked conjugates. Clinically important substrates include benzoic acid, phenylacetic acid, and salicylic acid.
R-HSA-177162 Conjugation of phenylacetate with glutamine Phenylacetate metabolism is of clinical importance because its conjugation with glutamine to form phenylacetylglutamine, which can be excreted in the urine, provides an alternative pathway for nitrogen excretion in patients with urea cycle defects (James et al. 1972; Batshaw et al. 2001; Brusilow and Horwich 2001). This conjugation proceeds in two steps. First, phenylacetate and ATP react with coenzyme A to form phenylacetyl CoA, AMP, and pyrophosphate (Vessey et al. 1999). Two human CoA ligases have been characterized that catalyze this reaction efficiently in vitro: acyl-CoA synthetase medium-chain family member 1 (BUCS1) (Fujino et al. 2001) and xenobiotic/medium-chain fatty acid:CoA ligase (Vessey et al. 2003). Their relative contributions to phenylacetate metabolism in vivo are unknown. Second, phenylacetyl CoA and glutamine react to form phenyacetyl glutamine and Coenzyme A. The enzyme that catalyzes this reaction has been purified from human liver mitochondria and shown to be a distinct polypeptide species from glycine-N-acyltransferase (Webster et al. 1976). This human glutamine-N-acyltransferase activity has not been characterized by sequence analysis at the protein or DNA level, however, and thus cannot be associated with a known human protein in the annotation of phenylacetate conjugation.
R-HSA-177128 Conjugation of salicylate with glycine In the body, aspirin (acetylsalicylic acid) is hydrolyzed to salicylate (ST). ST can then be hydroxylated to yield gentisic acid, conjugated with glucuronate, or conjugated with glycine to yield molecules that are excreted by the kidneys. The third of these conjugation processes is annotated here. It is the major route of ST catabolism and accounts for 20–65% of the products (Hutt et al, 1986). The conjugation proceeds in two steps. First, ST and ATP react with coenzyme A to form salicylate-CoA (ST-CoA), AMP, and pyrophosphate in a reaction catalyzed by xenobiotic/medium-chain fatty acid:CoA ligase (Vessey et al. 2003). Second, ST-CoA and glycine react to form salicyluric acid and Coenzyme A (Mawal and Qureshi 1994).
R-HSA-5674400 Constitutive Signaling by AKT1 E17K in Cancer While AKT1 gene copy number, expression level and phosphorylation are often increased in cancer, only one low frequency point mutation has been repeatedly reported in cancer and functionally studied. This mutation represents a substitution of a glutamic acid residue with lysine at position 17 of AKT1, and acts by enabling AKT1 to bind PIP2. PIP2-bound AKT1 is phosphorylated by TORC2 complex and by PDPK1 that is always present at the plasma membrane, due to low affinity for PIP2. Therefore, E17K substitution abrogates the need for PI3K in AKT1 activation (Carpten et al. 2007, Landgraf et al. 2008).
R-HSA-2219530 Constitutive Signaling by Aberrant PI3K in Cancer Signaling by PI3K/AKT is frequently constitutively activated in cancer via gain-of-function mutations in one of the two PI3K subunits - PI3KCA (encoding the catalytic subunit p110alpha) or PIK3R1 (encoding the regulatory subunit p85alpha). Gain-of-function mutations activate PI3K signaling by diverse mechanisms. Mutations affecting the helical domain of PIK3CA and mutations affecting nSH2 and iSH2 domains of PIK3R1 impair inhibitory interactions between these two subunits while preserving their association. Mutations in the catalytic domain of PIK3CA enable the kinase to achieve an active conformation. PI3K complexes with gain-of-function mutations therefore produce PIP3 and activate downstream AKT in the absence of growth factors (Huang et al. 2007, Zhao et al. 2005, Miled et al. 2007, Horn et al. 2008, Sun et al. 2010, Jaiswal et al. 2009, Zhao and Vogt 2010, Urick et al. 2011).
R-HSA-5637810 Constitutive Signaling by EGFRvIII In glioblastoma, the most prevalent EGFR mutation, present in ~25% of tumors, is the deletion of the ligand binding domain of EGFR, accompanied with amplification of the mutated allele, which results in over-expression of the mutant protein known as EGFRvIII. EGFRvIII mutant is not able to bind a ligand, but dimerizes and autophosphorylates spontaneously and is therefore constitutively active (Fernandes et al. 2001). Point mutations in the extracellular domain of EGFR are also frequently found in glioblastoma, but ligand binding ability and responsiveness are preserved (Lee et al. 2006).
Similar to EGFR kinase domain mutants, EGFRvIII mutant needs to maintain association with the chaperone heat shock protein 90 (HSP90) for proper functioning (Shimamura et al. 2005, Lavictoire et al. 2003). CDC37 is a co-chaperone of HSP90 that acts as a scaffold and regulator of interaction between HSP90 and its protein kinase clients. CDC37 is frequently over-expressed in cancers involving mutant kinases and acts as an oncogene (Roe et al. 2004, reviewed by Gray Jr. et al. 2008).
Expression of EGFRvIII mutant results in aberrant activation of downstream signaling cascades, namely RAS/RAF/MAP kinase signaling and PI3K/AKT signaling, and possibly signaling by PLCG1, which leads to increased cell proliferation and survival, providing selective advantage to cancer cells that harbor EGFRvIII (Huang et al. 2007).
EGFRvIII mutant does not autophosorylate on the tyrosine residue Y1069 (i.e. Y1045 in the mature protein), a docking site for CBL, and is therefore unable to recruit CBL ubiquitin ligase, which enables it to escape degradation (Han et al. 2006)
R-HSA-1236382 Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants Signaling by EGFR is frequently activated in cancer through activating mutations in the coding sequence of the EGFR gene, resulting in expression of a constitutively active mutant protein.
Epidermal growth factor receptor kinase domain mutants are present in ~16% of non-small-cell lung cancers (NSCLCs), but are also found in other cancer types, such as breast cancer, colorectal cancer, ovarian cancer and thyroid cancer. EGFR kinase domain mutants harbor activating mutations in exons 18-21 which code for the kinase domain (amino acids 712-979) . Small deletions, insertions or substitutions of amino acids within the kinase domain lock EGFR in its active conformation in which the enzyme can dimerize and undergo autophosphorylation spontaneously, without ligand binding (although ligand binding ability is preserved), and activate downstream signaling pathways that promote cell survival (Greulich et al. 2005, Zhang et al. 2006, Yun et al. 2007, Red Brewer et al. 2009).
Point mutations in the extracellular domain of EGFR are frequently found in glioblastoma. Similar to kinase domain mutations, point mutations in the extracellular domain result in constitutively active EGFR proteins that signal in the absence of ligands, but ligand binding ability and responsiveness are preserved (Lee et al. 2006).
EGFR kinase domain mutants need to maintain association with the chaperone heat shock protein 90 (HSP90) for proper functioning (Shimamura et al. 2005, Lavictoire et al. 2003). CDC37 is a co-chaperone of HSP90 that acts as a scaffold and regulator of interaction between HSP90 and its protein kinase clients. CDC37 is frequently over-expressed in cancers involving mutant kinases and acts as an oncogene (Roe et al. 2004, reviewed by Gray Jr. et al. 2008).
Over-expression of the wild-type EGFR or EGFR cancer mutants results in aberrant activation of downstream signaling cascades, namely RAS/RAF/MAP kinase signaling and PI3K/AKT signaling, and possibly signaling by PLCG1, which leads to increased cell proliferation and survival, providing selective advantage to cancer cells that harbor activating mutations in the EGFR gene (Sordella et al. 2004, Huang et al. 2007).
While growth factor activated wild-type EGFR is promptly down-regulated by internalization and degradation, cancer mutants of EGFR demonstrate prolonged activation (Lynch et al. 2004). Association of HSP90 with EGFR kinase domain mutants negatively affects CBL-mediated ubiquitination, possibly through decreasing the affinity of EGFR kinase domain mutants for phosphorylated CBL, so that CBL dissociates from the complex upon phosphorylation and cannot perform ubiquitination (Yang et al. 2006, Padron et al. 2007).
Various molecular therapeutics are being developed to target aberrantly activated EGFR in cancer. Non-covalent (reversible) small tyrosine kinase inhibitors (TKIs), such as gefitinib and erlotinib, selectively bind kinase domain of EGFR, competitively inhibiting ATP binding and subsequent autophosphorylation of EGFR dimers. EGFR kinase domain mutants sensitive to non-covalent TKIs exhibit greater affinity for TKIs than ATP compared with the wild-type EGFR protein, and are therefore preferential targets of non-covalent TKI therapeutics (Yun et al. 2007). EGFR proteins that harbor point mutations in the extracellular domain also show sensitivity to non-covalent tyrosine kinase inhibitors (Lee et al. 2006). EGFR kinase domain mutants harboring small insertions in exon 20 or a secondary T790M mutation are resistant to reversible TKIs (Balak et al. 2006) due to increased affinity for ATP (Yun et al. 2008), and are targets of covalent (irreversible) TKIs that form a covalent bond with EGFR cysteine residue C397. However, effective concentrations of covalent TKIs also inhibit wild-type EGFR, causing severe side effects (Zhou et al. 2009). Hence, covalent TKIs have not shown much promise in clinical trials (Reviewed by Pao and Chmielecki in 2010).
R-HSA-2691232 Constitutive Signaling by NOTCH1 HD Domain Mutants The heterodimerization (HD) domain of NOTCH1, responsible for association of NOTCH1 extracellular and transmembrane regions after furin-mediated cleavage of NOTCH1 precursor, is one of the hotspots for gain-of-function NOTCH1 mutations in T-cell acute lymphoblastic leukemia (T-ALL) (Weng et al. 2004). NOTCH1 HD domain mutants are responsive to ligand binding, but the activation (through cleavage of S2 and S3 sites and release of the intracellular domain NICD1) also happens spontaneously, in the absence of DLL and JAG ligands (Malecki et al. 2006). The following NOTCH1 HD domain mutants were directly functionally studied by Malecki et al.: NOTCH1 V1576E, NOTCH1 F1592S, NOTCH1 L1593P, NOTCH1 L1596H, NOTCH1 R1598P, NOTCH1 I1616N, NOTCH1 I1616T, NOTCH1 V1676D, NOTCH1 L1678P, NOTCH1 I1680N, NOTCH1 A1701P and NOTCH1 I1718T; other frequent NOTCH1 HD domain mutants (NOTCH1 L1574P, NOTCH1 L1574Q and NOTCH1 L1600P) are assumed to behave in a similar way.
R-HSA-2894862 Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants When found in cis, HD and PEST domain mutations act synergistically, increasing NOTCH1 transcriptional activity up to ~40-fold, compared with up to ~10-fold and up to ~2-fold increase with HD mutations alone and PEST domain mutations alone, respectively (Weng et al. 2004). HD domain mutations enable spontaneous, ligand-independent, proteolytic release of the NICD1 fragment, although mutants remain responsive to ligand binding (Malecki et al. 2006), while PEST domain mutations prolong NICD1 half-life and transcriptional activity through interference with FBXW7 (FBW7)-mediated ubiquitination and degradation (Thompson et al. 2007, O'Neil et al. 2007). NOTCH1 HD+PEST domain mutants annotated here are NOTCH1 L1600P;P2514Rfs*4, NOTCH1 L1600P;Q2440*, NOTCH1 L1600P;Q2395* and NOTCH1 L1574P;P2474Afs*4.
R-HSA-2644606 Constitutive Signaling by NOTCH1 PEST Domain Mutants As NOTCH1 PEST domain is intracellular, NOTCH1 PEST domain mutants are expected to behave as the wild-type NOTCH1 with respect to ligand binding and proteolytic cleavage mediated activation of signaling. However, once the NICD1 fragment of NOTCH1 is released, PEST domain mutations prolong its half-life and transcriptional activity through interference with FBXW7 (FBW7)-mediated ubiquitination and degradation of NICD1 (Weng et al. 2004, Thompson et al. 2007, O'Neil et al. 2007). All NOTCH1 PEST domain mutants annotated here (NOTCH1 Q2395*, NOTCH1 Q2440*, NOTCH1 P2474Afs*4 and NOTCH1 P2514Rfs*4) either have a truncated PEST domain or lack the PEST domain completely.
R-HSA-2660826 Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant NOTCH1 t(7;9)(NOTCH1:M1580_K2555) mutant is expressed in a small subset of T-cell acute lymphoblastic leukemia (T-ALL) patients. This mutant protein results from a translocation that joins a portion of intron 24 of the NOTCH1 gene to the promoter sequence of T-cell receptor beta (TCRB), leading to overexpression of a truncated NOTCH1 protein in T-cells and their precursors. The truncated NOTCH1 contains amino acids 1580 to 2555 of the wild-type NOTCH1, lacking almost the entire extracellular domain, including EGF and LIN12 repeats (Ellisen et al. 1991). As EGF repeats are needed for NOTCH1 interaction with its ligands (DLL1, DLL4, JAG1, JAG2), the mutant NOTCH1 t(7;9)(NOTCH1:M1580_K2555) does not bind a ligand. The constitutive activity of NOTCH1 t(7;9)(NOTCH1:M1580_K2555) is based on its constitutive proteolytic processing into NOTCH1 intracellular domain (NICD1) by ADAM10/17 protease and gamma-secretase complex, as proteolytic cleavage sites are exposed in the absence of ligand binding in the mutant protein. Constitutively produced NICD1 accumulates in the nucleus, leading to aberrant activation of NOTCH1 target genes which play important roles in the development of T lymphocytes (Washburn et al. 1997. Radtke et al. 1999, Maillard et al. 2004, Sambandam et al. 2005, Tan et al. 2005). Infection of bone marrow cells with recombinant retroviruses that code for truncated NOTCH1 that resembles t(7;9)(NOTCH1:M1580_K2555) resulted in T-ALL-like illness in a portion of mice that received the infected bone-marrow transplant, with all tumors overexpressing truncated forms of NOTCH1 (Pear et al. 1996).
R-HSA-9634285 Constitutive Signaling by Overexpressed ERBB2 Overexpression of ERBB2 (HER2), usually as a consequence of ERBB2 gene amplification, results in formation of ERBB2 homodimers. Under normal conditions, only ERBB2 heterodimers form, as ERBB2 is expressed at low levels.
ERBB2 homodimerization leads to activation of ERBB2 signaling in the absence of growth factors. Signaling by ERBB2 homodimers mainly activates the RAS/RAF/MAPK signaling cascade, while PI3K/AKT signaling is not significantly affected (Pickl and Ries 2009).
Trastuzumab (Herceptin), a recombinant antibody clinically approved as an anti-cancer therapeutic for ERBB2-overexpressing cancers, preferentially binds to ERBB2 homodimers (Pickl and Ries 2009).
Accurate functional analysis of ERBB2 signaling may require 3D instead of 2D cell culture (Pickl and Ries 2009).
R-HSA-176407 Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase The activity of the APC/C must be appropriately regulated during the cell cycle to ensure the timely degradation of its substrates. Of particular importance is the conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase. Phosphorylation of both the APC/C complex and Cdh1 regulate this conversion. During mitosis, several APC/C subunits are phosphorylated increasing the activity of APC/C:Cdc20. However, phosphorylation of Cdh1 by mitotic Cyclin:Cdk complexes prevents it from activating the APC/C. Dephosphorylation of Cdh1 in late anaphase by Cdc14a results in the activation of APC/C:Cdh1 (reviewed in Castro et al, 2005).
R-HSA-6814122 Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding The chaperonin complex TRiC/CCT is needed for the proper folding of all five G-protein beta subunits (Wells et al. 2006). TRiC/CCT cooperates with the phosducin-like protein PDCL (commonly known as PhLP or PhLP1), which interacts with both TRiC/CCT and G-protein beta subunits 1-5 (GNB1, GNB2, GNB3, GNB4, GNB5) (Dupre et al. 2007, Howlett et al. 2009). PDCL enables completion of G-protein beta folding by TRiC/CCT, promotes release of folded G-protein beta subunits 1-4 (GNB1, GNB2, GNB3, GNB4) from the chaperonin complex, and facilitates the formation of the heterodimeric G-protein beta:gamma complex between G-protein beta subunits 1-4 and G-protein gamma subunits 1-12 (Lukov et al. 2005, Lukov et al. 2006, Howlett et al. 2009, Lai et al. 2013, Plimpton et al. 2015, Xie et al. 2015). In the case of G-protein beta 5 (GNB5), PDCL stabilizes the interaction of GNB5 with the TRiC/CCT and promotes GNB5 folding, thus positively affecting formation of GNB5 dimers with RGS family proteins (Howlett et al. 2009, Lai et al. 2013, Tracy et al. 2015). However, over-expression of PDCL interferes with formation of GNB5:RGS dimers as PDCL and RGS proteins bind to the same regions of the GNB5 protein (Howlett et al. 2009).
R-HSA-389958 Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding In the case of actin and tubulin folding, and perhaps other substrates, the emerging polypeptide chain is transferred from the ribosome to TRiC via Prefoldin (Vainberg et al., 1998).
R-HSA-71288 Creatine metabolism In humans, creatine is synthesized primarily in the liver and kidney, from glycine, arginine, and S-adenosylmethionine, in a sequence of two reactions. From the liver, creatine is exported to tissues such as skeletal muscle and brain, where it undergoes phosphorylation and serves as a short-term energy store. The mechanism by which creatine leaves producer tissues is unclear, but its uptake by consumer tissues is mediated by the SLC6A8 transporter.
Once formed, phosphocreatine undergoes a slow spontaneous reaction to form creatinine, which is excreted from the body.
R-HSA-166786 Creation of C4 and C2 activators Two pathways lead to a complex capable of activating C4 and C2.
The classical pathway is triggered by activation of the C1-complex, which consists of hexameric molecule C1q and a tetramer comprising two C1r and two C1s serine proteinases. This occurs when C1q binds to IgM or IgG complexed with antigens, a single IgM can initiate the pathway while multiple IgGs are needed, or when C1q binds directly to the surface of the pathogen. Binding leads to conformational changes in C1q, activating the serine protease activity of C1r, which then cleaves C1s, another serine protease. The C1r:C1s component is now capable of splitting C4 and C2 to produce the classical C3-convertase C4b2a. C1r and C1s are additionally controlled by C1-inhibitor.(Kerr MA 1980)
The lectin pathway is similar in operation but has different components.
Mannose-binding lectin (MBL) or ficolins (L-ficolin, M-ficolin and H-ficolin) initiate the lectin pathway cascade by binding to specific carbohydrate patterns on pathogenic cell surfaces. MBL and ficolins circulate in plasma in complexes with homodimers of MBL-associated serine proteases (MASP) (Fujita et al. 2004; Hajela et al. 2002). Upon binding of human lectin (MBL or ficolins) to the target surface the complex of lectin:MASP undergoes conformational changes, which results in the activation of MASPs by cleavage (Matsushita M et al. 2000; Fujita et al. 2004). Activated MASPs become capable of C4 and C2 cleavage, giving rise to the same C3 convertase C4b:C2a as the classical pathway.
R-HSA-8949613 Cristae formation Cristae are invaginations of the inner mitochondrial membrane that extend into the matrix and are lined with cytochrome complexes and F1Fo ATP synthase complexes. Cristae increase the surface area of the inner membranes allowing greater numbers of respiratory complexes. Cristae are also believed to serve as "proton pockets" to generate localized regions of higher membrane potential. The steps in the biogenesis of cristae are not yet completely elucidated (reviewed in Zick et al. 2009) but the formation of the Mitochondrial Contact Site and Cristae Organizing System (MICOS, formerly also known as MINOS, reviewed in Rampelt et al. 2016, Kozjak-Pavlovic 2016, van der Laan et al. 2016) and localized concentrations of cardiolipin are known to define the inward curvature of the inner membrane at the bases of cristae. MICOS also links these regions of the inner membrane with complexes (the SAM complex and, in fungi, the TOM complex) embedded in the outer membrane. CHCHD3 (MIC19) and IMMT (MIC60) subunits of MICOS also interact with OPA1 at the inner membrane (Darshi et al. 2011, Glytsou et al. 2016).
Formation of dimers or oligomers of the F1Fo ATP synthase complex causes extreme curvature of the inner membrane at the apices of cristae (reviewed in Seelert and Dencher 2011, Habersetzer et al. 2013). Defects in either MICOS or F1Fo ATP synthase oligomerization produce abnormal mitochondrial morphologies.
R-HSA-1236973 Cross-presentation of particulate exogenous antigens (phagosomes) Dendritic cells (DCs) take up and process exogenous particulate or cell-associated antigens such as microbes or tumor cells for MHC-I cross-presentation. Particulate antigens have been reported to be more efficiently cross-presented than soluble antigens by DCs (Khor et al. 2008). Particulate antigens are internalized by phagosomes. There are two established models that explain the mechanism by which exogenous particulate antigens are presented through MHC I; the cytosolic pathway where internalized antigens are somehow translocated from phagosomes into cytosol for proteasomal degradation and the vacuolar pathway (Lin et al. 2008, Amigorena et al. 2010).
R-HSA-1236978 Cross-presentation of soluble exogenous antigens (endosomes) Exogenous soluble antigens are cross-presented by dendritic cells, albeit with lower efficiency than for particulate substrates. Soluble antigens destined for cross-presentation are taken up by distinct endocytosis mechanisms which route them into stable early endosomes and then to the cytoplasm for proteasomal degradation and peptide loading.
R-HSA-2243919 Crosslinking of collagen fibrils After removal of the N- and C-procollagen propeptides, fibrillar collagen molecules aggregate into microfibrillar arrays, stabilized by covalent intermolecular cross-links. These depend on the oxidative deamination of specific lysine or hydroxylysine residues in the telopeptide region by lysyl oxidase (LOX) with the subsequent spontaneous formation of covalent intermolecular cross-links (Pinnell & Martin 1968, Siegel et al. 1970, 1974, Maki 2009, Nishioka et al. 2012). Hydroxylysine is formed intracellularly by lysine hydroxylases (LH). There are different forms of LH responsible for hydroxylation of helical and telopeptide lysines (Royce & Barnes 1985, Knott et al.1997, Takaluoma et al. 2007, Myllyla 2007). The chemistry of the cross-links formed depends on whether lysines or hydroxylysines are present in the telopeptides (Barnes et al. 1974), which depends on the proportion of collagen lysines post-translationally converted to hydroxylysine by LH. The lysine pathway predominates in adult skin, cornea and sclera while the hydroxylysine pathway occurs primarily in bone, cartilage, ligament, tendons, embryonic skin and most connective tissues (Eyre 1987, Eyre & Wu 2005, Eyre et al. 2008). Oxidative deamination of lysine or hydroxylysine residues by LOX generates the allysine and hydroxyallysine aldehydes respectively. These can spontaneously react with either another aldehyde to form an aldol condensation product (intramolecular cross-link), or with an unmodified lysine or hydroxylysine residue to form intermolecular cross-links.
The pathway of cross-linking is regulated primarily by the hydroxylation pattern of telopeptide and triple-helix domain lysine residues. When lysine residues are the source of aldehydes formed by lysyl oxidase the allysine cross-linking pathway leads to the formation of aldimine cross-links (Eyre & Wu 2005). These are stable at physiological conditions but readily cleaved at acid pH or elevated temperature. When hydroxylysine residues are the source of aldehydes formed by lysyl oxidase the hydroxyallysine cross-linking pathway leads to the formation of more stable ketoimine cross-links.
Telopeptide lysine residues can be converted by LOX to allysine, which can react with a helical hydroxylysine residue forming the lysine aldehyde aldimine cross-link dehydro hydroxylysino norleucine (deHHLNL) (Bailey & Peach 1968, Eyre et al. 2008). If the telopeptide residue is hydroxylysine, the hydroxyallysine formed by LOX can react with a helical hydroxylysine forming the Schiff base, which spontaneously undergoes an Amadori rearrangement resulting in the ketoimine cross link hydroxylysino 5 ketonorleucine (HLKNL). This stable cross-link is formed in tissues where telopeptide residues are predominanly hydroxylated, such as foetal bone and cartilage, accounting for the relative insolubility of collagen from these tissues (Bailey et al. 1998). In bone, telopeptide hydroxyallysines can react with the epsilon-amino group of a helical lysine (Robins & Bailey 1975). The resulting Schiff base undergoes Amadori rearrangement to form lysino-hydroxynorleucine (LHNL). An alternative mechanism of maturation of ketoimine cross-links has been reported in cartilage leading to the formation of arginoline (Eyre et al. 2010).
These divalent crosslinks greatly diminish as connective tissues mature, due to further spontaneous reactions (Bailey & Shimokomaki 1971, Robins & Bailey 1973) with neighbouring peptides that result in tri- and tetrafunctional cross-links. In mature tissues collagen cross-links are predominantly trivalent. The most common are pyridinoline or 3-hydroxypyridinium cross-links, namely hydroxylysyl-pyridinoline (HL-Pyr) and lysyl-pyridinoline (L-Pyr) cross-links (Eyre 1987, Ogawa et al. 1982, Fujimoto et al. 1978). HL-Pyr is formed from three hydroxylysine residues, HLKNL plus a further hydroxyallysine. It predominates in highly hydroxylated collagens such as type II collagen in cartilage. L-Pyr is formed from two hydroxylysines and a lysine, LKNL plus a further hydroxyallysine, found mostly in calcified tissues (Bailey et al. 1998). Trivalent collagen cross-links can also form as pyrroles, either Lysyl-Pyrrole (L-Pyrrole) or hydroxylysyl-pyrrole (HL-Pyrrole), respectively formed when LKNL or HLKNL react with allysine (Scott et al. 1981, Kuypers et al. 1992). A further three-way crosslink can form when DeH-HLNL reacts with histidine to form histidino-hydroxylysinonorleucine (HHL), found in skin and cornea (Yamauchi et al. 1987, 1996). This can react with an additional lysine to form the tetrafunctional cross-link histidinohydroxymerodesmosine (Reiser et al. 1992, Yamauchi et al. 1996).
Another mechanism which could be involved in the cross-linking of collagen IV networks is the sulfilimine bond (Vanacore et al. 2009), catalyzed by peroxidasin, an enzyme found in basement membrane (Bhave 2012).
To improve clarity inter-chain cross-linking is represented here for Collagen type I only. Although the formation of each type of cross-link is represented here as an independent event, the partial and random nature of lysine hydroxylation and subsequent lysyl oxidation means that any combination of these cross-linking events could occur within the same collagen fibril .
R-HSA-69273 Cyclin A/B1/B2 associated events during G2/M transition Cell cycle progression is regulated by cyclin-dependent protein kinases at both the G1/S and the G2/M transitions. The G2/M transition is regulated through the phosphorylation of nuclear lamins and histones (reviewed in Sefton, 2001).
The two B-type cyclins localize to different regions within the cell and are thought to have specific roles as CDK1-activating subunits (see Bellanger et al., 2007). Cyclin B1 is primarily cytoplasmic during interphase and translocates into the nucleus at the onset of mitosis (Jackman et al., 1995; Hagting et al., 1999). Cyclin B2 colocalizes with the Golgi apparatus and contributes to its fragmentation during mitosis (Jackman et al., 1995; Draviam et al., 2001).
R-HSA-69656 Cyclin A:Cdk2-associated events at S phase entry Cyclin A:Cdk2 plays a key role in S phase entry by phosphorylation of proteins including Cdh1, Rb, p21 and p27. During G1 phase of the cell cycle, cyclin A is synthesized and associates with Cdk2. After forming in the cytoplasm, the Cyclin A:Cdk2 complexes are translocated to the nucleus (Jackman et al.,2002). Prior to S phase entry, the activity of Cyclin A:Cdk2 complexes is negatively regulated through Tyr 15 phosphorylation of Cdk2 (Gu et al., 1995) and also by the association of the cyclin kinase inhibitors (CKIs), p27 and p21. Phosphorylation of cyclin-dependent kinases (CDKs) by the CDK-activating kinase (CAK) is required for the activation of the CDK2 kinase activity (Aprelikova et al., 1995). The entry into S phase is promoted by the removal of inhibitory Tyr 15 phosphates from the Cdk2 subunit of Cyclin A:Cdk2 complex by the Cdc25 phosphatases (Blomberg and Hoffmann, 1999) and by SCF(Skp2)-mediated degradation of p27/p21 (see Ganoth et al., 2001). While Cdk2 is thought to play a primary role in regulating entry into S phase, recent evidence indicates that Cdk1 is equally capable of promoting entry into S phase and the initiation of DNA replication (see Bashir and Pagano, 2005). Thus, Cdk1 complexes may also play a significant role at this point in the cell cycle.
R-HSA-69231 Cyclin D associated events in G1 Three D-type cyclins are essential for progression from G1 to S-phase. These D cyclins bind to and activate both CDK4 and CDK6. The formation of all possible complexes between the D-type cyclins and CDK4/6 is promoted by the proteins, p21(CIP1/WAF1) and p27(KIP1). The cyclin-dependent kinases are then activated due to phosphorylation by CAK. The cyclin dependent kinases phosphorylate the RB1 protein and RB1-related proteins p107 (RBL1) and p130 (RBL2). Phosphorylation of RB1 leads to release of activating E2F transcription factors (E2F1, E2F2 and E2F3). After repressor E2Fs (E2F4 and E2F5) dissociate from phosphorylated RBL1 and RBL2, activating E2Fs bind to E2F promoter sites, stimulating transcription of cell cycle genes, which then results in proper G1/S transition. The binding and sequestration of p27Kip may also contribute to the activation of CDK2 cyclin E/CDK2 cyclin A complexes at the G1/S transition (Yew et al., 2001).
R-HSA-69202 Cyclin E associated events during G1/S transition The transition from the G1 to S phase is controlled by the Cyclin E:Cdk2 complexes. As the Cyclin E:Cdk2 complexes are formed, the Cdk2 is phosphorylated by the Wee1 and Myt1 kinases. This phosphorylation keeps the Cdk2 inactive. In yeast this control is called the cell size checkpoint control. The dephosphorylation of the Cdk2 by Cdc25A activates the Cdk2, and is coordinated with the cells reaching the proper size, and with the DNA synthesis machinery being ready. The Cdk2 then phosphorylates G1/S specific proteins, including proteins required for DNA replication initiation. The beginning of S-phase is marked by the first nucleotide being laid down on the primer during DNA replication at the early-firing origins.Failure to appropriately regulate cyclin E accumulation can lead to accelerated S phase entry, genetic instability, and tumorigenesis. The amount of cyclin E protein in the cell is controlled by ubiquitin-mediated proteolysis (see Woo, 2003).This pathway has not yet been annotated in Reactome.
R-HSA-1614603 Cysteine formation from homocysteine Transsulfuration is the interconversion of homocysteine and cysteine, and it fully takes place in bacteria and some plants and fungi. Animals however have only one direction of this bidirectional path, the synthesis of cysteine from homocysteine via cystathionine. Because excess cysteine is degraded to hydrogen sulfide, which is now known as a neuromodulator and smooth muscle relaxant, this pathway is also the main source of its production, which takes place in the cytosol, as well as in extracellular space (Dominy & Stipanuk 2004, Bearden et al. 2010).
R-HSA-211897 Cytochrome P450 - arranged by substrate type
The P450 isozyme system is the major phase 1 biotransforming system in man, accounting for more than 90% of drug biotransformations. This system has huge catalytic versatility and a broad substrate specificity, acting upon xenobiotica and endogenous compounds. It is also called the mixed-function oxidase system, the P450 monooxygenases and the heme-thiolate protein system. All P450 enzymes are a group of heme-containing isozymes which are located on the membrane of the smooth endoplasmic reticulum. They can be found in all tissues of the human body but are most concentrated in the liver. The name "cytochrome P450" (CYP) is derived from the spectral absorbance maximum at 450nm when carbon monoxide binds to CYP in its reduced (ferrous, Fe2+) state. The basic reaction catalyzed by CYP is mono-oxygenation, that is the transfer of one oxygen atom from molecular oxygen to a substrate. The other oxygen atom is reduced to water during the reaction with the equivalents coming from the cofactor NADPH. The basic reaction is;
RH (substrate) + O2 + NADPH + H+ = ROH (product) + H2O + NADP+
The end results of this reaction can be (N-)hydroxylation, epoxidation, heteroatom (N-, S-) oxygenation, heteroatom (N-, S-, O-) dealkylation, ester cleavage, isomerization, dehydrogenation, replacement by oxygen or even reduction under anaerobic conditions.
The metabolites produced from these reactions can either be mere intermediates which have relatively little reactivity towards cellular sysytems and are readily conjugated, or, they can be disruptive to cellular systems. Indeed, inert compounds need to be prepared for conjugation and thus the formation of potentially reactive metabolites is in most cases unavoidable.
There are 57 human CYPs (in 18 families and 42 subfamilies), mostly concentrated in the endoplasmic reticulum of liver cells although many tissues have them to some extent (Nelson DR et al, 2004). CYPs are grouped into 14 families according to their sequence similarity. Generally, enzymes in the same family share 40% sequence similarity and 55% within a subfamily. Nomenclature of P450s is as follows. CYP (to represent cytochrome P450 superfamily), followed by an arabic number for the family, a capital letter for the subfamily and finally a second arabic number to denote the isoenzyme. An example is CYP1A1 which is the first enzyme in subfamily A of cytochrome P450 family 1.
The majority of the enzymes are present in the CYP1-4 families. CYP1-3 are primarily concerned with xenobiotic biotransformation whereas the other CYPs deal primarily with endogenous compounds. The CYP section is structured by the typical substrate they act upon. Of the 57 human CYPs, 7 encode mitochondrial enzymes, all involved in sterol biosynthesis. Of the remaining 50 microsomal enzymes, 20 act upon endogenous compounds, 15 on xenobiotics and 15 are the so-called "orphan enzymes" with no substrate identified.
The P450 catalytic cycle (picture) shows the steps involved when a substrate binds to the enzyme.
(1) The normal state of a P450 with the iron in its ferric [Fe3+] state.
(2) The substrate binds to the enzyme.
(3) The enzyme is reduced to the ferrous [Fe2+] state by the addition of an electron from NADPH cytochrome P450 reductase. The bound substrate facilitates this process.
(4,5) Molecular oxygen binds and forms an Fe2+OOH complex with the addition of a proton and a second donation of an electron from either NADPH cytochrome P450 reductase or cytochrome b5. A second proton cleaves the Fe2+OOH complex to form water.
(6) An unstable [FeO]3+ complex donates its oxygen to the substrate (7). The oxidised substrate is released and the enzyme returns to its initial state (1).
R-HSA-111461 Cytochrome c-mediated apoptotic response Upon its release from the mitochondrial intermembrane space, cytochrome c (CYSC) binds to and causes an ATP-mediated conformational change in the cytoplasmic adaptor protein apoptotic protease‑activating factor 1 (APAF1). This conformational change triggers the formation of procaspase-9-activating oligomeric protein complex named apoptosome. The active caspase‑9 holoenzyme activates downstream effector caspases‑3 and ‑7. The activated effector caspases then cleave various cellular proteins. R-HSA-1280215 Cytokine Signaling in Immune system Cytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concentrations. Cytokines bind to specific membrane receptors, which then signal the cell via second messengers, to regulate cellular activity. R-HSA-9707564 Cytoprotection by HMOX1 Expression of heme oxygenase 1 (HMOX1) is regulated by various indicators of cell stress, while HMOX2 is expressed constitutively. Both catalyze the breakdown of heme into biliverdin (BV), carbon monoxide (CO), and ferrous iron. Biliverdin is immediately reduced to bilirubin (BIL). Both bilirubin and carbon monoxide can localize to different compartments and outside the cell. Cytoprotection by HMOX1 is exerted directly by HMOX1 and by the antioxidant metabolites produced through the degradation of heme. Additionally, due to the reactive nature of labile heme, its degradation is intrinsically protective.Detection of cytosolic DNA requires multiple and possibly redundant sensors leading to activation of the transcription factor NF-kappaB and TBK1-mediated phosphorylation of the transcription factor IRF3. Cytosolic DNA also activates caspase-1-dependent maturation of the pro-inflammatory cytokines interleukin IL-1beta and IL-18. This pathway is mediated by AIM2. R-HSA-156584 Cytosolic sulfonation of small molecules Two groups of sulfotransferease (SULT) enzymes catalyze the transfer of a sulfate group from 3-phosphoadenosine 5-phosphosulfate (PAPS) to a hydroxyl group on an acceptor molecule, yielding a sulfonated acceptor and 3-phosphoadenosine 5-phosphate (PAP). One is localized to the Golgi apparatus and mediates the sulfonation of proteoglycans. The second, annotated here, is cytosolic and mediates the sulfonation of a diverse array of small molecules, increasing their solubilities in water and modifying their physiological functions. There are probably thirteen or more human cytosolic SULT enzymes; eleven of these have been purified and characterized enzymatically, and are annotated here (Blanchard et al. 2004; Gamage et al. 2005). These enzymes appear to be active as dimers. Their substrate specificities are typically broad, and not related in an obvious way to their structures; indeed, apparently orthologous human and rodent SULT enzymes can have different substrate specificities (Glatt 2000), and none has been exhaustively characterized. The substrates listed in the table and annotated here are a sample of the known ones, chosen to indicate the range of activity of these enzymes and to capture some of their known physiologically important targets. Absence of a small molecule - enzyme pair from the table, however, may only mean that it has not yet been studied. R-HSA-379716 Cytosolic tRNA aminoacylation Cytosolic tRNA synthetases catalyze the reactions of tRNAs encoded in the nuclear genome, their cognate amino acids, and ATP to form aminoacyl-tRNAs, AMP, and pyrophosphate. Eight of the tRNA synthetases, those specific for arginine, aspartate, glutamate and proline, glutamine, isoleucine, leucine, lysine, and methionine, associate to form a complex with three accessory proteins. Each of the component synthetases is active in vitro as a purified protein; complex formation is thought to channel aminoacylated tRNAs more efficiently to the site of protein synthesis in mRNA:ribosome complexes (Quevillon et al. 1999; Wolfe et al. 2003, 2005). R-HSA-1489509 DAG and IP3 signaling This pathway describes the generation of DAG and IP3 by the PLCgamma-mediated hydrolysis of PIP2 and the subsequent downstream signaling events. R-HSA-2172127 DAP12 interactions DNAX activation protein of 12kDa (DAP12) is an immunoreceptor tyrosine-based activation motif (ITAM)-bearing adapter molecule that transduces activating signals in natural killer (NK) and myeloid cells. It mediates signalling for multiple cell-surface receptors expressed by these cells, associating with receptor chains through complementary charged transmembrane amino acids that form a salt-bridge in the context of the hydrophobic lipid bilayer (Lanier et al. 1998). DAP12 homodimers associate with a variety of receptors expressed by macrophages, monocytes and myeloid cells including TREM2, Siglec H and SIRP-beta, as well as activating KIR, LY49 and the NKG2C proteins expressed by NK cells. DAP12 is expressed at the cell surface, with most of the protein lying on the cytoplasmic side of the membrane (Turnbull & Colonna 2007, Tessarz & Cerwenka 2008). R-HSA-2424491 DAP12 signaling In response to receptor ligation, the tyrosine residues in DAP12's immunoreceptor tyrosine-based activation motif (ITAM) are phosphorylated by Src family kinases. These phosphotyrosines form the docking site for the protein tyrosine kinase SYK in myeloid cells and SYK and ZAP70 in NK cells. DAP12-bound SYK autophosphorylates and phosphorylates the scaffolding molecule LAT, recruiting the proximal signaling molecules phosphatidylinositol-3-OH kinase (PI3K), phospholipase-C gamma (PLC-gamma), GADS (GRB2-related adapter downstream of SHC), SLP76 (SH2 domain-containing leukocyte protein of 76 kDa), GRB2:SOS (Growth factor receptor-bound protein 2:Son of sevenless homolog 1) and VAV. All of these intermediate signalling molecules result in the recruitment and activation of kinases AKT, CBL (Casitas B-lineage lymphoma) and ERK (extracellular signal-regulated kinase), and rearrangement of the actin cytoskeleton (actin polymerization) finally leading to cellular activation. PLC-gamma generates the secondary messengers diacylglycerol (DAG) and inositol-1,4,5-trisphosphate (InsP3), leading to activation of protein kinase C (PKC) and calcium mobilization, respectively (Turnbull & Colonna 2007, Klesney-Tait et al. 2006). R-HSA-180024 DARPP-32 events Dopamine- and cAMP-regulated phosphoprotein, Mr 32 kDa (DARPP-32), was identified as a major target for dopamine and protein kinase A (PKA) in striatum. Recent advances now indicate that regulation DARPP-32 phosphorylation provides a mechanism for integrating information arriving at dopaminoceptive neurons, in multiple brain regions, via a variety of neurotransmitters, neuromodulators, neuropeptides, and steroid hormones. Activation of PKA or PKG stimulates DARPP-32 phosphorylation at Thr34, converting DARPP-32 into a potent inhibitor of protein phosphatase-1 (PP-1). DARPP-32 is also phosphorylated at Thr75 by Cdk5, converting DARPP-32 into an inhibitor of PKA. Thus, DARPP-32 has the unique property of being a dual-function protein, acting either as an inhibitor of PP-1 or of PKA. R-HSA-418885 DCC mediated attractive signaling The DCC family includes DCC and neogenin in vertebrates. DCC is required for netrin-induced axon attraction. DCC is a transmembrane protein lacking any identifiable catalytic activity. Protein tyrosine kinase 2/FAK and src family kinases bind constitutively to the cytoplasmic domain of DCC and their activation couples to downstream intracellular signaling complex that directs the organization of actin. R-HSA-168928 DDX58/IFIH1-mediated induction of interferon-alpha/beta RIG-I-like helicases (RLHs) the retinoic acid inducible gene-I (RIG-I, DDX58) and melanoma differentiation associated gene 5 (MDA5, IFIH1) are RNA helicases that recognize viral double-stranded RNA (dsRNA) present within the cytoplasm (Yoneyama M & Fujita T 2007, 2008). Upon viral infection dsRNA is generated by positive-strand RNA virus families such as Flaviviridae and Coronaviridae, negative-strand RNA virus families including Orthomyxoviridae and Paramyxoviridae, and DNA virus families such as Herpesviridae and Adenoviridae (Weber F et al. 2006; Son KN et al. 2015). Functionally RIG-I (DDX58) and MDA5 (IFIH1) positively regulate the IFN genes in a similar fashion, however they differ in their response to different viral species. DDX58 (RIG-I) is essential for detecting influenza virus, Sendai virus, VSV and Japanese encephalitis virus (JEV), whereas IFIH1 (MDA5) is essential in sensing encephalomyocarditis virus (EMCV), Mengo virus and Theiler's virus, all of which belong to the picornavirus family. RIG-I and MDA5 signalling results in the activation of IKK epsilon and (TKK binding kinase 1) TBK1, two serine/threonine kinases that phosphorylate interferon regulatory factor 3 and 7 (IRF3 and IRF7). Upon phosphorylation, IRF3 and IRF7 translocate to the nucleus and subsequently induce interferon alpha (IFNA) and interferon beta (IFNB) gene transcription (Yoneyama M et al. 2004; Yoneyama M & Fujita T 2007, 2008). R-HSA-3134963 DEx/H-box helicases activate type I IFN and inflammatory cytokines production DHX36 and DHX9 are aspartate-glutamate-any amino acid aspartate/histidine (DExD/H) box helicase (DHX) proteins that localize in the cytosol. The DHX RNA helicases family includes a large number of proteins that are implicated in RNA metabolism. Members of this family, RIG-1 and MDA5, have been shown to sense a non-self RNA leading to type I IFN production. RNA helicases DHX36 and DHX9 were found to trigger host responses to non-self DNA in MyD88-dependent manner. DHX36 sensed CpG class A, while DHX9 sensed CpG class B. Both DHX36 and DHX9 were critical for antiviral immune responses in viral DNA-stimulated human plasmacytoid dendritic cells (pDC) (Kim T et al. 2010). R-HSA-73893 DNA Damage Bypass In addition to various processes for removing lesions from the DNA, cells have developed specific mechanisms for tolerating unrepaired damage during the replication of the genome. These mechanisms are collectively called DNA damage bypass pathways. The Y family of DNA polymerases plays a key role in DNA damage bypass.
Y family DNA polymerases, REV1, POLH (DNA polymerase eta), POLK (DNA polymerase kappa) and POLI (DNA polymerase iota), as well as the DNA polymerase zeta (POLZ) complex composed of REV3L and MAD2L2, are able to carry out translesion DNA synthesis (TLS) or replicative bypass of damaged bases opposite to template lesions that arrest high fidelity, highly processive replicative DNA polymerase complexes delta (POLD) and epsilon (POLE). REV1, POLH, POLK, POLI and POLZ lack 3'->5' exonuclease activity and exhibit low fidelity and weak processivity. The best established TLS mechanisms are annotated here. TLS details that require substantial experimental clarification have been omitted. For recent and past reviews of this topic, please refer to Lehmann 2000, Friedberg et al. 2001, Zhu and Zhang 2003, Takata and Wood 2009, Ulrich 2011, Saugar et al. 2014. R-HSA-5696394 DNA Damage Recognition in GG-NER In global genome nucleotide excision repair (GG-NER), the DNA damage is recognized by two protein complexes. The first complex consists of XPC, RAD23A or RAD23B, and CETN2. This complex probes the DNA helix and recognizes damage that disrupts normal Watson-Crick base pairing, which results in binding of the XPC:RAD23:CETN2 complex to the undamaged DNA strand. The second complex is a ubiquitin ligase UV-DDB that consists of DDB2, DDB1, CUL4A or CUL4B and RBX1. The UV-DDB complex is necessary for the recognition of UV-induced DNA damage and may contribute to the retention of the XPC:RAD23:CETN2 complex at the DNA damage site. The UV-DDB complex binds the damaged DNA strand (Fitch et al. 2003, Wang et al. 2004, Moser et al. 2005, Camenisch et al. 2009, Oh et al. 2011). R-HSA-73942 DNA Damage Reversal DNA damage can be directly reversed by dealkylation (Mitra and Kaina 1993). Three enzymes play a major role in reparative DNA dealkylation: MGMT, ALKBH2 and ALKBH3. MGMT dealkylates O-6-methylguanine in a suicidal reaction that inactivates the enzyme (Daniels et al. 2000, Rasimas et al. 2004, Duguid et al. 2005, Tubbs et al. 2007), while ALKBH2 and ALKBH3 dealkylate 1-methyladenine, 3-methyladenine, 3-methylcytosine and 1-ethyladenine (Duncan et al. 2002, Dango et al. 2011). R-HSA-2559586 DNA Damage/Telomere Stress Induced Senescence Reactive oxygen species (ROS), whose concentration increases in senescent cells due to oncogenic RAS-induced mitochondrial dysfunction (Moiseeva et al. 2009) or due to environmental stress, cause DNA damage in the form of double strand breaks (DSBs) (Yu and Anderson 1997). In addition, persistent cell division fueled by oncogenic signaling leads to replicative exhaustion, manifested in critically short telomeres (Harley et al. 1990, Hastie et al. 1990). Shortened telomeres are no longer able to bind the protective shelterin complex (Smogorzewska et al. 2000, de Lange 2005) and are recognized as damaged DNA.
The evolutionarily conserved MRN complex, consisting of MRE11A (MRE11), RAD50 and NBN (NBS1) subunits, binds DSBs (Lee and Paull 2005) and shortened telomeres that are no longer protected by shelterin (Wu et al. 2007). Once bound to the DNA, the MRN complex recruits and activates ATM kinase (Lee and Paull 2005, Wu et al. 2007), leading to phosphorylation of ATM targets, including TP53 (p53) (Banin et al. 1998, Canman et al. 1998, Khanna et al. 1998). TP53, phosphorylated on serine S15 by ATM, binds the CDKN1A (also known as p21, CIP1 or WAF1) promoter and induces CDKN1A transcription (El-Deiry et al. 1993, Karlseder et al. 1999). CDKN1A inhibits the activity of CDK2, leading to G1/S cell cycle arrest (Harper et al. 1993, El-Deiry et al. 1993).
SMURF2 is upregulated in response to telomere attrition in human fibroblasts and induces senecscent phenotype through RB1 and TP53, independently of its role in TGF-beta-1 signaling (Zhang and Cohen 2004). The exact mechanism of SMURF2 involvement is senescence has not been elucidated. R-HSA-5693606 DNA Double Strand Break Response DNA double-strand break (DSB) response involves sensing of DNA DSBs by the MRN complex which triggers ATM activation. ATM phosphorylates a number of proteins involved in DNA damage checkpoint signaling, as well as proteins directly involved in the repair of DNA DSBs. For a recent review, please refer to Ciccia and Elledge, 2010. R-HSA-5693532 DNA Double-Strand Break Repair Double-strand breaks (DSBs), one of the most deleterious types of DNA damage along with interstrand crosslinks, are caused by ionizing radiation or certain chemicals such as bleomycin. DSBs also occur physiologically, during the processes of DNA replication, meiotic exchange, and V(D)J recombination.
DSBs are sensed (detected) by the MRN complex. Binding of the MRN complex to the DSBs usually triggers ATM kinase activation, thus initiating the DNA double strand break response. ATM phosphorylates a number of proteins involved in DNA damage checkpoint signaling, as well as proteins directly involved in the repair of DNA DSBs. DSBs are repaired via homology directed repair (HDR) or via nonhomologous end-joining (NHEJ).
HDR requires resection of DNA DSB ends. Resection creates 3'-ssDNA overhangs which then anneal with a homologous DNA sequence. This homologous sequence can then be used as a template for DNA repair synthesis that bridges the DSB. HDR preferably occurs through the error-free homologous recombination repair (HRR), but can also occur through the error-prone single strand annealing (SSA), or the least accurate microhomology-mediated end joining (MMEJ). MMEJ takes place when DSB response cannot be initiated.
While HRR is limited to actively dividing cells with replicated DNA, error-prone NHEJ pathway functions at all stages of the cell cycle, playing the predominant role in both the G1 phase and in S-phase regions of DNA that have not yet replicated. During NHEJ, the Ku70:Ku80 heterodimer (also known as the Ku complex or XRCC5:XRCC6) binds DNA DSB ends, competing away the MRN complex and preventing MRN-mediated resection of DNA DSB ends. The catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs, PRKDC) is then recruited to DNA-bound Ku to form the DNA-PK holoenzyme. Two DNA-PK complexes, one at each side of the break, bring DNA DSB ends together, joining them in a synaptic complex. DNA-PK complex recruits DCLRE1C (ARTEMIS) to DNA DSB ends, leading to trimming of 3'- and 5'-overhangs at the break site, followed by ligation.
For review of this topic, please refer to Ciccia and Elledge 2010. R-HSA-73894 DNA Repair DNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, environmental chemicals and radiation that damage their DNA, thus corrupting genetic information. In addition, normal cellular pH and temperature create conditions that are hostile to the integrity of DNA and its nucleotide components. DNA damage can also arise as a consequence of spontaneous errors during DNA replication. The DNA repair machinery continuously scans the genome and maintains genome integrity by removing or mending any detected damage.
Depending on the type of DNA damage and the cell cycle status, the DNA repair machinery utilizes several different pathways to restore the genome to its original state. When the damage and circumstances are such that the DNA cannot be repaired with absolute fidelity, the DNA repair machinery attempts to minimize the harm and patch the insulted genome well enough to ensure cell viability.
Accumulation of DNA alterations that are the result of cumulative DNA damage and utilization of "last resort" low fidelity DNA repair mechanisms is associated with cellular senescence, aging, and cancer. In addition, germline mutations in DNA repair genes are the underlying cause of many familial cancer syndromes, such as Fanconi anemia, xeroderma pigmentosum, Nijmegen breakage syndrome and Lynch syndrome, to name a few.
When the level of DNA damage exceeds the capacity of the DNA repair machinery, apoptotic cell death ensues. Actively dividing cells have a very limited time available for DNA repair and are therefore particularly sensitive to DNA damaging agents. This is the main rationale for using DNA damaging chemotherapeutic drugs to kill rapidly replicating cancer cells.
There are seven main pathways employed in human DNA repair: DNA damage bypass, DNA damage reversal, base excision repair, nucleotide excision repair, mismatch repair, repair of double strand breaks and repair of interstrand crosslinks (Fanconi anemia pathway). DNA repair pathways are intimately associated with other cellular processes such as DNA replication, DNA recombination, cell cycle checkpoint arrest and apoptosis.
The DNA damage bypass pathway does not remove the damage, but instead allows translesion DNA synthesis (TLS) using a damaged template strand. Translesion synthesis allows cells to complete DNA replication, postponing the repair until cell division is finished. DNA polymerases that participate in translesion synthesis are error-prone, frequently introducing base substitutions and/or small insertions and deletions.
The DNA damage reversal pathway acts on a very narrow spectrum of damaging base modifications to remove modifying groups and restore DNA bases to their original state.
The base excision repair (BER) pathway involves a number of DNA glycosylases that cleave a vast array of damaged bases from the DNA sugar-phosphate backbone. DNA glycosylases produce a DNA strand with an abasic site. The abasic site is processed by DNA endonucleases, DNA polymerases and DNA ligases, the choice of which depends on the cell cycle stage, the identity of the participating DNA glycosylase and the presence of any additional damage. Base excision repair yields error-free DNA molecules.
Mismatch repair (MMR) proteins recognize mismatched base pairs or small insertion or deletion loops during DNA replication and correct erroneous base pairing by excising mismatched nucleotides exclusively from the nascent DNA strand, leaving the template strand intact.
Nucleotide excision repair pathway is involved in removal of bulky lesions that cause distortion of the DNA double helix. NER proteins excise the oligonucleotide that contains the lesion from the affected DNA strand, which is followed by gap-filling DNA synthesis and ligation of the repaired DNA molecule.
Double strand breaks (DSBs) in the DNA can be repaired via a highly accurate homologous recombination repair (HRR) pathway, or through error-prone nonhomologous end joining (NHEJ), single strand annealing (SSA) and microhomology-mediated end joining (MMEJ) pathways. DSBs can be directly generated by some DNA damaging agents, such as X-rays and reactive oxygen species (ROS). DSBs can also be intermediates of the Fanconi anemia pathway.
Interstrand crosslinking (ICL) agents damage the DNA by introducing covalent bonds between two DNA strands, which disables progression of the replication fork. The Fanconi anemia proteins repair the ICLs by unhooking them from one DNA strand. TLS enables the replication fork to bypass the unhooked ICL, resulting in two replicated DNA molecules, one of which contains a DSB and triggers double strand break repair, while the sister DNA molecule contains a bulky unhooked ICL, which is removed through NER.
Single strand breaks (SSBs) in the DNA, generated either by DNA damaging agents or as intermediates of DNA repair pathways such as BER, are converted into DSBs if the repair is not complete prior to DNA replication. Simultaneous inhibition of DSB repair and BER through cancer mutations and anti-cancer drugs, respectively, is synthetic lethal in at least some cancer settings, and is a promising new therapeutic strategy.
For reviews of DNA repair pathways, please refer to Lindahl and Wood 1999 and Curtin 2012.
R-HSA-69306 DNA Replication Studies in the past decade have suggested that the basic mechanism of DNA replication initiation is conserved in all kingdoms of life. Initiation in unicellular eukaryotes, in particular Saccharomyces cerevisiae (budding yeast), is well understood, and has served as a model for studies of DNA replication initiation in multicellular eukaryotes, including humans. In general terms, the first step of initiation is the binding of the replication initiator to the origin of replication. The replicative helicase is then assembled onto the origin, usually by a helicase assembly factor. Either shortly before or shortly after helicase assembly, some local unwinding of the origin of replication occurs in a region rich in adenine and thymine bases (often termed a DNA unwinding element, DUE). The unwound region provides the substrate for primer synthesis and initiation of DNA replication. The best-defined eukaryotic origins are those of S. cerevisiae, which have well-conserved sequence elements for initiator binding, DNA unwinding and binding of accessory proteins. In multicellular eukaryotes, unlike S. cerevisiae, these loci appear not to be defined by the presence of a DNA sequence motif. Indeed, choice of replication origins in a multicellular eukaryote may vary with developmental stage and tissue type. In cell-free models of metazoan DNA replication, such as the one provided by Xenopus egg extracts, there are only limited DNA sequence specificity requirements for replication initiation (Kelly & Brown 2000; Bell & Dutta 2002; Marahrens & Stillman 1992; Cimbora & Groudine 2001; Mahbubani et al 1992, Hyrien & Mechali 1993).
R-HSA-69002 DNA Replication Pre-Initiation Although, DNA replication occurs in the S phase of the cell cycle, the formation of the DNA replication pre-initiation complex begins during G1 phase.
R-HSA-5334118 DNA methylation Methylation of cytosine is catalyzed by a family of DNA methyltransferases (DNMTs): DNMT1, DNMT3A, and DNMT3B transfer methyl groups from S-adenosylmethionine to cytosine, producing 5-methylcytosine and homocysteine (reviewed in Klose and Bird 2006, Ooi et al. 2009, Jurkowska et al. 2011, Moore et al. 2013). (DNMT2 appears to methylate RNA rather than DNA.) DNMT1, the first enzyme discovered, preferentially methylates hemimethylated CG motifs that are produced by replication (template strand methylated, synthesized strand unmethylated). Thus it maintains existing methylation through cell division. DNMT3A and DNMT3B catalyze de novo methylation at unmethylated sites that include both CG dinucleotides and non-CG motifs.
DNA from adult humans contains about 0.76 to 1.00 mole percent 5-methylcytosine (Ehrlich et al. 1982, reviewed in Klose and Bird 2006, Ooi et al. 2009, Moore et al. 2013). Methylation of DNA occurs at cytosines that are mainly located in CG dinucleotides. CG dinucleotides are unevenly distributed in the genome. Promoter regions tend to have a high CG-content, forming so-called CG-islands (CGIs), while the CG-content in the remaining part of the genome is much lower. CGIs tend to be unmethylated, while the majority of CGs outside CGIs are methylated. Methylation in promoters and first exons tends to repress transcription while methylation in gene bodies (regions of genes downstream of the promoter and first exon) correlates with transcription (reviewed in Ehrlich and Lacey 2013, Kulis et al. 2013). Proteins such as MeCP2 and MBDs specifically bind 5-methylcytosine and may recruit other factors.
Mammalian development has two major episodes of genome-wide demethylation and remethylation (reviewed in Zhou 2012, Guibert and Weber 2013, Hackett and Surani 2013, Dean 2014). In mice about 1 day after fertilization the paternal genome is actively demethylated by TET proteins together with thymine DNA glycosylase and the maternal genome is demethylated by passive dilution during replication, however methylation at imprinted sites is maintained. The genome has its lowest methylation level about 3.5 days post-fertilization. Remethylation occurs by 6.5 days post-fertilization. The second demethylation-remethylation event occurs in primordial germ cells of the developing embryo about 12.5 days post-fertilization. DNMT3A and DNMT3B, together with the non-catalytic DNMT3L, play major roles in the remethylation events (reviewed in Chen and Chan 2014). How the methyltransferases are directed to particular regions of the genome remains an area of active research. The mechanisms at each locus may differ in detail but a connection between histone modifications and DNA methylation has been observed (reviewed in Rose and Klose 2014).
R-HSA-68952 DNA replication initiation DNA polymerases are not capable of de novo DNA synthesis and require synthesis of a primer, usually by a DNA-dependent RNA polymerase (primase) to begin DNA synthesis. In eukaryotic cells, the primer is synthesized by DNA polymerase alpha:primase. First, the DNA primase portion of this complex synthesizes approximately 6-10 nucleotides of RNA primer and then the DNA polymerase portion synthesizes an additional 20 nucleotides of DNA (Frick & Richardson 2002; Wang et al 1984).
R-HSA-69190 DNA strand elongation Accurate and efficient genome duplication requires coordinated processes to replicate two template strands at eucaryotic replication forks. Knowledge of the fundamental reactions involved in replication fork progression is derived largely from biochemical studies of the replication of simian virus and from yeast genetic studies. Since duplex DNA forms an anti-parallel structure, and DNA polymerases are unidirectional, one of the new strands is synthesized continuously in the direction of fork movement. This strand is designated as the leading strand. The other strand grows in the direction away from fork movement, and is called the lagging strand. Several specific interactions among the various proteins involved in DNA replication underlie the mechanism of DNA synthesis, on both the leading and lagging strands, at a DNA replication fork. These interactions allow the replication enzymes to cooperate in the replication process (Hurwitz et al 1990; Brush et al 1996; Ayyagari et al 1995; Budd & Campbell 1997; Bambara et al 1997).
R-HSA-376172 DSCAM interactions DSCAM (Down syndrome cell adhesion molecule) is one of the members of the Ig superfamily CAMs with a domain architecture comprising 10 Ig domains, 6 fibronectin type III (FN) repeats, a single transmembrane and a C terminal cytoplasmic domain. DSCAM is implicated in Down syndrome (DS) due to the chromosomal location of the DSCAM gene, but no evidence supports a direct involvement of DSCAM with DS. It likely functions as a cell surface receptor mediating axon pathfinding. Besides these important implications, little is known about the physiological function or the molecular mechanism of DSCAM signal transduction in mammalian systems. A closely related DSCAM paralogue Down syndrome cell adhesion moleculelike protein 1 (DSCAML1) is present in humans. Both these proteins are involved in homophilic intercellular interactions.
R-HSA-9669914 Dasatinib-resistant KIT mutants Dasatinib is a type II tyrosine kinase inhibitor that is active against KIT receptors with mutations in the juxtamembrane and activation loop domains, but shows only partial activity against KIT receptors with mutations at residue V654 (Schittenhelm et al, 2006; Serrano et al, 2019).
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex The mechanisms involved in downregulation of TCF-dependent transcription are not yet very well understood. beta-catenin is known to recruit a number of transcriptional repressors, including Reptin, SMRT and NCoR, to the TCF/LEF complex, allowing the transition from activation to repression (Bauer et al, 2000; Weiske et al, 2007; Song and Gelmann, 2008). CTNNBIP1 (also known as ICAT) and Chibby are inhibitors of TCF-dependent signaling that function by binding directly to beta-catenin and preventing interactions with critical components of the transactivation machinery (Takemaru et al, 2003; Li et al, 2008; Tago et al, 2000; Graham et al, 2002; Daniels and Weiss, 2002). Chibby additionally promotes the nuclear export of beta-catenin in conjunction with 14-3-3/YWHAZ proteins (Takemura et al, 2003; Li et al, 2008). A couple of recent studies have also suggested a role for nuclear APC in the disassembly of the beta-catenin activation complex (Hamada and Bienz, 2004; Sierra et al, 2006). It is worth noting that while some of the players involved in the disassembly of the beta-catenin transactivating complex are beginning to be worked out in vitro, the significance of their role in vivo is not yet fully understood, and some can be knocked out with little effect on endogenous WNT signaling (see for instance Voronina et al, 2009).
R-HSA-429947 Deadenylation of mRNA Deadenylation of mRNA proceeds in two steps. According to current models, in the first step the poly(A) tail is shortened from about 200 adenosine residues to about 80 residues by the PAN2-PAN3 complex. In the second step the poly(A) tail is further shortened to 10-15 residues by either the CCR4-NOT complex or by the PARN exoribonuclease. How a particular mRNA is targeted to CCR4-NOT or PARN is unknown.
A number of other deadenylase enzymes can be identified in genomic searches. One particularly interesting one is nocturin, a protein that is related to the CCR-1 deadenylase and plays a role in circadian rhythms.
There is also evidence for networking between deadenylation and other aspects of gene expression. CCR4-NOT, for example, is known to be a transcription factor. PARN is part of a complex that regulates poly(A) tail length and hence translation in developing oocytes.
R-HSA-429914 Deadenylation-dependent mRNA decay After undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by the PAN2-PAN3 complex that shortens the poly(A) tail from about 200 adenosine residues to about 80 residues and one catalyzed by the CCR4-NOT complex or by the PARN enzyme that shortens the tail to about 10-15 residues.
After deadenylation the mRNA is then hydrolyzed by either the 5' to 3' pathway or the 3' to 5' pathway. It is unknown what determinants target a mRNA to one pathway or the other.
The 5' to 3' pathway is initiated by binding of the Lsm1-7 complex to the 3' oligoadenylate tail followed by decapping by the DCP1-DCP2 complex. The 5' to 3' exoribonuclease XRN1 then hydrolyzes the remaining RNA.
The 3' to 5' pathway is initiated by the exosome complex at the 3' end of the mRNA. The exosome processively hydrolyzes the mRNA from 3' to 5', leaving only a capped oligoribonucleotide. The cap is then removed by the scavenging decapping enzyme DCPS.
R-HSA-73887 Death Receptor Signaling The death receptors (DR), all cell-surface receptors, that belong to the TNF receptor superfamily (TNFRSF). The term death receptor refers to those members of the TNFRSF that contain a "death domain" (DD) within their cytoplasmic tail which provides the capacity for protein–protein interactions with other DD-containing proteins suach as FADD. The main signals transmitted from TNF death receptors such as TNFR1, TRAIL-R, and CD95/FAS in response to their cognate ligand binding result in an apoptotic signaling pathway characterized by direct activation of intracellular cysteine proteases (caspases), without directly involving the mitochondrial death pathway. However, these death receptors have also been shown to initiate survival signals via the activation of transcription factors NFκappaB and AP1. This project describes an assembly of the death-inducing signaling complex (DISC) downstream of TNFR1, TRAIL-R, and CD95/FAS and shows protein composition and stoichiometry within the DISC. However, the DISC signaling complex may vary in its components stoichiometry. DR signaling may trigger formation of higher order receptor structures or signaling through rearrangement of receptor chains, which is not reflected here. The project also describes neuron-type-specific signaling by the p75NTR death receptor (also known as NGFR) that can regulate a number of different biological activities in response to ligand binding, including cell death and/or survival, axonal growth and synaptic plasticity.
R-HSA-5607761 Dectin-1 mediated noncanonical NF-kB signaling In addition to the activation of canonical NF-kB subunits, activation of SYK pathway by Dectin-1 leads to the induction of the non-canonical NF-kB pathway, which mediates the nuclear translocation of RELB-p52 dimers through the successive activation of NF-kB-inducing kinase (NIK) and IkB kinase-alpha (IKKa) (Geijtenbeek & Gringhuis 2009, Gringhuis et al. 2009). Noncanonical activity tends to build more slowly and remain sustained several hours longer than does the activation of canonical NF-kB. The noncanonical NF-kB pathway is characterized by the post-translational processing of NFKB2 (Nuclear factor NF-kappa-B) p100 subunit to the mature p52 subunit. This subsequently leads to nuclear translocation of p52:RELB (Transcription factor RelB) complexes to induce cytokine expression of some genes (C-C motif chemokine 17 (CCL17) and CCL22) and transcriptional repression of others (IL12B) (Gringhuis et al. 2009, Geijtenbeek & Gringhuis 2009, Plato et al. 2013).
R-HSA-5621480 Dectin-2 family Dendritic cell-associated C-type lectin-2 (Dectin-2) family of C-type lectin receptors (CLRs) includes Dectin-2 (CLEC6A), blood dendritic antigen 2 (BDCA2/CLEC4C), macrophage C-type lectin (MCL/CLEC4D), Dendritic cell immunoreceptor (DCIR/CLEC4A) and macrophage inducible C-type lectin (Mincle/CLEC4E). These receptors possesses a single extracellular conserved C-type lectin domain (CTLD) with a short cytoplasmic tail that induces intracellular signalling indirectly by binding with the FCERG (High affinity immunoglobulin epsilon receptor subunit gamma) except for DCIR that has a longer cytoplasmic tail with an integral inhibitory signalling motif (Graham & Brown. 2009, Kerschera et al. 2013). CLEC6A (Dectin-2) binds to high mannose containing pathogen-associated molecular patterns (PAMPs) expressed by fungal hyphae, and CLEC4E (mincle) binds to alpha-mannaosyl PAMPs on fungal, mycobacterial and necrotic cell ligands. Both signaling pathways lead to Toll-like receptor (TLR)-independent production of cytokines such as tumor necrosis factor (TNF) and interleukin 6 (IL6). Similarities with Dectin-1 (CLC7A) signaling pathway suggests that both these CLRs couple SYK activation to NF-kB activation using a complex involving CARD9, BCL10 and MALT1 (Geijtenbeek & Gringhuis 2009).
R-HSA-5682113 Defective ABCA1 causes TGD In an ATP-dependent reaction, ATP-binding cassette sub-family A member 1 (ABCA1) mediates the movement of intracellular cholesterol to the extracellular face of the plasma membrane. Cholesterol associated with cytosolic vesicles is a substrate for this reaction. Under physiologocal conditions, the active form of ABCA1 is post-translationally modified (palmitoylated and phosphorylated), predominantly a tetramer and is associated with apolipoprotein A-I (APOA1). Defects in ABCA1 can cause Tangier disease (TGD; MIM:205400 aka high density lipoprotein deficiency type 1), an autosomal recessive disorder characterised by significantly reduced levels of plasma high density lipoproteins (HDL) resulting in tissue accumulation of cholesterol esters (Brooks-Wilson et al. 1999). Low HDL levels are among the most common biochemical abnormalities observed in coronary heart disease (CHD) patients (Kolovou et al. 2006, Iatan et al. 2008, Iatan et al. 2012).
R-HSA-5682294 Defective ABCA12 causes ARCI4B ATP-binding cassette sub-family A member 12 (ABCA12) is thought to function as an epidermal keratinocyte lipid transporter. These lipids form extracellular lipid layers in the stratum corneum of the epidermis, essential for skin barrier function. Defects in ABCA12 results in the loss of the skin lipid barrier, leading to autosomal recessive congenital ichthyosis 4B (ARCI4B; MIM:242500, aka harlequin ichthyosis, HI). ARCI4B shows the most severe phenotype of the congenital ichthyoses, with newborns having a thick covering of armour-like scales. The skin dries out to form hard diamond-shaped plaques separated by fissures. Affected babies are often born prematurely and rarely survive the perinatal period (Akiyama et al. 2005, Akiyama 2010, 2014).
R-HSA-5688399 Defective ABCA3 causes SMDP3 ATP-binding cassette sub-family A member 3 (ABCA3) plays an important role in the formation of pulmonary surfactant, probably by transporting phospholipids such as phosphatidylcholine (PC) and phosphatidylglycerol (PG) from the ER membrane to lamellar bodies (LBs). PC and PG are the major phospholipid constituents of pulmonary surfactant. LBs are the surfactant storage organelles of type II epithelial cells from where phospholipids can be secreted together with surfactant proteins (SFTPs) into the alveolar airspace. Defects in ABCA3 can cause pulmonary surfactant metabolism dysfunction type 3 (SMDP3; MIM:610921), resulting in respiratory distress in newborns and interstitial lung disease (ILD) in children (Whitsett et al. 2015).
R-HSA-5683678 Defective ABCA3 causes SMDP3 ATP-binding cassette sub-family A member 3 (ABCA3) is thought to play a role in the formation of pulmonary surfactant by transporting lipids such as cholesterol into lamellar bodies (LBs) in alveolar type II cells. In LBs, surfactant proteins and lipids are assembled into bilayer membranes that are secreted into the alveolar airspace, where they form a surface film at the air–liquid interface. Defects in ABCA3 can cause pulmonary surfactant metabolism dysfunction 3 (SMDP3), a usually fatal pulmonary disease in newborns, characterised by the absence of normal LBs and the presence of electron-dense inclusions within small vesicular structures. Loss of secretion of lipid pulmonary surfactants causes excessive lipoprotein accumulation in the alveoli resulting in severe respiratory distress (Shulenin et al. 2004, Quazi & Molday 2011, Tarling et al. 2014, Whitsett et al. 2015).
R-HSA-5678520 Defective ABCB11 causes PFIC2 and BRIC2 The bile salt export pump ABCB11 mediates the release of bile salts from liver cells into bile. Defects in ABCB11 can cause two clinically distinct forms of cholestasis; progressive familial intrahepatic cholestasis 2 (PFIC2; MIM:601847) and benign recurrent intrahepatic cholestasis 2 (BRIC2; MIM:605479). Cholestasis is characterized by the retention of bile acids or salts. Bile acids can damage hepatocytes and bile duct cells leading to inflammation, fibrosis, cirrhosis and eventually carcinogenesis. PFIC2 patients suffer from chronic cholestasis and develop liver fibrosis, cirrhosis and end-stage liver disease before adulthood. BRIC2 patients experience intermittent episodes of cholestasis that resolve spontaneously after weeks or months (Strubbe et al. 2012, Cuperus et al. 2014).
R-HSA-5678771 Defective ABCB4 causes PFIC3, ICP3 and GBD1 Multidrug resistance protein 3 (ATP-binding cassette sub-family B member 4, ABCB4 aka MDR3) mediates the ATP-dependent export of organic anions, phospholipids and drugs from hepatocytes into the canalicular lumen in the presence of bile salts, especially the export of phospholipids such as phosphatidylcholine (PC). Biliary phospholipids associate with bile salts and cholesterol in mixed micelles, thereby reducing the detergent activity and cytotoxicity of bile salts and preventing cholesterol crystallisation. Thus, ABCB4 plays a crucial role in bile formation and lipid homeostasis. Defects in ABCB4 result in a wide spectrum of cholestasis phenotypes, from progressive familial intrahepatic cholestasis 3 (PFIC3; MIM:602347) and intrahepatic cholestasis of pregnancy 3 (ICP3; MIM:614972) to gallbladder disease 1 (GBD1; MIM:600803) (Jacquemin et al. 2001, Davit-Spraul et al. 2010, Jacquemin 2012). In PFIC3, the biliary phospholipid level is substantially decreased despite the presence of bile acids. Cholestasis may be caused by the toxicity of detergent bile salts that are not associated with phospholipids, leading to bile canaliculus and biliary epithelium damage. ICP3 is a reversible form of cholestasis in the third trimester of pregnancy and quickly disappears after childbearing. GBD1 is one of the major digestive diseases. Gallstones composed of cholesterol (cholelithiasis) are the common manifestations of GBD1 in western countries. Most people with gallstones remain asymptomatic throughout their lifetimes but approximately 10-50% of individuals eventually develop symptoms.
R-HSA-5683371 Defective ABCB6 causes MCOPCB7 ATP-binding cassette sub-family B member 6 (ABCB6), uniquely located on the outer mitochondrial membrane in homodimeric form, plays a crucial role in haem synthesis by mediating porphyrin uptake into the mitochondria. Defects in ABCB6 can cause isolated colobomatous microphthalmia 7 (MCOPCB7; MIM:614497), a developmental defect of the eye resulting from abnormal or incomplete fusion of the optic fissure with associated microphthalmia (eyeballs are abnormally small). Coloboma is thought to play an important role in the early development of the CNS, including that of the eye (Wang et al. 2012).
R-HSA-5679001 Defective ABCC2 causes DJS Canalicular multispecific organic anion transporter 1 (ABCC2 aka multidrug resistance-associated protein 2, MRP2), in addition to transporting many organic anions, mediates the ATP-dependent transport of glutathione and glucuronate conjugates from hepatocytes into bile. ABCC2 transports with high affinity and efficiency mono- and di-glucuronated bilirubin into bile. Bilirubin, the end product of heme breakdown, is an important constituent of bile and is responsible for its characteristic colour. Defects in ABCC2 can cause Dubin-Johnson syndrome (DJS; MIM:237500), an autosomal recessive disorder characterised by conjugated hyperbilirubinemia (Dubin & Johnson 1954, Keppler 2014, Erlinger et al. 2014).
R-HSA-5690338 Defective ABCC6 causes PXE The multidrug resistance associated protein (MRPs) subfamily of the ABC transporter family can transport a wide and diverse range of organic anions that can be endogenous compounds and xenobiotics and their metabolites. The multidrug resistance-associated protein 6 (ABCC6 aka MOAT-E) can actively transport organic anions. Defects in ABCC6 can cause pseudoxanthoma elasticum (PXE; MIM:264800), a rare multisystem disorder characterized by accumulation of mineralized and fragmented elastic fibers in the skin, vasculature and the Burch membrane of the eye (Finger et al. 2009).
R-HSA-5683177 Defective ABCC8 can cause hypo- and hyper-glycemias ATP-binding cassette sub-family C member 8 (ABCC8) is a subunit of the beta-cell ATP-sensitive potassium channel (KATP). KATP channels play an important role in the control of insulin release. Elevation of the ATP:ADP ratio closes KATP channels leading to cellular depolarisation, calcium influx and exocytosis of insulin from its storage granules. Defects in ABCC8 can cause dysregulation of insulin secretion resulting in hyperglycemias or hypoglycemias. Specific phenotypes observed are noninsulin-dependent diabetes mellitus (NIDDM; MIM:125853), permanent neonatal diabetes mellitus (PNDM; MIM:606176), transient neonatal diabetes mellitus 2 (TNDM2; MIM:610374), familial hyperinsulinemic hypoglycemia 1 (HHF1; MIM:256450) and leucine-induced hypoglycemia (LIH; MIM:240800) (Edghill et al. 2010, Flanagan et al. 2009, Yorifuji 2014, Yang et al. 2010, Chandran et al. 2014).
R-HSA-5678420 Defective ABCC9 causes CMD10, ATFB12 and Cantu syndrome ATP-binding cassette sub-family C member 9 (ABCC9) forms cardiac and smooth muscle-type KATP channels with ATP-sensitive inward rectifier potassium channel 11 (KCNJ11). KCNJ11 forms the channel pore while ABCC9 is required for activation and regulation (Babenko et al. 1998, Tammaro & Ashcroft 2007). Inward rectifier potassium channels favor the flow of potassium into the cell rather than out of it. KATP channels open and close in response to intracellular changes in the ADP/ATP ratio, thereby linking the metabolic state of the cell to its membrane potential. Inhibition of KATP channel activity causes membrane depolarization and thereby activation of voltage-dependent Ca2+ channels, leading to Ca2+ influx and a rise in intracellular Ca2+ concentration. Correct maintenance of calcium balance is essential for the normal functioning of the heart.
Defects in ABCC9 can cause dilated cardiomyopathy 10 (CMD10: MIM:608569), a disorder characterised by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia (Bienengraeber et al. 2004). Defects in ABCC9 can also cause familial atrial fibrillation 12 (ATFB12; MIM:614050), characterised by disorganized atrial electrical activity and ineffective atrial contraction resulting in blood stasis in the atria and reduces ventricular filling. It can result in palpitations, syncope, thromboembolic stroke, and congestive heart failure (Olson et al. 2007). Defects in ABCC9 can also cause hypertrichotic osteochondrodysplasia (Cantu syndrome; MIM:239850), a rare disorder characterised by congenital hypertrichosis, neonatal macrosomia, a distinct osteochondrodysplasia and cardiomegaly (van Bon et al. 2012, Harakalova et al. 2012).
R-HSA-5684045 Defective ABCD1 causes ALD The 70-kDa peroxisomal membrane protein (PMP70) and the adrenoleukodystrophy protein (ALDP aka ABCD1) are half ATP binding cassette (ABC) transporters in the peroxisome membrane. They are involved in metabolic transport of long and very long chain fatty acids into peroxisomes. Mutations in the ALD gene result in the X-linked neurodegenerative disorder adrenoleukodystrophy (ALD; MIM:300100). ABCD1 deficiency impairs the peroxisomal beta-oxidation of very long-chain fatty acids (VLCFA) and facilitates their further chain elongation by ELOVL1 resulting in accumulation of VLCFA in plasma and tissues. While all patients with ALD have mutations in the ABCD1 gene, there is no general genotype-phenotype correlation. In addition to ABCD1, other genes and environmental factors determine clinical features of ALD (Kemp et al. 2012, Berger et al. 2014).
R-HSA-5683329 Defective ABCD4 causes MAHCJ ATP-binding cassette sub-family D member 4 (ABCD4) is thought to mediate the lysosomal export of cobalamin (Cbl aka vitamin B12) into the cytosol, making it available for the production of Cbl cofactors. Cbl is an important cofactor for correct haematological and neurological functions. Defects in ABCD4 can cause methylmalonic aciduria and homocystinuria, cblJ type (MAHCJ; MIM:614857), a genetically heterogeneous metabolic disorder of Cbl metabolism characterised by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl). Clinically, symptoms include feeding difficulties, poor growth, hypotonia, lethargy, anaemia and delayed development (Coelho et al. 2012).
R-HSA-5679096 Defective ABCG5 causes sitosterolemia ATP-binding cassette sub-family G member 5 (ABCG5 aka sterolin-1), is a "half transporter", that forms a complex with another half transporter ABCG8 (aka sterolin-2) in the endoplasmic reticulum. This complex translocates to the plasma membrane to mediate the ATP-dependent intestinal absorption and facilitation of biliary secretion of cholesterol and phytosterols (e.g. sitosterol). Defects in either of these half transporters result in loss of enterocyte discrimination between cholesterol and sitosterol causing sterol accumulation and predisposition for atherosclerosis. Defects in ABCG5 are the cause of sitosterolemia (MIM:210250), characterised by unrestricted intestinal absorption of both cholesterol and plant-derived sterols causing hypercholesterolemia and premature coronary atherosclerosis. Patients with sitosterolemia absorb between 15 and 60% of ingested sitosterol and excrete only a fraction of this into the bile (Berge et al. 2000, Othman et al. 2013, Yu et al. 2014).
R-HSA-5679090 Defective ABCG8 causes GBD4 and sitosterolemia ATP-binding cassette sub-family G member 8 (ABCG8 aka sterolin-2), is a "half transporter", that forms a complex with another half transporter ABCG5 in the endoplasmic reticulum. This complex translocates to the plasma membrane to mediate the ATP-dependent intestinal absorption and facilitation of biliary secretion of cholesterol and phytosterols (eg sitosterol). Defects in either of these half transporters result in loss of enterocyte discrimination between cholesterol and sitosterol causing sterol accumulation and predisposition for atherosclerosis. Defects in ABCG8 are the cause of gallbladder disease 4 (GBD4; MIM:611465), one of the major digestive diseases. Gallstones are composed of cholesterol (cholelithiasis) and are the common manifestations of GBD in western countries (Buch et al. 2007, Rudkowska & Jones 2008, Jakulj et al. 2010). Defects in ABCG8 also cause sitosterolemia (MIM:210250), characterised by unrestricted intestinal absorption of both cholesterol and plant-derived sterols causing hypercholesterolemia and premature coronary atherosclerosis. Patients with sitosterolemia absorb between 15 and 60% of ingested sitosterol, and they excrete only a fraction into the bile (Berge et al. 2000, Othman et al. 2013, Yu et al. 2014).
R-HSA-5579031 Defective ACTH causes obesity and POMCD The precursor peptide pro-opiomelanocortin (POMC) gives rise to many peptide hormones through cleavage. The cleavage products corticotropin (ACTH) and beta-lipotropin give rise to smaller peptides that have distinct biologic activities: alpha-melanotropin and corticotropin-like intermediate lobe peptide (CLIP) are formed from ACTH; gamma-LPH and beta-endorphin are formed from beta-LPH. ACTH (POMC(138-176) stimulates the adrenal glands to release cortisol, a glucocorticoid released in response to stress whose primary functions are to stimulate gluconeogenesis, suppress the immune system and aid metabolism of fats, proteins and carbohydrates.
Defects in ACTH can cause obesity (MIM:601665) resulting in excessive accumulation of body fat (Challis et al. 2002, Millington 2013). Defects in ACTH can also cause pro-opiomelanocortinin deficiency (POMCD; MIM:609734) where affected individuals present early-onset obesity, adrenal insufficiency and red hair (Krude et al. 1998, Krude et al. 2003).
R-HSA-5579007 Defective ACY1 causes encephalopathy Aminoacylase 1 (ACY1) is a cytosolic, homodimeric zinc-binding metalloenzyme with a wide range of tissue expression. It hydrolyses acylated L-amino acids (except L-aspartate) into L-amino acids and an acyl group. It can also hydrolyse N-acetylcysteine-S-conjugates. Defects in ACY1 can cause aminoacylase-1 deficiency (ACY1D; MIM:609924) resulting in encephalopathy, delay in psychomotor development, seizures and increased urinary excretion of several N-acetylated amino acids (Sass et al. 2006, Sass et al. 2007).
R-HSA-9734735 Defective ADA disrupts (deoxy)adenosine deamination Normally in humans, adenosine and deoxyadenosine can be deaminated to inosine and deoxyinosine, catalyzed by ADA (adenosine deaminase). In the absence of ADA activity, however, accumulated nucleosides disrupt lymphoid cell function, leading to severe combined immunodeficiency (Hirschhorn et al. 1989, 1990).
R-HSA-5578997 Defective AHCY causes HMAHCHD Adenosylhomocysteinase (AHCY) is a tetrameric, NAD+-bound, cytosolic protein that regulates all adenosylmethionine (AdoMet) dependent transmethylations by hydrolysing the feedback inhibitor adenosylhomocysteine (AdoHcy) to homocysteine (HCYS) and adenosine (Ade-Rib). Defects in AHCY cause Hypermethioninemia with S-adenosylhomocysteine hydrolase deficiency (HMAHCHD; MIM:613752), a metabolic disorder characterised by hypermethioninemia associated with failure to thrive, psychomotor retardation, facial dysmorphism with abnormal hair and teeth and myocardiopathy (Baric et al. 2004).
R-HSA-4549380 Defective ALG1 causes CDG-1k Chitobiosyldiphosphodolichol beta-mannosyltransferase (ALG1) normally tranfers a mannose moiety to the lipid-linked oligosaccharide (LLO aka N-glycan precursor) which is required for subsequent N-glycosylation of proteins. Defects in ALG1 can cause congenital disorder of glycosylation 1k (ALG1-CDG, previously known as CDG1k; MIM:608540), a multisystem disorder characterised by under-glycosylated serum glycoproteins. CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. Compared to other CDGs, ALG1-CDG has a very severe phenotype, which can result in an early death (Schwarz et al. 2004, Kranz et al. 2004, Dupre et al. 2010).
R-HSA-4551295 Defective ALG11 causes CDG-1p GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase (ALG11) transfers the fourth and fifth mannoses (Man) to the N-glycan precursor in an alpha-1,2 orientation. These additions are the last two on the cytosolic side of the ER membrane before the N-glycan is flipped to the luminal side of the membrane. Recently discovered defects in ALG11 have been linked to congential disorder of glycosylation, type 1p (ALG11-CDG, CGD1p) (Rind et al. 2010, Thiel et al. 2012). The disease is a multi-system disorder characterised by under-glycosylated serum glycoproteins. Early-onset developmental retardation, dysmorphic features, hypotonia, coagulation disorders and immunodeficiency are reported features of this disorder (Rind et al. 2010, Thiel et al. 2012).
R-HSA-4720489 Defective ALG12 causes CDG-1g Dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase (ALG12) (Chantret et al. 2002) normally tranfers the 8th mannose moiety to the lipid-linked oligosaccharide (LLO aka N-glycan precursor) which is required for subsequent N-glycosylation of proteins. Defects in ALG12 are associated with congenital disorder of glycosylation 1g (ALG12-CDG, CDG1g; MIM:607143), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins (Chantret et al. 2002, Grubenmann et al. 2002). CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency.
R-HSA-5633231 Defective ALG14 causes ALG14-CMS UDP-N-acetylglucosamine transferase subunit ALG14 homolog (ALG14) forms a complex with ALG13 protein and is required for the addition of the second N-acetylglucosamine (GlcNAc) to the lipid linked oligosaccharide (LLO) intermediate (GlcNAcDOLDP) (Gao et al. 2005). Defects in ALG14 can cause congenital myasthenic syndrome (ALG14-CMS), which is due to a defect in neuromuscular signal transmission (Cossins et al. 2013). The most commonly affected muscles include proximal limb muscles. Mutations causing ALG14-CMS include p.P65L and p.R104* (Cossins et al. 2013).
R-HSA-4549349 Defective ALG2 causes CDG-1i Alpha 1,3/1,6 mannosyltransferase ALG2 (ALG2) is a bifunctional mannosyltransferase normally tranfers a mannose moiety to the lipid linked oligosaccharide (LLO aka N glycan precursor) which is required for subsequent N glycosylation of proteins. Defects in ALG2 can cause congenital disorder of glycosylation 1i (ALG2-CDG, previously known as CDG1i; MIM:607906), a multisystem disorder characterised by under glycosylated serum glycoproteins. CDG type 1 diseases result in a wide phenotypic spectrum, from poor neurological development, psychomotor retardation and dysmorphic features to hypotonia, coagulation abnormalities and immunodeficiency (Thiel et al. 2003). Defect in ALG2 can also cause congenital myasthenic syndrome (ALG2-CMS), which is due to a defect in neuromuscular signal transmission (Cossins et al. 2013). The most commonly affected muscles include proximal limb muscles. Mutations causing ALG2-CMS include p.V68G and p.72_75delinsSPR (Cossins et al. 2013).
R-HSA-4720475 Defective ALG3 causes CDG-1d Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase (ALG3) adds the sixth mannose (although the first to be derived from dolichyl-phosphate-mannose, DOLPman) to the lipid-linked oligosaccharide (LLO) intermediate GlcNAc(2) Man(5) (PPDol)1 (Korner et al. 1999). Defects in ALG3 are associated with congenital disorder of glycosylation 1d (ALG3-CDG, CDG1d; MIM:601110), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins. CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency (Sun et al. 2005).
R-HSA-4724289 Defective ALG6 causes CDG-1c Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase (ALG6) normally adds the first glucose moiety to the lipid-linked oligosaccharide precursor (LLO aka N-glycan precursor) which is required for subsequent N-glycosylation of proteins (Imbach et al. 1999). Defects in ALG6 can cause congenital disorder of glycosylation 1c (ALG6-CDG, CDG-1c; MIM:603147), a multisystem disorder characterised by under-glycosylated serum glycoproteins (Imbach et al. 1999, Imbach et al. 2000, Westphal et al. 2000, Sun et al. 2005). ALG6 deficiency is accompanied by an accumulation of the N-glycan precursor (GlcNAc)2 (Man)9 (PP-Dol)1 and is the second most common CDG disease subtype after PMM2-CDG (CDG-1a) (Imbach et al. 1999). CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency.
R-HSA-4724325 Defective ALG8 causes CDG-1h The probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase (ALG8) (Stanchi et al. 2001, Chantret et al. 2003) normally adds the second glucose moiety to the lipid-linked oligosaccharide precursor (LLO aka N-glycan precursor) which is required for subsequent N-glycosylation of proteins. Defects in ALG8 can cause congenital disorder of glycosylation 1h (ALG8-CDG, CDG-1h; MIM:608104), a multisystem disorder characterised by under-glycosylated serum glycoproteins (Chantret et al. 2003, Schollen et al. 2004). ALG8 deficiency is accompanied by an accumulation of the N-glycan precursor (Glc)1 (GlcNAc)2 (Man)9 (PP-Dol)1. CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency.
R-HSA-4720454 Defective ALG9 causes CDG-1l Alpha-1,2-mannosyltransferase ALG9 (ALG9) normally catalyses the transfer of mannose to the lipid-linked oligosaccharide (LLO) precursor. It adds the 7th and 9th mannose moieties to LLO. Defects in ALG9 are associated with congenital disorder of glycosylation 1l (ALG9-CDG, CDG1l; MIM:608776), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins. CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency (Frank et al. 2004, Weinstein et al. 2005). The LLO profile showed accumulation of (GlcNAc)2 (Man)6 (PP-Dol)1 and (GlcNAc)2 (Man)8 (PP-Dol)1 fragments, suggesting a defect in ALG9 and correlating with the normal function of ALG9 in adding the 7th and 9th mannose moieties (Frank et al. 2004).
R-HSA-3359462 Defective AMN causes MGA1 Defects in AMN cause recessive hereditary megaloblastic anemia 1 (RH-MGA1 aka MGA1 Norwegian type or Imerslund-Grasbeck syndrome, I-GS; MIM:261100). The Norwegian cases described by Imerslund were due to defects in AMN (Imerslund 1960). The resultant malabsorption of Cbl (vitamin B12) leads to impaired B12-dependent folate metabolism and ultimately impaired thymine synthesis and DNA replication.
R-HSA-9734195 Defective APRT disrupts adenine salvage Normally in humans, adenine formed in processes such as polyamine biosynthesis can be salvaged by conversion to AMP, catalyzed by APRT (adenine phosphoribosyltransferase). In the absence of APRT activity, however, accumulated adenine is instead converted to 2,8-dioxo-adenine. Accumulation of insoluble crystals of 2,8-dioxo-adenine in the kidneys causes the kidney damage that is a major symptom of APRT deficiency in humans (Van Acker et al. 1977; Bollée et al. 2012).
R-HSA-5619099 Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) Arginine vasopressin (AVP(20-28)) is a 9 amino-acid long signal peptide produced by cleavage of the precursor protein AVP in the hypothalamus. It mediates the reabsorption of water in the kidney and its synthesis and release are physiologically regulated by plasma osmolarity, blood pressure and/or blood volume. AVP(20-28) binds to vasopressin receptors AVPR1 and 2, located on the basolateral surface of the kidney collecting duct. This binding results in interaction of AVPRs with the G protein alpha-s. Following a cascade of downstream events, ultimately the water channel aquaporin 2 (AQP2) translocates from intracellular stores to the apical surface where it functions as the entry site for water reabsorption. When water balance is achieved, plasma levels of AVP(20-28) drop and AQP2 levels in the apical plasma membrane are decreased.
Mutations in AVP make it unavailable to its AVPRs in the kidney, resulting in dysregulation of water reabsorption. This can cause familial neurohypophyseal diabetes insipidus (FNDI), an autosomal dominant disorder characterised by persistent excessive thirst resulting in constant drinking (polydipsia) and passage of large volumes of urine (polyuria). In FNDI, the production and release of AVP from the posterior pituitary gland is impaired (Moeller et al. 2013).
R-HSA-9036092 Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) Arginine vasopressin (AVP(20-28)) is a 9 amino-acid long signal peptide produced by cleavage of the precursor protein AVP in the hypothalamus. It mediates the reabsorption of water in the kidney and its synthesis and release are physiologically regulated by plasma osmolarity, blood pressure and/or blood volume. AVP(20-28) binds to vasopressin receptors AVPR1 and 2, located on the basolateral surface of the kidney collecting duct. This binding results in interaction of AVPRs with the G protein alpha-s. Following a cascade of downstream events, ultimately the water channel aquaporin 2 (AQP2) translocates from intracellular stores to the apical surface where it functions as the entry site for water reabsorption. When water balance is achieved, plasma levels of AVP(20-28) drop and AQP2 levels in the apical plasma membrane are decreased.
Mutations in AVP make it unavailable to its AVPRs in the kidney, resulting in dysregulation of water reabsorption. This can cause familial neurohypophyseal diabetes insipidus (FNDI), an autosomal dominant disorder characterised by persistent excessive thirst resulting in constant drinking (polydipsia) and passage of large volumes of urine (polyuria). In FNDI, the production and release of AVP from the posterior pituitary gland is impaired (Moeller et al. 2013).
R-HSA-4420332 Defective B3GALT6 causes EDSP2 and SEMDJL1 The biosynthesis of dermatan sulfate/chondroitin sulfate and heparin/heparan sulfate glycosaminoglycans (GAGs) starts with the formation of a tetrasaccharide linker sequence attached to the core protein. Beta-1,3-galactosyltransferase 6 (B3GALT6) is one of the critical enzymes involved in the formation of this linker sequence. Defects in B3GALT6 causes Ehlers-Danlos syndrome progeroid type 2 (EDSP2; MIM:615349), a severe disorder resulting in a broad spectrum of skeletal, connective tissue and wound healing problems. Defects in B3GALT6 can also cause spondyloepimetaphyseal dysplasia with joint laxity type 1 (SEMDJL1; MIM:271640), characterised by spinal deformaty and lax joints, especially of the hands and respiratory compromise resulting in early death (Nakajima et al. 2013, Malfait et al. 2013).
R-HSA-5083635 Defective B3GALTL causes PpS Human beta-1,3-glucosyltransferase like protein (B3GALTL, HGNC Approved Gene Symbol: B3GLCT; MIM:610308; CAZy family GT31), localised on the ER membrane, glucosylates O-fucosylated proteins. The resultant glc-beta-1,3-fuc disaccharide modification on thrombospondin type 1 repeat (TSR1) domain-containing proteins is thought to assist in the secretion of many of these proteins from the ER lumen, and mediate an ER quality-control mechanism of folded TSRs (Vasudevan et al. 2015). Defects in B3GALTL can cause Peters plus syndrome (PpS; MIM:261540), an autosomal recessive disorder characterised by anterior eye chamber defects, short stature, delay in growth and mental developmental and cleft lip and/or palate (Heinonen & Maki 2009).
R-HSA-3560801 Defective B3GAT3 causes JDSSDHD Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferases1, 2 and 3 (B3GAT1-3) are involved in forming the linker tetrasaccharide present in heparan sulfate and chondroitin sulfate. Defects in B3GAT3 cause multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defects (JDSSDHD; MIM:245600). This is an autosomal recessive disease characterized by dysmorphic facies, elbow, hip and knee dislocations, clubfeet, short stature and cardiovascular defects (Steel & Kohl 1972, Bonaventure et al. 1992, Baasanjav et al. 2011). JDSSDHD has phenotypic similarities to Larsen syndrome (Larsen et al. 1950).
R-HSA-3656244 Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) Congenital disorders of glycosylation (CDG, previously called carbohydrate-deficient glycoprotein syndromes, CDGSs), are a group of hereditary multisystem disorders. They are characterized biochemically by hypoglycosylation of glycoproteins, diagnosed by isoelectric focusing (IEF) of serum transferrin. There are two types of CDG, types I and II. Type I CDG has defects in the assembly of lipid-linked oligosaccharides or their transfer onto nascent glycoproteins, whereas type II CDG comprises defects of trimming, elongation, and processing of protein-bound glycans. Clinical symptoms are dominated by severe psychomotor and mental retardation, as well as blood coagulation abnormalities (Jaeken 2013). B4GALT1-CDG (CDG type IId) is a multisystem disease, characterized by dysmorphic features, hydrocephalus, hypotonia and blood clotting abnormalities (Hansske et al. 2002).
R-HSA-4793953 Defective B4GALT1 causes CDG-2d Congenital disorders of glycosylation (CDG, previously called carbohydrate-deficient glycoprotein syndromes, CDGSs), are a group of hereditary multisystem disorders. They are characterized biochemically by hypoglycosylation of glycoproteins, diagnosed by isoelectric focusing (IEF) of serum transferrin. There are two types of CDG, types I and II. Type I CDG has defects in the assembly of lipid-linked oligosaccharides or their transfer onto nascent glycoproteins, whereas type II CDG comprises defects of trimming, elongation, and processing of protein-bound glycans. Clinical symptoms are dominated by severe psychomotor and mental retardation, as well as blood coagulation abnormalities (Jaeken 2013). B4GALT1-CDG (CDG type IId) is a multisystem disease, characterized by dysmorphic features, hydrocephalus, hypotonia and blood clotting abnormalities (Hansske et al. 2002).
R-HSA-3560783 Defective B4GALT7 causes EDS, progeroid type Ehlers–Danlos syndrome (EDS) is a group of inherited connective tissue disorders, caused by a defect in the synthesis of collagen types I or III. Abnormal collagen renders connective tissues more elastic. The severity of the mutation can vary from mild to life-threatening. There is no cure and treatment is supportive, including close monitoring of the digestive, excretory and particularly the cardiovascular systems. Defective B4GALT7, a galactosyltransferase important in proteoglycan synthesis, causes the progeroid variant of EDS (MIM:130070). Features include an aged appearance, developmental delay, short stature, generalized osteopenia, defective wound healing, hypermobile joints, hypotonic muscles, and loose but elastic skin (Okajima et al. 1999).
R-HSA-3371598 Defective BTD causes biotidinase deficiency BTD deficiency is an autosomal recessive disorder in which the body is unable to recycle and reuse biotin (Btn). This results in a secondary Btn deficiency that leads to juvenile-onset multiple carboxylase deficiency (MIM:253260) (Wolf 2012, Wolf et al. 1983). Patients present with neurological and cutaneous symptoms, including seizures, hypotonia, skin rash, and alopecia, usually between the second and fifth months of life (Wolf 2010). Children with profound BTD deficiency are treated with pharmacological doses of biotin (5-20 mg daily). Neonatal screening for BTD deficiency is performed in most states of the United States and many other countries.
R-HSA-9605310 Defective Base Excision Repair Associated with MUTYH MUTYH gene is located on chromosome 1 and encodes a DNA glycosylase involved in base excision repair (BER). MUTYH (MYH) functions as an adenine DNA glycosylase and removes adenines and 2-hydroxyadenines on the newly synthesized DNA strand mispaired with guanines or 8-oxoguanines. 8-oxogunanines are produced by oxidation of guanines in DNA or by incorporation of 8-oxodGTP from the nucleotide pool into the newly synthesized DNA strand. Germline mutations in MUTYH cause the MUTYH-associated polyposis (MAP), a syndrome that resembles the familial adenomatous polyposis (FAP) syndrome, caused by mutations in the APC tumor suppressor gene. MAP is also known as the familial adenomatous polyposis 2 (FAP2) (OMIM:608456). MAP-affected individuals are predisposed to development of multiple colorectal adenomas and colorectal cancer. MAP is largely inherited in an autosomally recessive manner, with both MUTYH alleles affected. The predisposition of heterozygous MUTYH mutation carriers to MAP has not been completely ruled out (Fleischmann et al. 2004).
MUTYH is most frequently affected by missense mutations in MAP patients, with two major mutations, Y165C and G382D, reported in about 80% of MAP patients of European origin. In Japanese patients, the most frequently reported mutation was Q324H (Yanaru-Fujisawa et al. 2008). Residues Y165C and G382D in the abundant MUTYH isoform MUTYH alpha-3 (MUTYH-3), used in the majority of functional studies, correspond to Y176C and G393D, respectively, in the canonical UniProt isoform (MUTYH alpha-1) and to Y179C and G396, respectively, in the longest NCBI isoform, which is used as a reference isoform in the database InSiGHT (International Society for Gastrointestinal Hereditary Tumours Database). However, both the canonical UniProt and NCBI MUTYH isoforms are expressed at very low levels or not at all (Plotz et al. 2012). In addition to the isoform MUTYH alpha-3, the other two abundant MUTYH isoforms are MUTYH beta-3 and MUTYH gamma-3 (Plotz et al. 2012), which differ from MUTYH alpha-3 in the first exon used. Exons 1-alpha and 1-beta contain sequences that resemble a mitochondrial targeting signal (MTS). It was reported that MUTYH alpha-3 and MUTYH beta-3 predominantly localize to mitochondria, while MUTYH gamma-3 predominantly localizes to the nucleus (Takao et al. 1999). However, a nuclear localization signal is located at the C-terminus of all MUTYH isoforms and other studies suggested that all isoforms can localize to the nucleus and only a small fraction of MUTYH is targeted to the mitochondria (Ohtsubo et al. 2000, Ichinoe et al. 2004). A small number of functional studies of MUTYH mutants uses the MUTYH isoform gama-3 (Goto et al. 2010, Shinmura et al. 2012). Nuclear localization of MUTYH may be affected by a splicing site variant (Tao et al. 2004).
MAP, compared with APC-associated FAP, is characterized by a later age of onset and a smaller number and size of polyps. Germline MUTYH mutations are associated with an increased incidence of duodenal polyps, gastric cancer, melanoma, breast cancer, dental and dermoid cysts, and osteomas. MUTYH mutations are rarely reported in the sporadic colorectal cancer. Tumors that develop in MAP patients are characterized with an excess of G:C -> T:A transversions in tumor suppressor genes, such as APC, and oncogenes, such as KRAS, which is a consequence of MUTYH functional impairment.
A single nucleotide polymorphism (SNP) at the splice donor site was reported to affect translation efficiency of MUTYH transcript, but its relevance for cancer predisposition has not been clarified (Yamaguchi et al. 2002). Catalytic activity of MUTYH and its mutants may be affected by posttranslational modifications (Parker et al. 2003, Kundu et al. 2010). Some MUTYH mutations reported in colorectal cancer do not affect MUTYH catalytic activity but disrupt the interaction of MUTYH with other proteins involved in DNA repair (Tominaga et al. 2004, Turco et al. 2013).
For review, please refer to Chow et al. 2004, Nielsen et al. 2011, Venesio et al. 2012, Mazzei et al. 2013.
R-HSA-9616334 Defective Base Excision Repair Associated with NEIL1 NEIL1 is an enzyme with dual DNA glycosylase and beta/delta lyase activity involved in base excision repair pathway (BER), the primary repair pathway for oxidative DNA damage. NEIL1 can detect and remove DNA damage resulting from oxidation of adenine, guanine and thymine, in the form of 4,6-diamino-5-formamidopyrimidine (FapyA), 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG), and thymine glycol (Tg), respectively. NEIL1 can also detect and remove dihydrouracil (DHU), which results from deamination of cytosine. Several low frequency NEIL1 polymorphisms, present in about 1% of general population in the United States have been reported. Different polymorphisms have different effects on NEIL1 function, and it was suggested that NEIL1 polymorphisms and NEIL1 deficiency or haploinsuficiency may be involved in predisposition to cancer and in metabolic syndrome (Roy et al. 2007, Vartanian et al. 2006, Sampath et al. 2011, Prakash et al. 2014). One polymorphism, NEIL1 G83D, is associated with primary sclerosing cholangitis and cholangiocarcinoma (Forsbring et al. 2009). NEIL1 G83D variant exhibits impaired DNA glycosylase activity towards different damaged DNA bases (Roy et al. 2007, Prakash et al. 2014) and induces genomic instability (Galick et al. 2017).
NEIL1 E28del, an in frame deletion variant of NEIL1 reported in gastric (stomach) cancer, where glutamate at position 28 is deleted, does not cleave Tg from damaged DNA (Shinmura et al. 2004).
NEIL1 Q282TER, a NEIL1 variant which lacks the putative nuclear localization signal (NLS), localizes to the cytosol and is therefore not able to access damaged DNA substrates, but its involvement in cancer is uncertain (Shinmura et al. 2015).
Reduced expression of NEIL1 and NEIL2 genes, accompanied with increased NEIL3 gene expression was detected in various cancers. NEIL1 gene silencing by promoter hypermethylation may be one of the underlying mechanisms for reduced NEIL1 expression in cancer (Shinmura et al. 2016).
Infection with the Hepatitis C virus (HCV) leads to decreased NEIL1 expression in liver cells, through an unknown mechanism (Pal et al. 2010).
Mice that are double knockout for Neil1 and Nthl1 genes accumulate DNA damage in the form of FapyA and FapyG and are more prone to development of lung adenocarcinoma than single Neil1 or Nthl1 gene knockouts (Chan et al. 2009). Another study reported that Neil1 knockout mice did not show a predisposition to tumour formation, and neither did double knockouts of Neil1 and Neil2, nor triple knockouts of Neil1, Neil2 and Neil3. Neil1 knockout mice are obese, consistent with the metabolic syndrome, but double knockouts of Neil1 and Neil2 do not display obesity (Rolseth et al. 2017).
R-HSA-9629232 Defective Base Excision Repair Associated with NEIL3 NEIL3 is a DNA N-glycosylase involved in base excision repair (BER), the primary repair pathway for oxidative DNA damage. NEIL3 can detect and remove oxidized guanine, in the form of 5-guanidinohydatoin and spiroiminodihydantoin, and oxidized thymine, in the form of thymine glycol. NEIL3 has a preference for single strand DNA (ssDNA) and is implicated in repair of oxidative DNA damage at telomeres (Zhou et al. 2013). A NEIL3 disease variant NEIL3 D132 is unable to cleave 5 guanidinohydantoin (Gh) from oxidatively damaged DNA. Individuals harboring a NEIL3 D132V homozygous mutation are predisposed to development of autoimmune diseases (Massaad et al. 2016) and NEIL3 depletion is also associated with an increase in telomere damage and loss (Zhou et al. 2017). NEIL3 unhooks DNA interstrand cross-links (ICLs) during DNA replication. NEIL3 resolves psoralen- and abasic site-induced ICLs in a Fanconi anemia (FA) pathway-independent manner (Semlow et al. 2016, Martin et al. 2017).
A polymorphism in one of the NEIL3 gene splice sites may increase the risk of myocardial infarction (Skarpengland et al. 2015). NEIL3 expression in the heart increases after heart failure in humans and after myocardial infarction in mouse disease models. Neil3 knockout mice show increased mortality after myocardial infarction, but there is no increase in the amount of DNA damage in Neil3 knockout hearts. In the heart, NEIL3 may function in the epigenetic regulation of gene expression and facilitate transcriptional response to myocardial infarction (Olsen et al. 2017). NEIL3 mRNA expression is increased in human carotid plaques and Neil3 deficiency accelerates plaque formation in Apoe knockout mice, but it appears that this is not correlated with oxidative DNA damage (Skarpengland et al. 2016).
The function of NEIL3 in removal of hydantoins from single strand DNA may be important for removal of replication blocks in proliferating cells. Mouse embryonic fibroblasts and neuronal stem cell derived from Neil3 knockout mouse embryos show decreased proliferation capacity and increased sensitivity to DNA damaging agents (Rolseth et al. 2013). NEIL3 may be required for maintenance of adult neurogenesis, as Neil3 knockout mice exhibit learning and memory deficits and synaptic irregularities in the hippocampus (Regnell et al. 2012). In addition, NEIL3 deficient neuronal stem cells exhibits signs of premature senescence (Reis and Hermanson 2012) and Neil3 knockout mice show reduced ability to augment neurogenesis to repair damage induced hypoxia ischemia (Sejersted et al. 2011).
Mice that are triple knockout for Neil1, Neil2 and Neil3 do not show a predisposition to tumour formation or changes in telomere length (Rolseth et al. 2017).
R-HSA-9616333 Defective Base Excision Repair Associated with NTHL1 NTHL1 is a DNA N-glycosylase that catalyzes the first step in base excision repair (BER), the primary repair pathway for oxidative DNA damage. NTHL1 can recognize and remove oxidized cytosine, adenine and thymine, in the form of cytosine glycol (Cg), 4,6-diamino-5-formamidopyrimidine (FapyA), and thymine glycol (Tg), respectively. NTHL1 can also recognize and remove dihydrouracil (DHU), produced by cytosine deamination. Germline mutations that impair function of NTHL1 predispose affected patients to a cancer syndrome (NTHL1 syndrome) that involves adenomatous polyposis and colorectal cancer, similar to MUTYH-associated polyposis (MAP), but also causes development of tumors in other organs, such as breast, bladder, skin, uterus and brain. Only patients with mutations in both alleles of NTHL1 are affected, indicative of an autosomally recessive inheritance (Weren et al. 2015, Rivera et al. 2015, Broderick et al. 2017, Grolleman et al. 2019). Some common NTHL1 polymorphisms may results in reduced NTHL1 function, but predisposition of affected individuals to cancer has not been studied in full (Galick et al. 2013). Mice that are double knockout for Neil1 and Nthl1 genes accumulate DNA damage in the form of FapyA and FapyG and are more prone to development of lung adenocarcinoma than single Neil1 or Nthl1 gene knockouts (Chan et al. 2009). Biallelic loss-of-function mutations in NTHL1 result in a mutational signature characterized by C>T transitions at non-CpG sites (Grolleman et al. 2019). For review, please refer to Weren et al. 2018.
Besides loss-of-function mutations, NTHL1 is amplified and overexpressed in some cancers. NTHL1 overexpression leads to genomic instability in non-transformed human bronchial epithelial cells and may lead to malignant transformation (Limpose et al. 2018).
R-HSA-9656249 Defective Base Excision Repair Associated with OGG1 OGG1 is the main DNA glycosylase responsible for removal of 8-oxoguanine (8oxoG), the most frequent type of oxidative DNA damage, from DNA and initiation of the base excision repair (Klungland et al. 1999, Minowa et al. 2000). A frequent OGG1 polymorphism increases the risk of breast and lung cancer in affected individuals, and inactivating mutations in OGG1 have been reported in various cancer types and in Alzheimer's disease. Ogg1 knockout mice are predisposed to cancer. For review, please refer to Boiteux et al. 2017.
R-HSA-5083632 Defective C1GALT1C1 causes TNPS Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 (C1GALT1; MIM:610555) mediates the transfer of Galactose (Gal) from UDP-galactose to single O-linked GalNAc residues (Tn antigens) to form Core 1 structures on glycoproteins. C1GALT1 is active when in complex with the molecular chaperone C1GALT1C1 (aka COSMC; MIM:300611) which assists the folding and/or stability of C1GALT1. Defects in C1GALT1C1 causes somatic Tn polyagglutination syndrome (TNPS; MIM:300622), characterised by the polyagglutination of erythrocytes by naturally occurring anti-Tn antibodies following exposure of the Tn antigen on their surface. Defects in C1GALT1C1 render C1GALT1 inactive and results in the accumulation of the incompletely glycosylated Tn antigen. The Tn antigen is tumour-associated, found in a majority of human carcinomas, and is not normally expressed in peripheral tissues or blood cells (Crew et al. 2008, Ju et al. 2014). C1GALT1 and C1GALT1C1 belong to the CAZy family GT31 (www.cazy.org).
R-HSA-3359457 Defective CBLIF causes IFD Defects in cobalamin binding intrinsic factor CBLIF, aka gastric intrinsic factor GIF) cause hereditary intrinsic factor deficiency (IFD, aka congenital pernicious anemia; MIM:261000). IFD is an autosomal recessive disorder characterized by megaloblastic anemia (Tanner et al. 2005).
R-HSA-3359485 Defective CD320 causes MMATC Defects in CD320 cause methylmalonic aciduria type TCblR (MMATC aka methylmalonic aciduria; MIM:613646) resulting in elevated methylmalonic acid (MMA) and homocysteine (HCYS) in newborns (Quadros et al. 2010).
R-HSA-5678895 Defective CFTR causes cystic fibrosis Cystic fibrosis transmembrane conductance regulator (CFTR) is a low conductance chloride-selective channel that mediates the transport of chloride ions in human airway epithelial cells. Chloride ions plays a key role in maintaining homoeostasis of epithelial secretions in the lungs. Defects in CFTR can cause cystic fibrosis (CF; MIM:602421), a common generalised disorder in Caucasians affecting the exocrine glands. CF results in an ionic imbalance that impairs clearance of secretions, not only in the lung, but also in the pancreas, gastrointestinal tract and liver. Wide-ranging manifestations of the disease include chronic lung disease, exocrine pancreatic insufficiency, blockage of the terminal ileum, male infertility and salty sweat. The median survival of CF patients in North America and Western Europe is around 40 years (Davis 2006, Radlovic 2012).
R-HSA-3595174 Defective CHST14 causes EDS, musculocontractural type Carbohydrate sulfotransferase 14 (CHST14 also known as D4ST-1) mediates the transfer of sulfate to position 4 of further N-acetylgalactosamine (GalNAc) residues of dermatan sulfate (DS). Defects in CHST14 cause Ehlers-Danlos syndrome, musculocontractural type (MIM:601776). The Ehlers-Danlos syndromes (EDS) are a group of connective tissue disorders that share common features such as skin hyperextensibility, articular hypermobility and tissue fragility (Beighton et al. 1998). The musculocontractural form of EDS (MIM:601776) include distinctive characteristics such as craniofacial dysmorphism, congenital contractures of fingers and thumbs, clubfeet, severe kyphoscoliosis and muscular hypotonia (Malfait et al. 2010).
R-HSA-3595172 Defective CHST3 causes SEDCJD Carbohydrate sulfotransferase 3 (CHST3) transfers sulfate (SO4(2-)) to position 6 of N-acetylgalactosamine (GalNAc) residues of chondroitin-containg proteins resulting in chondroitin sulfate (CS), the predominant glycosaminoglycan present in cartilage. Defects in CHST3 result in spondyloepiphyseal dysplasia with congenital joint dislocations (SEDCJD; MIM:143095), a bone dysplasia clinically characterized by severe progressive kyphoscoliosis (abnormal curvature of the spine), arthritic changes with joint dislocations and short stature in adulthood (Unger et al. 2010).
R-HSA-3656225 Defective CHST6 causes MCDC1 Carbohydrate sulfotransferase 6 (CHST6) catalyzes the transfer of sulfate to position 6 of non-reducing ends of N-acetylglucosamine (GlcNAc) residues on keratan sulfate (KS). KS plays a central role in maintaining corneal transparency. Defective CHST6 (Nakazawa et al. 1984) results in unsulfated keratan deposited within the intracellular space and the extracellular corneal stroma leading to macular dystrophy, corneal type I (MCDC1; MIM:217800). MCDC1 is an early-onset, ocular disease characterized by bilateral, progressive corneal opacification, and reduced corneal sensitivity (Jones & Zimmerman 1961). MCD can be subdivided into 2 types on the basis of immunohistochemical studies and serum analysis for keratan sulfate; MCD type I, in which there is a virtual absence of sulfated KS-specific antibody response in the serum and cornea and MCD type II, in which the normal KS-specific antibody response is present in cornea and serum (Yang et al. 1988).
R-HSA-3595177 Defective CHSY1 causes TPBS Chondroitin sulfate synthases (CHSY) are involved in the synthesis of chondroitin sulfate, adding alternatingly glucuronate (GlcA) and N-acetylgalactosamine (GalNAc) to the growing chondroitin polymer (Mizumoto et al. 2013). Defects in CHSY1 cause temtamy preaxial brachydactyly syndrome (TPBS; MIM:605282), a syndrome characterized by multiple congenital anomalies, mental retardation, sensorineural deafness, growth retardation and bilateral symmetric digital anomalies mainly in the form of preaxial brachydactyly (literally, shortness of fingers and toes) and hyperphalangism (Temtamy et al. 1998, Race et al. 2010, Tian et al. 2010).
R-HSA-5619060 Defective CP causes aceruloplasminemia (ACERULOP) Ceruloplasmin (CP), synthesised in the liver and secreted into plasma, is a copper-binding (6-7 atoms per molecule) glycoprotein involved in iron trafficking in vertebrates. CP is essential for SLC40A1 (ferroportin) stability at the cell surface, the protein that mediates iron efflux from cells. CP also possesses ferroxidase activity, which oxidises ferrous iron (Fe2+) to ferric iron (Fe3+) following its transfer out of the cell. Fe3+ can then be loaded on to extracellular transferrin which transports it around the body to sites where it is required. Iron is vital for many metabolic processes such as electron transport and the transport and storage of oxygen.
Defects in CP (or indeed SLC40A1) can lead to the phenotype of iron overload as seen in the disorder aceruloplasminemia (ACERULOP; MIM:604290). It is a rare autosomal recessive disorder of iron metabolism characterised by iron accumulation mainly in the brain, but also in liver, pancreas and retina. Patients develop retinal degeneration, diabetes mellitus and neurological disturbance. ACERULOP belongs to a group of disorders known as NBIA (neurodegeneration with brain iron accumulation), distinguishing it from hereditary hemochromatosis (serum iron is high but the brain is usually not affected) and from disorders of copper metabolism such as Menkes and Wilson disease (Harris et al. 1995, Kono 2012, Musci et al. 2014).
R-HSA-5688890 Defective CSF2RA causes SMDP4 Surfactant catabolism by alveolar macrophages plays a small but critical part in surfactant recycling and metabolism. Upon ligand binding, granulocyte-macrophage colony-stimulating factor receptor (GM-CSFR), a heterodimer of alpha (CSF2RA) and beta (CSF2RB) subunits, initiates a signalling process that not only induces proliferation, differentiation and functional activation of hematopoietic cells but can also determine surfactant uptake into alveolar macrophages and its degradation via clathrin-coated vesicles. Defects in human CSF2RA can cause pulmonary surfactant metabolism dysfunction 4 (SMDP4; MIM:300770, aka congenital pulmonary alveolar proteinosis, (PAP)), a rare lung disorder due to impaired surfactant homeostasis characterised by alveoli filling with floccular material. Cellular responses to the misfolded pro-SFTPC products include ER stress, the activation of reactive oxygen species and autophagy. Excessive lipoprotein accumulation in the alveoli results in a form of respiratory distress syndrome in premature infants (RDS; MIM:267450) (Whitsett et al. 2015).
R-HSA-5688849 Defective CSF2RB causes SMDP5 Surfactant catabolism by alveolar macrophages plays a small but critical part in surfactant recycling and metabolism. Upon ligand binding, granulocyte-macrophage colony-stimulating factor receptor (GM-CSFR), a heterodimer of alpha (CSF2RA) and beta (CSF2RB) subunits, initiates a signalling process that not only induces proliferation, differentiation and functional activation of hematopoietic cells but can also determine surfactant uptake into alveolar macrophages and its degradation via clathrin-coated vesicles. Defects in human CSF2RB can cause pulmonary surfactant metabolism dysfunction 5 (SMDP5; MIM:614370, aka pulmonary alveolar proteinosis 5, PAP5), a rare lung disorder due to impaired surfactant homeostasis characterised by alveoli filling with floccular material causing respiratory failure (Greenhill & Kotton 2009, Whitsett et al. 2015).
R-HSA-3359463 Defective CUBN causes MGA1 Defects in the CUBN gene cause recessive hereditary megaloblastic anemia 1 (RH-MGA1 aka MGA1 Finnish type or Imerslund-Grasbeck syndrome, I-GS; MIM:261100). The Finnish cases described by Grasbeck et al. were caused by defects in CUBN (Grasbeck et al. 1960). The resultant malabsorption of Cbl (cobalamin, vitamin B12) leads to impaired B12-dependent folate metabolism and ultimately impaired thymine synthesis and DNA replication.
R-HSA-5579026 Defective CYP11A1 causes AICSR Cholesterol side-chain cleavage enzyme, mitochondrial (CYP11A1) normally catalyses the side-chain cleavage of cholesterol to form pregnenolone. Defects in CYP11A1 can cause Adrenal insufficiency, congenital, with 46,XY sex reversal (AICSR; MIM:613743). This is a rare disorder that can present as acute adrenal insufficiency in infancy with elevated ACTH and plasma renin activity and low or absent adrenal steroids. The severest phenotype is loss-of-function mutations associated with prematurity, complete under-androgenisation and severe, early-onset adrenal failure (Kim et al. 2008).
R-HSA-5579017 Defective CYP11B1 causes AH4 Cytochrome P450 11B1, mitochondrial (CYP11B1) possesses steroid 11-beta-hydroxylase activity which can convert 11-deoxycortisol to cortisol. 11-beta-hydroxylase deficiency is one of the main causes of congenital adrenal hyperplasia (CAH) (5-8%), second only to 21-hydroxylase deficiency which accounts for more than 90% of CAH (Zhao et al. 2008). Defects in CYP11B1 can cause Adrenal hyperplasia 4 (AH4; MIM:202010), a form of congenital adrenal hyperplasia which is a common recessive disease due to failure to convert 11-deoxycortisol to cortisol. This impaired corticosteroid biosynthesis results in androgen excess, virilization and hypertension (White et al. 1991).
R-HSA-5579009 Defective CYP11B2 causes CMO-1 deficiency Cytochrome P450 11B2, mitochondrial (CYP11B2 aka aldosterone hydroxylase) is an enzyme necessary for aldosterone biosynthesis via corticosterone (CORST) and 18-hydroxycorticosterone (18HCORST). Defects in CYP11B2 results in disorders of aldosterone synthesis. Corticosterone methyloxidase 1 and 2 deficiencies (CMO-1; MIM:203400 and CMO-2 deficiency; MIM:61060) are autosomal recessive disorders of aldosterone biosynthesis (Mitsuuchi et al. 1993, Bureik et al. 2002). In CMO-1 deficiency, aldosterone is undetectable in plasma, while its immediate precursor, 18HCORST, is low or normal. In CMO-2 deficiency, aldosterone can be low or normal, but at the expense of increased secretion of 18HCORST. Patients with CMO-2 deficiency have elevated plasma 18-hydroxycorticosterone/aldosterone ratios.
R-HSA-5579028 Defective CYP17A1 causes AH5 Steroid 17-alpha-hydroxylase/17,20 lyase (CYP17A1) mediates both 17-alpha-hydroxylase and 17,20-lyase activity, allowing the adrenal glands and gonads to synthesise both 17-alpha-hydroxylated glucocorticoids and sex steroids respectively (Kagimoto et al. 1998). Defects in CYP17A1 can cause Adrenal hyperplasia 5 (AH5), a form of congenital adrenal hyperplasia (CAH), a common recessive disease due to defective synthesis of cortisol and sex steroids. Common symptoms include mild hypocortisolism, ambiguous genitalia in genetic males or failure of the ovaries to function at puberty in genetic females, metabolic alkalosis due to hypokalemia and low-renin hypertension. CYP17A1 can have defects in either or both of 17-alpha-hydroxylase and 17,20-lyase activities thus patients can show combined partial 17-alpha-hydroxylase/17,20-lyase deficiency or isolated 17,20-lyase deficiency traits (Yanase et al. 1992, Kater & Biglieri 1994, Fluck & Miller 2006, Miller 2012).
R-HSA-5579030 Defective CYP19A1 causes AEXS Aromatase (CYP19A1) catalyses the conversion of androstenedione (ANDST) to estrone (E1). Defects in CYP19A1 can cause aromatase excess syndrome (AEXS; MIM:139300) and aromatase deficiency (AROD; MIM:613546). Affected individuals cannot synthesise endogenous estrogens. In females the lack of estrogen leads to pseudohermaphroditism and progressive virilization at puberty, whereas in males pubertal development is normal (Bulun 2014).
R-HSA-5579000 Defective CYP1B1 causes Glaucoma Cytochrome P450 1B1 (CYP1B1) can oxidise a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics as well as activating a range of procarcinogens. A specific substrate is the female sex hormone estradiol-17beta (EST17b) which is 4-hydroxylated to 4-hydroxyestradiol-17beta 4OH-EST17b). Defects in CYP1B1 can cause glaucoma disorders such as Glaucoma 3, primary congenital, A (GLC3A; MIM:231300), Glaucoma, primary open angle (POAG; MIM:137760), Glaucoma 1, open angle, A (GLC1A; MIM:137750) and Peters anomaly (PAN; MIM:604229). These disorders cause a progressive optic neuropathy characterised by visual field defects that ultimately lead to irreversible blindness (Li et al. 2011, Sarfarazi et al. 2003, Vincent et al. 2001).
R-HSA-5579021 Defective CYP21A2 causes AH3 Steroid 21-hydroxylase (CYP21A2) specifically catalyses the 21-hydroxylation of steroids which is required for the adrenal synthesis of mineralocorticoids and glucocorticoids. Defects in CYP21A2 can cause adrenal hyperplasia 3 (AH3; MIM:201910), a form of congenital adrenal hyperplasia (CAH) where cortisol synthesis is defective. This results in increased ACTH levels, causing overproduction and accumulation of cortisol precursors, particularly 17-hydroxyprogesterone (17HPROG). The resultant excessive production of androgens causes virilization. 21-hydroxylase deficiency accounts for more than 90% of CAH cases and ranges from mild to complete loss of activity (White et al. 2000, White & Bachega 2012).
R-HSA-5579010 Defective CYP24A1 causes HCAI Catabolic inactivation of the active, hormonal form of vitamin D3 (calcitriol, CALTOL, 1,25-dihydroxyvitamin D3) is initially carried out by 24-hydroxylation, mediated by 1,25-dihydroxyvitamin D3 24-hydroxylase (CYP24A1). The product formed is eventually transformed to calcitroic acid, the major water-soluble metabolite that can be excreted in bile. Defects in CYP24A1 can cause hypercalcemia infantile (HCAI; MIM:143880), a disorder characterised by abnormally high level of calcium in the blood, failure to thrive, vomiting, dehydration, and nephrocalcinosis (Schlingmann et al. 2011).
R-HSA-5579015 Defective CYP26B1 causes RHFCA Retinoic acid (RA) is a biologically active analogue of vitamin A (retinol). RA plays an important role in regulating cell growth and differentiation.CYP26A1 and B1 are involved in the metabolic breakdown of RA by 4-hydroxylation. High expression levels of CYP26B1 in the cerebellum and pons of human brain suggests a protective role of specific tissues against retinoid damage (White et al. 2000). Defects in CYP26B1 can cause radiohumeral fusions with other skeletal and craniofacial anomalies (RHFCA; MIM:614416), a disease characterised by craniofacial malformations and multiple skeletal anomalies (Laue et al. 2011).
R-HSA-5579004 Defective CYP26C1 causes FFDD4 Retinoic acid (RA) is a biologically active analogue of vitamin A (retinol). RA plays an important role in regulating cell growth and differentiation. CYP26C1 is involved in the metabolic breakdown of RA by 4-hydroxylation. While CYP26C1 can hydroxylate the trans form, it is unique in hydroxylating the 9-cis isomer of RA (9cRA) (Taimi et al. 2004). Defects in CYP26C1 can cause focal facial dermal dysplasia 4 (FFDD4; MIM:614974), a rare syndrome characterised by facial lesions.
R-HSA-5578996 Defective CYP27A1 causes CTX CYP27A1, a mitochondrial matrix sterol hydroxylase, catalyses the 27-hydroxylation of side-chains of sterol intermediates (Cali et al. 1991). In the bile acid synthesis pathway, CYP27A1 catalyses the first step in the oxidation of the side chain of sterol intermediates such as cholestane-triols (Pikuleva et al. 1998). Defects in CYP27A1 can cause Cerebrotendinous xanthomatosis (CTX; MIM:213700), a rare sterol storage disorder. Decreased bile acid production results in the accumulation of sterol intermediates in many tissues, including brain. The disorder is characterised by progressive neurologic dysfunction, premature atherosclerosis and cataracts (Gallus et al. 2006).
R-HSA-5579014 Defective CYP27B1 causes VDDR1A Vitamin D3 (cholecalciferol), synthesised in human skin by ultraviolet radiation action on 7-dehydrocholesterol, does not possess any biological activity. Vitamin D hormonal activity requires hydroxylation at the 25 and 1-alpha positions by cytochrome P450 enzymes CYP2R1 and CYP27B1 respectively. Vitamin D 25-hydroxylase (CYP2R1) catalyses the hydroxylation of vitamin D3 to calcidiol (CDL). Subsequent 1-alpha-hydroxylation of CDL by CYP27B1 produces calcitriol (CTL). CTL binds and activates the nuclear vitamin D receptor, with subsequent regulation of physiologic events such as calcium homeostasis, cellular differentiation and proliferation.
Defects in CYP27B1 can cause rickets, vitamin D-dependent 1A (VDDR1A; MIM:264700), a disorder caused by deficiency of the active form of vitamin D (CTL) resulting in defective bone mineralization and clinical features of rickets. To date, 47 mutations have been identified, the majority of them (28) being missense mutations (Kim 2011, Cui et al. 2012).
R-HSA-5579027 Defective CYP27B1 causes VDDR1B Vitamin D3 (cholecalciferol), synthesised in human skin by ultraviolet radiation action on 7-dehydrocholesterol, does not possess any biological activity. Vitamin D hormonal activity requires hydroxylation at the 25 and 1-alpha positions by cytochrome P450 enzymes CYP2R1 and CYP27B1 respectively.
Vitamin D 25-hydroxylase (CYP2R1) catalyses the hydroxylation of vitamin D3 to calcidiol (CDL). Subsequent 1-alpha-hydroxylation of CDL produces calcitriol (CTL). CTL binds and activates the nuclear vitamin D receptor, with subsequent regulation of physiologic events such as calcium homeostasis, cellular differentiation and proliferation.
Defects in CYP2R1 can cause rickets, vitamin D-dependent 1B (VDDR1B; MIM:600081), a disorder caused by a selective deficiency of the active form of vitamin D (CTL) resulting in defective bone mineralization and clinical features of rickets (Pikuleva et al. 2013).
R-HSA-5579011 Defective CYP2U1 causes SPG56 Cytochrome P450 2U1 (CYP2U1) catalyses the hydroxylation of arachidonic acid, docosahexaenoic acid and other long chain fatty acids, generating bioactive eicosanoid derivatives which may play an important physiological role in fatty acid signaling processes. Defects in CYP2U1 can cause Spastic paraplegia 56, autosomal recessive (SPG56; MIM:615030), a neurodegenerative disorder characterised by a slow, gradual, progressive weakness and spasticity of the lower limbs (Tesson et al. 2012, Fink 2013).
R-HSA-5579005 Defective CYP4F22 causes ARCI5 Cytochrome P450 4F22 (CYP4F22) is thought to 20-hydroxylate trioxilin A3 (TrXA3), an intermediary metabolite from the 12(R)-lipoxygenase pathway. This pathway is implicated in proliferative skin diseases. The major products of arachidonic acid in keratinocytes are 12- and 15-HETE which undergo biotransformation to products involved in skin hydration. CYP4F22 mutations can lead to autosomal recessive congenital ichthyosis 5 (ARCI5) (Lefevre et al. 2006, Lugassy et al. 2008).
R-HSA-5579013 Defective CYP7B1 causes SPG5A and CBAS3 Bile acids are synthesised from cholesterol via two pathways - a classic neutral pathway involving cholesterol 7-alpha-hydroxylase (CYP7A1), and an acidic pathway involving 25-hydroxycholesterol 7-alpha-hydroxylase (CYP7B1). Defects in CYP7B1 can cause spastic paraplegia 5A (SPG5A), a neurodegenerative disorder characterised by a slow, gradual, progressive weakness and spasticity of the lower limbs (Tsaousidou et al. 2008). Defects in CYP7B1 can also cause Congenital bile acid synthesis defect 3 (CBAS3; MIM:613812), a disorder resulting in severe cholestasis, cirrhosis and liver synthetic failure. Hepatic CYP7B1 activity is undetectable (Setchell et al. 1998).
R-HSA-4755609 Defective DHDDS causes RP59 The ER membrane-associated enzyme dehydrodolichyl diphosphate synthase (DHDDS) (Endo et al. 2003) normally mediates the sequential head-to-tail cis addition of multiple isopentyl pyrophosphate (IPP) molecules to farnesyl pyrophosphate (E,E-FPP) to produce polyprenol pyrophosphate (pPPP) (Shridas et al. 2003). Dolichol in humans contain homologues ranging from 17-23 isoprene units, the most common homologues contain 19 or 20 isoprene units (Freeman et al. 1980). Dolichol is an important substrate in the N-glycosylation of proteins, including rhodopsin.
Defects in DHDDS cause retinitis pigmentosa 59 (RP59; MIM:613861), a pigment retinopathy, characterised by retinal pigment deposits (visible on fundus examination) and primary loss of rod photoreceptors followed by secondary loss of cone photoreceptors. Sufferers typically have night vision blindness and loss of mid to peripheral vision. As the condition progresses, they lose far peripheral vision and eventually central vision (Zuchner et al. 2011).
R-HSA-9699150 Defective DNA double strand break response due to BARD1 loss of function Although germline mutations of BARD1 are implicated in some cases of hereditary breast and ovarian cancer (HBOC), they occur less frequently that those of the BRCA1 or BRCA2 genes (De Brakeleer et al. 2010, Alenezi et al. 2020). From animal studies, it is known that the loss of BARD1 function results in a phenotype very similar to that caused by loss of BRCA1 function, characterized by embryonic lethality (McCarthy et al. 2003), genomic instability (McCarthy et al. 2003) and defects in homology-directed repair (Lee et al. 2015). A small number of clinically-relevant BARD1 missense mutants that have been functionally characterized and shown to be impaired in BRCA1 binding (Xia et al. 2003, Lee et al. 2015) are annotated in this pathway.
R-HSA-9663199 Defective DNA double strand break response due to BRCA1 loss of function Germline mutations in the BRCA1 or BRCA2 tumor suppressor genes are implicated in up to 10% of breast cancers overall and 40% of familial breast cancers. Carriers of either BRCA1 or BRCA2 germline mutation are predisposed to hereditary breast and ovarian cancer (the HBOC syndrome), which is inherited in an autosomal dominant manner. Besides early onset breast and ovarian cancer, HBOC patients also have a modestly increased risk of developing other tumor types, including pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. The BRCA1 gene encodes a large protein of 1863 amino acids, which contains a RING finger domain at the N-terminus and two BRCT repeats at the C-terminus. The RING domain is responsible for heterodimerization with BARD1, which increases stability of BRCA1 and activates its E3 ubiquitin ligase activity. BRCA1 plays an important role in homology-directed repair of DNA double-strand breaks (DSBs). Brca1-null knockout mice die early during embryonic development and cells depleted of BRCA1 show genomic instability (reviewed by Roy et al. 2011). Cancer mutations that affect the RING domain of BRCA1 frequently result in the inability of BRCA1 to bind to BARD1 and participate in DNA DSB response (Wu et al. 1996, Ransburgh et al. 2010). Some mutations in the RING domain of BRCA1 were shown to affect the ubiquitin ligase activity of BRCA1 (Brzovic et al. 2001), but it is uncertain if the ubiquitin ligase activity is essential for the tumor suppressor role of BRCA1 (Shakya et al. 2011).
R-HSA-4755583 Defective DOLK causes DOLK-CDG Dolichol kinase (DOLK, TMEM15) normally mediates the phosphorylation of dolichol (DCHOL) to form dolichyl phosphate (DOLP) in the ER membrane (Fernandez et al. 2002). DOLP is an important substrate in the synthesis of N- and O-glycosylated proteins and GPI anchors. Defects in DOLK cause congenital disorder of glycosylation type 1m (DOLK-CDG, CDG1m, also known as dolichol kinase deficiency; MIM:610768), a severe mutisystem disorder characterised by under-glycosylated serum glycoproteins. This disorder has a very severe phenotype and death can occur in early life (Kranz et al. 2007).
R-HSA-4549356 Defective DPAGT1 causes CDG-1j, CMSTA2 UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) catalyses the initial committed step in the biosynthesis of dolichyl pyrophosphate-oligosaccharides. Defects in DPAGT1 cause congenital disorder of glycosylation 1j (DPAGT1-CDG, previously known as CDG-1j; MIM:608093), a multisystem disorder characterised by under-glycosylated serum glycoproteins (Wu et al. 2003, Timal et al. 2012). Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. Defects in DPAGT1 can also cause myasthenic syndrome, congenital, with tubular aggregates, 2 (CMSTA2; MIM:614750), characterised by muscle weakness of mainly the proximal limb muscles, with tubular aggregates present on muscle biopsy. Sufferers find walking difficult and fall frequently. Younger sufferers show hypotonia and poor head control. A disorder of neuromuscular transmission is detected on electromyography (Belaya et al. 2012, Finlayson et al. 2013).
R-HSA-4717374 Defective DPM1 causes DPM1-CDG Dolichyl-phosphate mannosyltransferase (DPM), a heterotrimeric protein embedded in the endoplasmic reticulum membrane, mediates the transfer of mannose (from cytosolic GDP-mannose) to dolichyl phosphate (DOLP) to form dolichyl-phosphate-mannose (DOLPman). The first subunit of the heterotrimer (DPM1) appears to be the actual catalyst, and the other two subunits (DPM2 and 3) appear to stabilise it (Maeda et al. 2000). Defects in DPM1 can cause congenital disorder of glycosylation 1e (DPM1-CDG, CDG-1e; MIM:608799), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins (Kim et al. 2000, Imbach et al. 2000, Garcia-Silva et al. 2004).
R-HSA-4719377 Defective DPM2 causes DPM2-CDG Dolichyl-phosphate mannosyltransferase (DPM), a heterotrimeric protein embedded in the endoplasmic reticulum membrane, mediates the transfer of mannose (from cytosolic GDP-mannose) to dolichyl phosphate (DOLP) to form dolichyl-phosphate-mannose (DOLPman). The first subunit of the heterotrimer (DPM1) appears to be the actual catalyst, and the other two subunits (DPM2 and 3) appear to stabilise it (Maeda et al. 2000). Defects in DPM2 can cause congenital disorder of glycosylation 1u (DPM2-CDG, CDG1u; MIM:615042), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins (Barone et al. 2012). CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency.
R-HSA-4719360 Defective DPM3 causes DPM3-CDG Dolichyl-phosphate mannosyltransferase (DPM), a heterotrimeric protein embedded in the endoplasmic reticulum membrane, mediates the transfer of mannose (from cytosolic GDP-mannose) to dolichyl phosphate (DOLP) to form dolichyl-phosphate-mannose (DOLPman). The first subunit of the heterotrimer (DPM1) appears to be the actual catalyst, and the other two subunits (DPM2 and 3) appear to stabilise it (Maeda et al. 2000). Defects in DPM3 can cause congenital disorder of glycosylation 1o (DPM3-CDG, CDG1o; MIM:612937), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins. CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency (Lefeber et al. 2009).
Four biosynthetic pathways depend on DOLPman; N-glycosylation, O-mannosylation, C-Mannosylation and GPI-anchor biosynthesis. A defect in DPM3 strongly reduces O-mannosylation of alpha-dystroglycan, explaining the clinical phenotype of muscular dystrophy and linking the congenital disorders of glycosylation with the dystroglycanopathies (Lefeber et al. 2009).
R-HSA-3656253 Defective EXT1 causes exostoses 1, TRPS2 and CHDS Heparan sulfate (HS) is involved in regulating various body functions functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Exostosin 1 and 2 (EXT1 and 2) glycosyltransferases are required to form HS. They are able to transfer N-acetylglucosamine (GlcNAc) and glucuronate (GlcA) to HS during its synthesis. The functional form of these enzymes appears to be a complex of the two located on the Golgi membrane. Defects in either EXT1 or EXT2 can cause hereditary multiple exostoses 1 (Petersen 1989) and 2 (McGaughran et al. 1995) respectively (MIM:133700 and MIM:133701), autosomal dominant disorders characterized by multiple projections of bone capped by cartilage resulting in deformed legs, forearms and hands. Trichorhinophalangeal syndrome, type II (TRPS2 aka Langer-Giedion syndrome, LGS) is a disorder that combines the clinical features of trichorhinophalangeal syndrome type I (TRPS1, MIM:190350) and multiple exostoses type I, caused by mutations in the TRPS1 and EXT1 genes, respectively (Langer et al. 1984, Ludecke et al. 1995). Defects in EXT1 may also be responsible for chondrosarcoma (CHDS; MIM:215300) (Schajowicz & Bessone 1967, Hecht et al. 1995).
R-HSA-3656237 Defective EXT2 causes exostoses 2 Heparan sulfate (HS) is involved in regulating various body functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Exostosin 1 and 2 (EXT1 and 2) glycosyltransferases are required to form HS. They are able to transfer N-acetylglucosamine (GlcNAc) and glucuronate (GlcA) to HS during its synthesis. The functional form of these enzymes appears to be a complex of the two located on the Golgi membrane. Defects in either EXT1 or EXT2 can cause hereditary multiple exostoses 1 (Petersen 1989) and 2 (McGaughran et al. 1995) respectively (MIM:133700 and MIM:133701), autosomal dominant disorders characterised by multiple projections of bone capped by cartilage resulting in deformed legs, forearms and hands.
R-HSA-9672387 Defective F8 accelerates dissociation of the A2 domain Retention of A2 polypeptide is required for normal stability of activated factor VIII (FVIIIa) and dissociation of A2 correlates with FVIIIa inactivation and consequent loss of FXase activity. Hemophilia A (HA)-associated mutations (R550H, A303E, S308L, N713I, R717W and R717L) within the predicted A1-A2 and A2-A3 interface are thought to disrupt potential intersubunit hydrogen bonds and have the molecular phenotype of increased rate of inactivation of FVIIIa due to increased rate of A2 subunit dissociation (Pipe SW et al. 1999; Hakeos WH et al. 2002)
R-HSA-9672395 Defective F8 binding to the cell membrane The Reactome event describes the defective interaction between the thrombin-activated FVIIIa protein and phospholipid membrane surfaces caused by hemophilia A-associated FVIII variants, such as A2220P, A2220del and Q2330P.
R-HSA-9672393 Defective F8 binding to von Willebrand factor Upon secretion from the cell, FVIII circulates in a tight complex with the multimeric glycoprotein von Willebrand Factor (vWF), which is essential for maintaining stable levels of FVIII in the circulation (reviewed by Pipe SW et al. 2016). Genetic mutations in the F8 gene can compromise FVIII binding to vWF thus decreasing FVIII values in the plasma causing hemophilia A (HA), an X-linked recessive bleeding disorder.
R-HSA-9672391 Defective F8 cleavage by thrombin In normal human plasma, thrombin cleaves factor VIII (FVIII) after arginine residues 391 (A1-A2 domain junction) and 759 (A2-B domain junction) to yield heavy chain fragments and at R1708 (a3-A3 junction) to yield the light chain fragment (Eaton D et al. 1986; Hill-Eubanks DC et al. 1989). Mutations affecting arginine residues located at the thrombin cleavage sites of factor VIII protein result in mild/moderate hemophilia A (HA) (Pattinson JK et al. 1990; Arai M et al. 1990; Schwaab R et al. 1991). The Reactome event describes failed thrombin-mediated activation of HA-associated FVIII variants (R391C, R391H, S392L, R1708C and R1708H) due to defects at or close to thrombin cleavage sites.
R-HSA-9672397 Defective F8 secretion Hemophilia A (HA) is a bleeding disorder caused by lack of or a defective factor VIII (FVIII) protein and results from defects in the F8 gene (Peyvandi F et al. 2016).
In healthy individuals, FVIII is synthesized as a large glycoprotein of 2351 amino acids with a discrete domain structure: A1-A2-B-A3-C1-C2 (Wood WI et al. 1984; Vehar GA et al. 1984; Toole JJ et al. 1984). Upon synthesis, FVIII is translocated into the lumen of the endoplasmic reticulum (ER), where it undergoes extensive processing including cleavage of a signal peptide and N-linked glycosylation at asparagine residues (Kaufman RJ et al. 1988, 1997; Kaufman RJ 1998). In the ER lumen of mammalian cells FVIII interacts with the protein chaperones calnexin (CNX), calreticulin (CRT), and immunoglobulin-binding protein (BiP or GRP78) that facilitate proper folding of proteins prior to trafficking to the Golgi compartment (Marquette KA et al. 1995; Swaroop M et al. 1997; Pipe SW et al. 1998; Kaufman RJ et al. 1997; Kaufman RJ 1998). Trafficking from the ER to the Golgi compartment is facilitated by LMAN1 and multiple combined factor deficiency 2 (MCFD2) cargo receptor complex (Zhang B et al. 2005; Zheng, C et al. 2010, 2013). Within the Golgi apparatus, FVIII is subject to further processing, including modification of the N-linked oligosaccharides to complex-type structures, O-linked glycosylation, and sulfation of specific Tyr-residues (Kaufman RJ 1998). Upon secretion from the cell, FVIII is cleaved at two sites in the B-domain to form a heterodimer consisting of the heavy chain containing the A1-A2-B domains in a metal ion-dependent complex with the light chain consisting of the A3-C1-C2 domains (Kaufman RJ et al. 1997; Kaufman RJ 1998).
The Reactome event describes defects within the secretory pathway due to mutations in the F8 gene that can impair FVIII synthesis, folding, intracellular processing and transport which result in a lack or reduced levels of the plasma FVIII protein. The module includes also an event of defective post-translational tyrosine sulfonation of FVIII in the Golgi apparatus that is required for the optimal interaction between the secreted FVIII and the von Willebrand factor (VWF). R-HSA-9674519 Defective F8 sulfation at Y1699 Hemophilia A (HA) is a bleeding disorder caused by lack of or a defective factor VIII (FVIII) protein and results from defects in the F8 gene (Peyvandi F et al. 2016).
In healthy individuals, FVIII is synthesized as a large glycoprotein of 2351 amino acids with a discrete domain structure: A1-A2-B-A3-C1-C2 (Wood WI et al. 1984; Vehar GA et al. 1984; Toole JJ et al. 1984). Upon synthesis, FVIII is translocated into the lumen of the endoplasmic reticulum (ER), where it undergoes extensive processing including cleavage of a signal peptide and N-linked glycosylation at asparagine residues (Kaufman RJ et al. 1988, 1997; Kaufman RJ 1998). In the ER lumen of mammalian cells FVIII interacts with the protein chaperones calnexin (CNX), calreticulin (CRT), and immunoglobulin-binding protein (BiP or GRP78) that facilitate proper folding of proteins prior to trafficking to the Golgi compartment (Marquette KA et al. 1995; Swaroop M et al. 1997; Pipe SW et al. 1998; Kaufman RJ et al. 1997; Kaufman RJ 1998). Trafficking from the ER to the Golgi compartment is facilitated by LMAN1 and multiple combined factor deficiency 2 (MCFD2) cargo receptor complex (Zhang B et al. 2005; Zheng, C et al. 2010, 2013). Within the Golgi apparatus, FVIII is subject to further processing, including modification of the N-linked oligosaccharides to complex-type structures, O-linked glycosylation, and sulfation of specific Tyr-residues (Kaufman RJ 1998). Upon secretion from the cell, FVIII is cleaved at two sites in the B-domain to form a heterodimer consisting of the heavy chain containing the A1-A2-B domains in a metal ion-dependent complex with the light chain consisting of the A3-C1-C2 domains (Kaufman RJ et al. 1997; Kaufman RJ 1998).
The Reactome event describes defects within the secretory pathway due to mutations in the F8 gene that can impair FVIII synthesis, folding, intracellular processing and transport which result in a lack or reduced levels of the plasma FVIII protein. The module includes also an event of defective post-translational tyrosine sulfonation of FVIII in the Golgi apparatus that is required for the optimal interaction between the secreted FVIII and the von Willebrand factor (VWF). R-HSA-9673221 Defective F9 activation Deficiency or dysfunction of FIX leads to hemophilia B (HB), an X-linked, recessive, bleeding disorder. On a molecular basis, HB is due to a heterogeneous spectrum of mutations spread throughout the F9 gene (Rallapalli PM et al. 2013).
The Reactome event describes the defective proteolytic activation of FIX by factor XIa due to the presence of HB-associated point mutations R191C, R191H, R226Q and R226W in the cleavage sites of FIX (Liddell MB et al. 1989; Monroe DM et al. 1989; Suehiro K et al. 1989; Diuguid DL et al. 1989; Bertina RM et al.1990). In addition, naturally occurring point mutations in the FIX propeptide sequence such as N43Q, N43L or N46S are also annotated here. These FIX variants are secreted into the circulation with a mutant 18-amino acid propeptide still attached (Bentley AK et al. 1986; Galeffi P & Brownlee GG 1987). The unprocessed FIX variants were found to affect the function of the protein by destabilizing the calcium-induced conformation of FIX (Wojcik EG et al. 1997) and showed delayed activation by FXIa (Liddell MB et al. 1989; Ware J et al. 1989; de la Salle C et al. 1993; Wojcik EG et al. 1997; Bristol JA et al. 1993).
R-HSA-9673218 Defective F9 secretion A deficiency or dysfunction of factor IX (FIX) caused by mutations in the F9 gene is associated with a blood clotting disorder hemophilia B (HB). The FIX protein level may be decreased in the circulation by F9 mutations affecting FIX protein synthesis, stability, or secretion (Kurachi S et al. 1997; Enjolras N et al. 2004; Branchini A et al. 2013, 2017; Tajnik M et al. 2016; Odaira K et al. 2019).
The Reactome event describes intracellular accumulation and/or decreased secretion of FIX due to different HB-related genetic alterations spread throughout the F9 gene.
R-HSA-9673202 Defective F9 variant does not activate FX Factor IX (FIX) deficiency is associated with mild to severe bleeding in hemophilia B (HB) patients (Rallapalli PM et al. 2013). HB is caused by a wide range of mutations that can include point mutations (nonsense and missense), insertions, deletions and other complex rearrangements of the F9 gene (Rallapalli PM et al. 2013). The Reactome event describes failed generation of FXa as the functional consequence of the defective serine protease activity of hemophilia B (HB)-associated FIX variants such as G363R & G363E (Lu Q et al. 2015), G357E (Miyata T et al. 1991), A436V (Usharani P et al. 1985), I443T (Hamaguchi N et al. 1991), G409V (Bajaj SP et al. 1990), D410H and S411G (Ludwig M et al. 1992).
R-HSA-5579019 Defective FMO3 causes TMAU Trimethylamine (TMA) is present in the diet (in fish) but primarily formed in vivo from the breakdown of choline. It is N-oxidised by FMO3 in the liver, the major isoform active towards TMA. Trimethylaminuria (TMAU; MIM:602079, fish-odour syndrome) is a human genetic disorder characterised by an impaired ability to convert the malodourous TMA to its odourless N-oxide. Patients emit a foul odour, which resembles that of rotting fish and can be a psychologically disabling condition (Messenger et al. 2013).
R-HSA-5609977 Defective GALE causes EDG Cytosolic UDP-galactose 4'-epimerase (GALE) catalyses the reversible interconversion of UDP-D-galactose (UDP-Gal) and UDP-glucose (UDP-Glc), the third reacton in the Leloir pathway of galactose metabolism. GALE can also catalyse the epimerisation of UDP-N-acetylglucosamine to UDP-N-acetylgalactosamine. The active form of the enzyme is a homodimer with one molecule of bound NAD per monomer (GALE:NAD+ dimer). Defects in GALE can cause Epimerase-deficiency galactosemia (EDG; MIM:230350), or type III galactosemia (diseases of galactose metabolism) whose clinical features include early-onset cataracts, liver damage, deafness and mental retardation. Historically, it was considered that there were two forms of GALE deficidency; a benign ("peripheral") form where there is no GALE activity in red blood cells and characterised by mild symptoms (Gitzelmann 1972) and a rarer "generalised" form with no detectable GALE activity in all tissues resulting in more severe symptoms (Holton et al. 1981). The disease is now considered to be a continuum (Openo et al. 2006).
R-HSA-5609976 Defective GALK1 causes GALCT2 Cytosolic galactokinase (GALK1) catalyses the first committed step in the Leloir pathway of galactose metabolism. GALK1 catalyses the phosphorylation of D-galactose (Gal) to form D-galactose 1-phosphate (Gal1P). Defects in GALK1 can cause type II galactosemia (GALCT2; MIM:230200), an autosomal recessive deficiency characterised by congenital cataracts during infancy and presenile cataracts in the adult population. Galactitol accumulation in the lens is the cause of these cataracts (Bosch et al. 2002).
R-HSA-5083636 Defective GALNT12 causes CRCS1 The family of UDP GalNAc:polypeptide N acetylgalactosaminyltransferases (GalNAc transferases, GALNTs) carry out the addition of N acetylgalactosamine on serine, threonine or possibly tyrosine residues on a wide variety of proteins, and most commonly associated with mucins (Wandall et al. 1997). This reaction takes place in the Golgi apparatus (Rottger et al. 1998). There are 20 known members of the GALNT family, 15 of which have been characterised and 5 candidate members which are thought to belong to this family based on sequence similarity (Bennett et al. 2012). The GALNT-family is classified as belonging to CAZy family GT27. Defects in one of the GALNT family, GALNT12 (Guo et al. 2002) (MIM: 610290) can result in decreased glycosylation of mucins, mainly expressed in the digestive organs such as the stomach, small intestine and colon, and may play a role in colorectal cancer 1 (CRCS1; MIM:608812). CRCS1 is a complex disease characterised by malignant lesions arising from the inner walls of the colon and rectum (Guda et al. 2009, Clarke et al. 2012).
R-HSA-5083625 Defective GALNT3 causes HFTC The family of UDP GalNAc:polypeptide N acetylgalactosaminyltransferases (GalNAc transferases, GALNTs) carry out the addition of N acetylgalactosamine (GalNAc) on serine, threonine or possibly tyrosine residues on a wide variety of proteins, most commonly associated with mucins. This is the initial reaction in the biosynthesis of GalNAc-type O linked oligosaccharides (Wandall et al. 1997). This reaction takes place in the Golgi apparatus (Rottger et al. 1998). There are 20 known members of the GALNT family, 15 of which have been characterised and 5 candidate members which are thought to belong to this family based on sequence similarity (Bennett et al. 2012). The GALNT-family is classified as belonging to CAZy family GT27. Defects in one of the GALNT family genes, GALNT3 (MIM:601756), can cause familial hyperphosphatemic tumoral calcinosis (HFTC; MIM:211900). HFTC is a rare autosomal recessive severe metabolic disorder characterised by the progressive deposition of calcium phosphate crystals in the skin, soft tissues and sometimes bone (Chefetz et al. 2005). The biochemical observation is hyperphosphatemia, caused by increased renal absorption of phosphate (Chefetz et al. 2005, Ichikawa et al. 2005). Some patients manifest recurrent, transient, painful swellings of the long bones with radiological evidence of periosteal reaction and cortical hyperostosis (Frishberg et al. 2005).
R-HSA-5609978 Defective GALT can cause GALCT Galactose-1-phosphate uridylyltransferase (GALT) is one of the enzymes involved in galactose metabolism in the Leloir pathway. GALT catalyses the transfer of uridine monophosphate (UMP) from UDP-glucose (UDP-Glc) to galactose-1-phosphate (Gal1P) to form UDP-galactose (UDP-Gal) and glucose 1-phosphate. Defects in GALT can cause Galactosemia (GALCT; MIM:230400), an autosomal recessive disorder of galactose metabolism presenting in neonatals that causes jaundice, cataracts and mental retardation (Bosch 2006).
R-HSA-5619073 Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) Cytosolic glucokinase (GCK) (and three isoforms of hexokinase) catalyse the irreversible reaction of alpha-D-glucose (Glc) and ATP to form alpha-D-glucose-6-phosphate (G6P) and ADP, the first step in glycolysis. In the body, GCK is found only in hepatocytes and pancreatic beta cells. GCK and the hexokinase enzymes differ in that GCK has a higher Km than the hexokinases and is less readily inhibited by the reaction product. As a result, GCK should be inactive in the fasting state when glucose concentrations are low but in the fed state should have an activity proportional to glucose concentration. These features are thought to enable efficient glucose uptake and retention in the liver, and to function as a sensor of glucose concentration coupled to insulin release in pancreatic beta cells. Defects in GCK are can cause maturity-onset diabetes of the young 2 (MODY2; MIM:125851), a heritable early onset form of type II diabetes (Hussain 2010, Osbak et al. 2009).
R-HSA-5578999 Defective GCLC causes HAGGSD In mammalian cells, many antioxidant defence systems exist which protect cells from subsequent exposure to oxidant stresses. One antioxidant is glutathione (GSH), a tripeptide present in virtually all cells that regulates the intracellular redox state and protects cells from oxidative injury. It is metabolised via the gamma-glutamyl cycle, which is catalysed by six enzymes. In man, hereditary deficiencies have been found in five of the six enzymes. Gamma-glutamylcysteine ligase (GCL) catalyses the first and rate-limiting step in GSH biosynthesis. GCL is a heterodimer of a catalytic heavy chain (GCLC) and a regulatory light chain (GCLM). Defects in the catalytic GCLC can cause hemolytic anemia due to gamma-glutamylcysteine synthetase deficiency (HAGGSD; MIM:230450), a disease characterised by hemolytic anemia, glutathione deficiency, myopathy, late-onset spinocerebellar degeneration, and peripheral neuropathy (Ristoff & Larsson 2007, Aoyama & Nakaki 2013).
R-HSA-4085023 Defective GFPT1 causes CMSTA1 Glucosamine-fructose 6-phosphate aminotransferases 1 and 2 (GFPT1,2) are the first and rate-limiting enzymes in the hexosamine synthesis pathway, and thus formation of hexosamines like N-acetylglucosamine (GlcNAc). These enzymes probably play a role in limiting the availability of substrates for the N- and O-linked glycosylation of proteins. GFPT1 and 2 are required for normal functioning of neuromuscular synaptic transmission. Defects in GFPT1 lead to myasthenia, congenital, with tubular aggregates 1 (CMSTA1; MIM:610542), characterised by altered muscle fibre morphology and impaired neuromuscular junction development. Sufferers of CMSTA1 show a good response to acetylcholinesterase inhibitors (Senderek et al. 2011). The missense mutations observed do not always result in significant reduction in enzyme activity, but biopsies show reduced amounts of GFPT1 protein suggesting increased turnover or defective translation (Senderek et al. 2011).
R-HSA-5579022 Defective GGT1 causes GLUTH To be excreted in urine, glutathione conjugates undergo several hydrolysis steps to form mercapturic acids which are readily excreted. The first step is the hydrolysis of a gamma-glutamyl residue from the conjugate catalysed by gamma-glutamyltransferases (GGTs). These are membrane-bound, heterodimeric enzymes composed of light and heavy peptide chains. Extracellular glutathione (GSH) or its conjugates can be hydrolysed to give cysteinylglycine (CG, or CG conjugates) and free glutamate (L-Glu). Hydrolysis of GSH provides cells with a local cysteine supply and contributes to intracellular GSH levels (Heisterkamp et al. 2008). Defects in GGT1 can cause glutathionuria (GLUTH; MIM:231950), an autosomal recessive disorder characterised by increased GSH concentration in the plasma and urine. Mutations that cause GLUTH can occur in both chains of the GGT1 dimer (Heisterkamp et al. 2008, Aoyama & Nakaki 2013).
R-HSA-9035968 Defective GGT1 in aflatoxin detoxification causes GLUTH To be excreted in urine, glutathione conjugates undergo several hydrolysis steps to form mercapturic acids which are readily excreted. The first step is the hydrolysis of a gamma-glutamyl residue from the conjugate catalysed by gamma-glutamyltransferases (GGTs). These are membrane-bound, heterodimeric enzymes composed of light and heavy peptide chains. Extracellular glutathione (GSH) or its conjugates can be hydrolysed to give cysteinylglycine (CG, or CG conjugates) and free glutamate (L-Glu). Hydrolysis of GSH provides cells with a local cysteine supply and contributes to intracellular GSH levels (Heisterkamp et al. 2008). Defects in GGT1 can cause glutathionuria (GLUTH; MIM:231950), an autosomal recessive disorder characterised by increased GSH concentration in the plasma and urine. Mutations that cause GLUTH can occur in both chains of the GGT1 dimer (Heisterkamp et al. 2008, Aoyama & Nakaki 2013).
R-HSA-4085011 Defective GNE causes sialuria, NK and IBM2 Sialuria (MIM:269921) is caused by a metabolic defect where the UDP?N?acetylglucosamine 2?epimerase, N?acetylmannosamine kinase (GNE) gene lacks feedback inhibition resulting in constitutive overproduction of free sialic acid (Neu5Ac) (Montreuil et al. 1968, Fontaine et al. 1968). Sialuria is characterised by a large cytoplasmic accumulation and urinary excretion of Neu5Ac (Kamerling et al. 1979). Sialurias differ from sialidoses, in which there is storage and excretion of 'bound' Neu5Ac. Defects in GNE also cause Nonaka myopathy (NK; MIM:605820), an early adult-onset disorder characterised by muscle weakness and wasting of distal muscles, especially the anterior tibial muscles (Nonaka et al. 1981, Asaka et al. 2001). Defects in GNE also cause inclusion body myopathy 2 (IBM2; MIM:600737), an autosomal recessive disorder with a similar phenotype to Nonaka myopathy (NK). IBM2 is an adult-onset, proximal and distal muscle weakness and wasting disorder. Muscle biospsy reveals from sufferers shows a rimmed vacuole myopathy and the degenerating muscle fibers contained abnormal amounts of beta-amyloid protein such as that found in neurodegenerative diorders. However, there is no neurological symptoms in these patients (Argov & Yarom 1984).
R-HSA-5579006 Defective GSS causes GSS deficiency In mammalian cells, many antioxidant defence systems exist which protect cells from subsequent exposure to oxidant stresses. One antioxidant is glutathione (GSH), a tripeptide present in virtually all cells that regulates the intracellular redox state and protects cells from oxidative injury. It is metabolised via the gamma-glutamyl cycle, which is catalysed by six enzymes. In man, hereditary deficiencies have been found in five of the six enzymes. Glutathione synthetase deficiency is the most frequently recognised disorder. Defects in GSS can cause glutathione synthetase deficiency (GSSD aka 5-oxoprolinase deficiency, MIM:266130), a severe autosomal recessive disorder characterised by an increased rate of haemolysis, 5-oxoprolinuria, CNS damage and recurrent bacterial infections. In this condition, decreased levels of cellular glutathione result in overstimulation of gamma-glutamylcysteine synthesis and its subsequent conversion to 5-oxoproline. Glutathione synthetase deficiency can be classed as mild, moderate or severe (Ristoff & Larsson 2007, Aoyama & Nakaki 2013).
R-HSA-9704331 Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function Mutations in the N-terminal coiled-coil domain of PALB2 (amino acids 9-44), involved in self-interaction and BRCA1 binding, impair the interaction of PALB2 with BRCA1 (Sy et al. 2009, Foo et al. 2017, Boonen et al. 2020). Phosphorylation of PALB2 by ATR on serine residue S59 promotes BRCA1-PALB2 interaction and the localization of PALB2 to DNA damage sites (Buisson et al. 2017). Mutations in the coiled-coil domain can also affect PALB2 self-interaction, recruitment to double-strand break sites, homologous recombination repair, and RAD51 foci formation (Buisson and Masson 2012). PALB2 missense mutants that do not bind to BRCA1 can still be recruited to DNA double-strand break repair (DSBR) sites, probably through interaction with other proteins involved in DSBR, but they are unable to restore efficient gene conversion in PALB2-deficient cells and they render cells hypersensitive to the DNA damaging agent mitomycin C (Sy et al. 2009). Some variants in this region are also sensitive to PARP inhibitors (Foo et al. 2017).
R-HSA-9704646 Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function Mutations affecting the C-terminal WD40 domain of PALB2 (amino acids 853-1186) impair its ability to interact with BRCA2, RAD51 and/or RAD51C (Erkko et al. 2007, Park et al. 2014). In addition, disruption of the WD40 domain can lead to the exposure of the nuclear export signal (NES) and cytoplasmic translocation of PALB2 (Pauty et al. 2017). Mutations affecting the C-terminal domain of PALB2 are more frequent than mutations that affect the N-terminus and have been observed, as germline mutations, in familial breast cancer and in Fanconi anemia, but somatic mutations also occur in sporadic cancers. Cells that express PALB2 mutants defective in BRCA2, RAD51 and/or RAD51C binding show reduced ability to perform DSBR via homologous recombination repair, form fewer RAD51 foci at DSBR sites, and are sensitive to DNA crosslinking agents such as mitomycin C (Erkko et al. 2007, Park et al. 2014).
R-HSA-3656234 Defective HEXA causes GM2G1 Beta-hexosaminidase (HEX) cleaves the terminal N-acetyl galactosamine (GalNAc) from glycosaminoglycans (GAGs) and any other molecules containing a terminal GalNAc. There are two forms of HEX; HEXA and B. The A form is a trimer of the subunits alpha, beta A and beta B. The B form is a tetramer of 2 beta A and 2 beta B subunits (O'Dowd et al. 1988). Defects in the two subunits cause lysosomal storage diseases marked by the accumulation of GM2 gangliosides in neuronal cells. Defects in the alpha subunits are the cause of GM2-gangliosidosis type 1 (GM2G1) (MIM:272800), also known as Tay-Sachs disease (Okada & O'Brien 1969, Nakano et al. 1988). Classical Tay-Sachs disease is characterised by infant-onset neurodegeneration followed by paralysis, dementia and blindness, Death occurs by the age of 2 or 3 (Okada et al. 1971). The two other forms of Tay-Sachs disease, juvenile- and adult-onset, are less commom and severe than the infant-onset form (Suzuki et al. 1970, Johnson et al. 1982).
R-HSA-3656248 Defective HEXB causes GM2G2 Beta-hexosaminidase (HEX) cleaves the terminal N-acetyl galactosamine (GalNAc) from glycosaminoglycans (GAGs) and any other molecules containing a terminal GalNAc. There are two forms of HEX; HEXA and B. The A form is a trimer of the subunits alpha, beta A and beta B. The B form is a tetramer of 2 beta A and 2 beta B subunits (O'Dowd et al. 1988). Defects in the two subunits cause lysosomal storage diseases marked by the accumulation of GM2 gangliosides in neuronal cells.
Defects in the beta subunits are the cause of GM2-gangliosidosis type 2 (GM2G2; MIM:268800), also known as Sandhoff disease (Sandhoff et al. 1968, Banerjee et al. 1991). Sandhoff disease is an autosomal recessive lysosomal storage disease clinically indistinguishable from GM2-gangliosidosis type 1, presenting early blindness with cherry-red spots on the macula, progressive motor and mental deterioration and macrocephaly. Death usually occurs by the age of 3 years.
R-HSA-5619056 Defective HK1 causes hexokinase deficiency (HK deficiency) Cytosolic hexokinase 1 (HK1), together with isoforms HK2 and 3 and glucokinase (GCK), catalyse the irreversible reaction of alpha-D-glucose (Glc) and ATP to form alpha-D-glucose-6-phosphate (G6P) and ADP, the first step in glycolysis. HK1 is the predominant isoform of the different HKs in tissues that utilise glucose for their physiological function such as brain, lymphocytes, erythrocytes, platelets and fibroblasts. Defects in HK1 can cause hexokinase deficiency (HK deficiency; MIM:235700), a rare, autosomal recessive disease with nonspherocytic hemolytic anemia as the predominant clinical feature (Kanno 2000).
R-HSA-3371599 Defective HLCS causes multiple carboxylase deficiency Defects in HLCS causes holocarboxylase synthetase deficiency (HLCS deficiency aka early onset multiple carboxylase deficiency; MIM:253270). HLCS deficiency is an autosomal recessive disorder whereby deficient HLCS activity results in reduced activity of all five biotin-dependent carboxylases. Symptoms include metabolic acidosis, organic aciduria, lethargy, hypotonia, convulsions and dermatitis (Suzuki et al. 2005). Patients can present symptoms shortly after birth to up to early childhood and will be prescribed oral biotin supplements, typically 10-20 mg daily. Two classes of HLCS deficiency have been reported depending on whether patients respond to biotin therapy. Most patients respond favourably to treatment and show complete reversal of biochemical and clinical symptoms (Morrone et al. 2002, Dupuis et al. 1999). Here mutations in the HLCS active site cause a reduced affinity for biotin that can be overcome by pharmacological doses of the vitamin (Pendini et al. 2008). Patients who display incomplete responsiveness to biotin therapy have a poor long-term prognosis (Bailey et al. 2008). Here mutations that reside outside of the enzyme's active site have no effect on biotin binding but do compromise the protein-protein interaction between the HLCS and its substrates, resulting in reduced biotinylation of all five carboxylases thus reducing their enzymatic activity (Mayende et al. 2012).
R-HSA-9734281 Defective HPRT1 disrupts guanine and hypoxanthine salvage Normally in humans, guanine and hypoxanthine can be salvaged by conversion to GMP and IMP, catalyzed by HPRT1 (hypoxanthine guanine phosphoribosyltransferase). In the absence of HPRT1 activity, however, accumulated guanine and hypoxanthine are catabolized by XDH (xanthine dehydrogenase / oxidase) to urate (Fu & Jinnah 2012).
R-HSA-9670621 Defective Inhibition of DNA Recombination at Telomere ATRX (Alpha thalassemia mental retardation X-lined) and DAXX (Death domain-associated protein 6) chromatin remodeling factors form a complex that binds to subtelomeric regions and plays a role in inhibition of DNA recombination at telomere ends, probably by mediating loading of H3F3A histone at telomere ends and by repressing transcription of TERRA (Telomeric repeat containing RNA), a long noncoding telomeric repeats-containing RNA. Tumors positive for alternative lengthening of telomeres (ALT) markers often harbor loss-of-function mutations in ATRX, and more rarely in DAXX or missense mutations in H3F3A, implying that the impairment of function of one of these three proteins may contribute to initiation of the ALT process. Additionally, mutations in IDH, the tumor suppressor TP53 and SMARCAL1 are also observed in the context of ALT in certain types of human cancers, particularly sarcomas and tumors of the central nervous system (Jiao et al. 2012, Nicolle et al. 2019). For review, please refer to Gocha et al. 2013, Pickett and Reddel 2015, Amorim et al. 2016).
R-HSA-9670615 Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations Many tumors that are positive for markers of alternative lengthening of telomeres (ALT) harbor loss-of-function mutations in the ATRX gene, encoding a chromatin remodeling protein ATRX. ATRX is thought to act together with DAXX and histone H3F3A to inhibit DNA recombination at telomere ends. For review, please refer to Heaphy et al. 2011, Gocha et al. 2014, Pickett and Reddel 2015, Amorim et al. 2016.
R-HSA-9670613 Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations A small portion of tumors that are positive for alternative lengthening of telomeres (ALT) markers and negative for mutations in the ATRX gene harbor loss-of-function mutations in the DAXX gene, which encodes the ATRX binding partner DAXX. For review, please refer to Gocha et al. 2013, and Pickett and Reddel 2015.
R-HSA-9734009 Defective Intrinsic Pathway for Apoptosis Defects in the regulation of the intrinsic pathway for apoptosis are involved in diseases associated with increased cell loss, such as neurodegenerative diseases, as well as in diseases associated with impaired elimination of harmful cells, such as cancer and autoimmunity. For review, please refer to Reed 2001, Lavrik et al. 2009, and Tuzlak et al. 2016.
So far, Reactome has annotated apoptosis defects associated with the loss of function of the CDKN2A gene product p14ARF in cancer, loss of function of TP53 in cancer, and CDK5 dysregulation in neurodegenerative diseases.
R-HSA-9645722 Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function Cancer-derived missense mutations in the CDKN2A gene that affect the C-terminal arginine-rich region of p14ARF (also known as CDKN2A transcription isoform 4, CDKN2A-4, p14 or ARF) impair p14ARF binding to the mitochondrial matrix protein C1QBP and interfere with p53-mediated apoptosis. Many mutations in the CDKN2A locus that affect C-terminal arginines of p14ARF are silent in p16INK4A (CDKN2A-1) (Itahana and Zhang 2008).
R-HSA-5083627 Defective LARGE causes MDDGA6 and MDDGB6 Glycosyltransferase-like protein LARGE (MIM:603590) is a bifunctional glycosyltransferase with both xylosyltransferase and beta-1,3-glucuronyltransferase activities involved in the biosynthesis of a phosphorylated O-mannosyl trisaccharide, a structure present in alpha-dystroglycan (DAG1; MIM:128239) which plays a key role in skeletal muscle function and regeneration. LARGE contains two substrate-specific GT-domains and belongs to the CAZy glycosyltransferase families GT8 and GT49. Defects in LARGE result in hypoglycosylation of DAG1 and cause several congenital muscular dystrophies (CMDs). Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A6 (MDDGA6; MIM:613154) is associated with brain anomalies, eye malformations, profound mental retardation, and death usually in the first years of life (Clement et al. 2008, Mercuri et al. 2009). Muscular dystrophy-dystroglycanopathy congenital with mental retardation B6 (MDDGB6; MIM:608840) is associated with profound mental retardation, white matter changes and structural brain abnormalities (Longman et al. 2003).
R-HSA-5083630 Defective LFNG causes SCDO3 The Fringe family (CAZy family GT31) of glycosyltransferases in mammals includes LFNG (lunatic fringe; MIM:602576), MFNG (manic fringe; MIM:602577) and RFNG (radical fringe; MIM:602578). Fringe enzymes function in the Golgi apparatus where they initiate the elongation of O-linked fucose on fucosylated peptides by the addition of a beta 1,3 N-acetylglucosaminyl group (GlcNAc) (Moloney et al. 2000). Fringe enzymes elongate conserved O fucosyl residues conjugated to EGF repeats of NOTCH, modulating NOTCH activity (Cohen et al. 1997, Johnston et al. 1997) by decreasing the affinity of NOTCH extracellular domain for JAG ligands (Bruckner et al. 2000).
The spondylocostal dysostoses (SCDs) are a group of disorders that arise during embryonic development by a disruption of somitogenesis. The Notch signalling pathway is essential for somitogenesis, the precursors of vertebra and associated musculature. Defects in one of the Fringe enzymes, beta-1,3-N-acetylglucosaminyltransferase lunatic fringe (LFNG), can cause spondylocostal dysostosis, autosomal recessive 3 (SCDO3, MIM:609813), a condition of variable severity associated with vertebral and rib segmentation defects (Sparrow et al. 2006).
R-HSA-4793950 Defective MAN1B1 causes MRT15 Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (MAN1B1) normally trims single mannose residues from misfolded glycoproteins, targeting them for degradation and thus providing a quality control process for N-glycoyslated proteins. Defects in MAN1B1 can cause mental retardation, autosomal recessive 15 (MRT15; MIM:614202), a disorder resulting in nonsyndromic moderate to severe mental retardation. It is characterised by significantly below average intellectual functioning associated with impaired adaptative behaviour during the developmental period (Rafiq et al. 2010, Rafiq et al. 2011).
R-HSA-5579012 Defective MAOA causes BRUNS Amine oxidase (flavin-containing) A (MAOA) catalyses the oxidative deamination of biogenic and dietary amines, the regulation of which is critical for mental state homeostasis. MAOA, located on the mitochondrial outer membrane and requiring FAD as cofactor (Weyler 1989), preferentially oxidises biogenic amines such as 5-hydroxytryptamine (5HT), dopamine, noradrenaline and adrenaline. Defects in MAOA can cause Brunner syndrome (BRUNS; MIM:300615), a form of X-linked non-dysmorphic mild mental retardation. Male patients are affected by mild mental retardation and exhibit abnormal behaviour, including impulsive aggression (Brunner et al. 1993, Shih et al. 1999, Shih 2004).
R-HSA-5579024 Defective MAT1A causes MATD S-adenosylmethionine (AdoMet, SAM) is an important methyl donor in most transmethylation reactions. S-adenosylmethionine synthase isoform type-1 (MAT1A) catalyses the formation of AdoMet from methionine and ATP. Defects in MAT1A can cause methionine adenosyltransferase deficiency (MATD; MIM:250850), an inborn error of metabolism resulting in hypermethioninemia. In this condition, methionine accumulates because its conversion to AdoMet is impaired (Furujo et al. 2012, Mudd 2011).
R-HSA-4793952 Defective MGAT2 causes CDG-2a Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (MGAT2) normally catalyses the transfer of a GlcNAc moiety onto the alpha-1,6 mannose of an alpha-1,4 branch of oligomannose N-glycans to form complex N-glycans (Tan et al. 1995). Defects in MGAT2 are associated with congenital disorder of glycosylation type IIa (MGAT2-CDG, CDG-2a; MIM:212066), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins (Tan et al. 1996, Cormier-Daire et al. 2000, Alkuraya 2010, Alazami et al. 2012). Type II CDGs refer to defects in the trimming and processing of protein-bound glycans.
R-HSA-3359475 Defective MMAA causes MMA, cblA type Defects in MMAA cause methylmalonic aciduria type cblA (cblA aka methylmalonic aciduria type A or vitamin B12-responsive methylmalonic aciduria of cblA complementation type; MIM:251100). Affected individuals accumulate methylmalonic acid in the blood and urine and are prone to potentially life threatening acidotic crises in infancy or early childhood (Dobson et al. 2002, Lerner-Ellis et al. 2004).
R-HSA-3359471 Defective MMAB causes MMA, cblB type Defects in MMAB cause methylmalonic aciduria type cblB (cblB aka methylmalonic aciduria type B or vitamin B12 responsive methylmalonicaciduria of cblB complementation type; MIM:251110). Affected individuals have methylmalonic aciduria and episodes of metabolic ketoacidosis, despite a functional methylmalonyl CoA mutase. In severe cases, newborns become severely acidotic and may die if acidosis is not treated promptly (Dobson et al. 2002).
R-HSA-3359474 Defective MMACHC causes MAHCC Defects in MMACHC cause methylmalonic aciduria and homocystinuria type cblC (MMAHCC; MIM:277400). MMAHCC is the most common disorder of cobalamin metabolism and is characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl). Affected individuals may have developmental, haematologic, neurologic, metabolic, ophthalmologic, and dermatologic clinical findings (Lerner-Ellis et al. 2006).
R-HSA-3359473 Defective MMADHC causes MMAHCD Defects in MMADHC cause methylmalonic aciduria and homocystinuria type cblD (MMAHCD; MIM:277410), a disorder of cobalamin metabolism characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl) (Coelho et al. 2008).
R-HSA-4793954 Defective MOGS causes CDG-2b After the lipid-linked oligosaccharide (LLO) precursor is attached to the protein, the outer alpha-1,2-linked glucose is removed by by mannosyl-oligosaccharide glucosidase (MOGS). This is a mandatory step for protein folding control and glycan extension. Defects in MOGS are associated with congenital disorder of glycosylation type IIb (CDGIIb), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins (De Praeter et al. 2000, Voelker et al. 2002). Type II CDGs refer to defects in the trimming and processing of protein-bound glycans.
R-HSA-4687000 Defective MPDU1 causes CDG-1f Mannose-P-dolichol utilisation defect 1 protein (MPDU1) is required for the efficient utilisation of the mannose donor dolichyl-phospho-mannose (DOLPman) in the synthesis of both lipid-linked oligosaccharides (LLOs) and glycosylphosphatidylinositols. Defects in MPDU1 can cause congenital disorder of glycosylation 1f (MPDU1-CDG, CDG-1f; MIM:609180), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins. CDG type 1 diseases result in a wide phenotypic spectrum, such as poor neurological development, psychomotor retardation, dysmorphic features, hypotonia, coagulation abnormalities and immunodeficiency. In this condition, DOLPman is no longer utilised in transferase reactions extending LLOs, even as substrate levels and transferase enzyme activities appear normal (Anand et al. 2001, Schenk et al. 2001).
R-HSA-4043916 Defective MPI causes MPI-CDG Mannose 6-phosphate isomerase (MPI) normally isomerises fructose 6-phosphate (Fru6P) to mannose 6-phosphate (Man6P) in the cytosol. Man6P is a precursor in the synthesis of GDP-mannose and dolichol-phosphate-mannose, required for mannosyl transfer reactions in the N-glycosylation of proteins. Defects in MPI cause congenital disorder of glycosylation 1b (MPI-CDG, previously known as CDG1b,; MIM:602579), a multisystem disorder characterised by under-glycosylated serum glycoproteins (Schollen et al. 2000). Unlike PMM2-CDG (CDG1a), there is no neurological involvement with MPI-CDG. Instead, patients present predominantly with diarrhoea, failure to thrive and protein-losing enteropathy (Pelletier et al. 1986). MPI-CDG is one of two CDGs that can be treated with oral mannose supplementation, but can be fatal if left untreated (Marquardt & Denecke 2003).
R-HSA-3359469 Defective MTR causes HMAG Defects in MTR cause methylcobalamin deficiency type G (cblG; MIM:250940), an autosomal recessive inherited disease that causes mental retardation, macrocytic anemia, and homocystinuria (Leclerc et al. 1996, Gulati et al. 1996, Watkins et al. 2002).
R-HSA-3359467 Defective MTRR causes HMAE Defects in MTRR cause methylcobalamin deficiency type E (cblE; methionine synthase reductase deficiency; MIM:236270) (Wilson et al. 1999). Patients with cblE exhibit megaloblastic anemia and hyperhomocysteinemia. SAM is used as a methyl donor in many biological reactions and demethylation of SAM produces S-adenosylhomocysteine, which is deadenosylated to form homocysteine. Homocysteine remethylation is carried out by MTR, which requires MTRR to maintain enzyme-bound cobalamin (Cbl) in its active form; but in cblE patients, MTR becomes inactivated and thus homocysteine accumulates.
R-HSA-3359478 Defective MUT causes MMAM Defects in MUT cause methylmalonic aciduria, mut type (MMAM; MIM:251000), an often fatal disorder of organic acid metabolism (Worgan et al. 2006).
R-HSA-9608287 Defective MUTYH substrate binding For a subset of MUTYH disease variants underlying MUTYH-associated polyposis (MAP), also known as familial adenomatous polyposis 2 (FAP2), it was shown that, in addition to impaired catalytic activity, they also exhibit reduced binding to their substrate, adenine mispaired with 8-oxoguanine (OGUA:Ade, also known as 8-oxoG:A). MUTYH alpha-3 isoform (MUTYH-3) mutants with demonstrated deficient binding to OGUA:Ade include missense variants MUTYH-3 Y165C, MUTYH-3 R227W, MUTYH-3 R231L, MUTYH-3 R231H, MUTYH-3 V232F, MUTYH-3 R260Q, MUTYH-3 P281L and MUTYH-3 G382D, nonsense variants MUTYH-3 Y90*, MUTYH-3 Q377*, MUTYH-3 E466*, and frameshift variant MUTYH-3 A368fs26* (commonly known as MUTYH 1103delC) (Chmiel et al. 2003, Parker et al. 2005, Ali et al. 2008, Molatore et al. 2010, D'Agostino et al. 2010).
R-HSA-9608290 Defective MUTYH substrate processing MUTYH disease variants underlying the MUTYH-associated polyposis (MAP), also known as familial adenomatous polyposis 2 (FAP2), show impaired catalytic activity with respect to cleaving adenine mispaired with 8-oxoguanine (OGUA:Ade, also known as 8-oxoG:A). For some of the mutants, defective substrate processing is further aggravated by reduced substrate binding. MUTYH alpha-3 isoform (MUTYH-3) mutants and MUTYH gamma-3 isoform (MUTYH-6) mutants with experimentally demonstrated deficiency in catalytic activity include missense mutants MUTYH-3 Y165C (MUTYH-6 Y151C), MUTYH-3 R171W, MUTYH-3 R227W, MUTYH-3 R231H, MUTYH-3 R231L, MUTYH-3 V232F, MUTYH-3 R260Q, MUTYH-3 G272E, MUTYH-3 P281L, MUTYH-3 P391L (MUTYH-6 P377L), MUTYH-3 Q324H, MUTYH-3 Q324R,, MUTYH-3 A359V, MUTYH-3 G382D (MUTYH-6 G368D), MUTYH-3 A459D, MUTYH-6 R154H, MUTYH-6 I195V, MUTYH-6 M255V and MUTYH-3 L360P, in-frame indel mutants MUTYH-3 W138_M139insIW (also known as MUTYH 137insIW) and MUTYH-3 E466del (MUTYH-6 E452del), nonsense mutants MUTYH-3 Y90*, MUTYH-3 Q377*, and MUTYH-3 E466*, and frameshift mutant MUTYH-3 A368fs26* (commonly known as MUTYH 1103delC) (Jones et al. 2002, Chmiel et al. 2003, Wooden et al. 2004, Parker et al. 2005, Bai et al. 2005, Alhopuro et al. 2005, Bai et al. 2007, Ali et al. 2008, Yanaru-Fujisawa et al. 2008, Kundu et al. 2009, Forsbring et al. 2009, Molatore et al. 2010, D'Agostino et al. 2010, Goto et al. 2010, Raetz et al. 2012, Shinmura et al. 2012).
R-HSA-5545483 Defective Mismatch Repair Associated With MLH1 The MLH1:PMS2 complex is homologous to the E. coli MutL gene and is involved in DNA mismatch repair. Heterozygous mutations in the MLH1 gene result in hereditary nonpolyposis colorectal cancer-2 (Papadopoulos et al., 1994).
R-HSA-5632928 Defective Mismatch Repair Associated With MSH2 MSH2 is homologous to the E. coli MutS gene and is involved in DNA mismatch repair (MMR) (Fishel et al., 1994). Heterozygous mutations in the MSH2 gene result in hereditary nonpolyposis colorectal cancer-1. Variants of MSH2 are associated with hereditary nonpolyposis colorectal cancer. Alteration of MSH2 is also involved in Muir-Torre syndrome and mismatch repair cancer syndrome.
R-HSA-5632927 Defective Mismatch Repair Associated With MSH3 MSH3 forms a heterodimer with MSH2 to form the MSH3:MSH2 complex, part of the post-replicative DNA mismatch repair system. This complex initiates mismatch repair by binding to a mismatch and then forming a complex with MutL alpha heterodimer. This gene contains a polymorphic 9 bp tandem repeat sequence in the first exon. Defects in this gene are a cause of susceptibility to endometrial cancer.
R-HSA-5632968 Defective Mismatch Repair Associated With MSH6 MSH6 encodes a G/T mismatch-binding protein encoded by a gene localized to within 1 megabase of the related hMSH2 gene on chromosome 2. Unlike other mismatch repair genes, the MSH6 deficient cells showed alterations primarily in mononucleotide tracts, indicating the role MSH6 plays in maintaining the integrity of the human genome. Cells deficient in MSH6, accrue mutations in tracts of repeated nucleotides. MSH6 defects seem to be less common than MLH1 and MSH2 defects. They have been mostly observed in atypical HNPCC families and are characterized by a weaker family history of tumor development, higher age at disease onset, and low degrees of microsatellite instability (MSI) that predominantly involving mononucleotide runs.
R-HSA-5632987 Defective Mismatch Repair Associated With PMS2 PMS2 heterodimerizes with MLH1 to form the MutL alpha complex involved in DNA mismatch repair. Mutations in this PMS2 are associated with hereditary nonpolyposis colorectal cancer, Turcot syndrome, and are a cause of supratentorial primitive neuroectodermal tumors. Heterozygous truncating mutations in PMS2 play a role in a small subset of hereditary nonpolyposis colorectal carcinoma (Lynch syndrome, HNPCC-like) families. PMS2 mutations lead to microsatellite instability with carriers showing a microsatellite instability high phenotype and loss of PMS2 protein expression in all tumors.
R-HSA-4341670 Defective NEU1 causes sialidosis Sialidases have important roles in the degradation of glycoconjugates by removing terminal sialic acid residues.
Defects in sialidase 1 (NEU1) cause sialidosis, a lysosomal storage disease characterised by the progressive lysosomal storage of sialidated glycopeptides and oligosaccharides and the accumulation and excretion of N-acetylneuraminic acid (Neu5Ac) covalently-linked ('bound') glycoconjugates (Lowden & O'Brien 1979). The sialidoses are distinct from the sialurias in which there is storage and excretion of 'free' Neu5Ac. Sialidosis manifests into types I and II forms. Type I is the milder form, also known as the 'normosomatic' type or the cherry red spot-myoclonus syndrome. Sialidosis type II is the more severe form with an earlier onset, and is also known as the 'dysmorphic' type.
R-HSA-9630222 Defective NTHL1 substrate binding Several different mutations that result in truncation of NTHL1 protein have been described and associated with cancer. NTHL1 Q90TER (NTHL1 Gln90*) truncation mutant results from a nonsense mutation that replaces codon for glutamine 90 with a STOP codon. NTHL1 Q90TER has not been studied at the protein level, but is predicted to lack the DNA binding domain and the glycosylase domain, thus resulting in a complete loss of the base excision repair (BER) related DNA glycosylase function. Homozygous or compound heterozygous germline NTHL1 Q90TER mutation result in a cancer syndrome (NTHL1 associated tumor syndrome) that involves adenomatous polyposis, colorectal cancer breast cancer and multiple other types of cancer and benign tumors (Weren et al. 2015, Rivera et al. 2015, Grolleman et al. 2019). Apart from NTHL1 Q90TER, at least seven other truncating variants have been identified in patients with NTHL1 associated tumor syndrome, such as NTHL1 A79fs (NTHL1 Ala79fs), NTHL1 Y130TER (NTHL1 Tyr130*), NTHL1 W182TER (NTHL1 Trp182*), NTHL1 c.709+1G>A, NTHL1 I245fs (NTHL1 Ile245fs), NTHL1 W269TER (NTHL1 Trp269*), NTHL1 Q287TER (NTHL1 Gln287*) (Rivera et al. 2015, Broderick et al. 2017, Grolleman et al. 2019).
R-HSA-9630221 Defective NTHL1 substrate processing NTHL1 D239Y is produced as a consequence of a single nucleotide polymorphism (SNP) rs3087468 in the NTHL1 gene. The frequency of this polymorphism varies in different populations. Substitution of aspartic acid residue at position 239 with tyrosine results in an NTHL1 protein that is still able to bind to damaged DNA but appears to have impaired glycosylase activity. Expression of NTHL1 D239Y in non-transformed human and mouse mammary epithelial cells increases genomic instability and leads to neoplastic transformation, acting as a dominant negative for wild-type NTHL1, through competition for substrate binding (Galick et al. 2013). It is uncertain if heterozygosity for NTHL1 D239Y polymorphism increases predisposition to cancer.
R-HSA-9657050 Defective OGG1 Localization OGG1 splicing isoform beta contains a mitochondrial targeting sequence at the N terminus and lacks the C terminal nuclear localization signal. OGG1beta localizes to mitochondria (Nishioka et al. 1999), where it might participate in the repair of mitochondrial DNA, although its role in mitochondrial base excision repair has not been confirmed. OGG1beta G12E mutant, reported in kidney cancer, is unable to translocate to the mitochondrion as the missense mutation disrupts the mitochondrial targeting sequence (Audebert et al. 2002).
R-HSA-9656255 Defective OGG1 Substrate Binding OGG1 missense mutants reported in Alzheimer's disease, OGG1 A53T and OGG1 A288V, show decreased binding to 8 oxoguanine substrate (Mao et al. 2007).
R-HSA-9656256 Defective OGG1 Substrate Processing The majority of OGG1 mutants have been tested for their ability to excise 8-oxoguanine (8oxoG) from damaged DNA, while a small number of mutants have been tested for the ability to remove FapyG from DNA.
The following OGG1 mutants show at least a partial loss of their ability to remove 8oxoG:
OGG1 R46Q (Audebert, Chevillard et al. 2000; Audebert, Radicella et al. 2000);
OGG1 R154H (Audebert, Radicella et al. 2000, Bruner et al. 2000);
OGG1 R131Q (Chevillard et al. 1998, Bruner et al. 2000, Anderson and Dagget 2009);
OGG1 R229Q (Hyun et al. 2000, Hyun et al. 2002, Hill and Evans 2007);
OGG1 P266fs139* (Mao et al. 2007).
OGG1 R46L and OGG1 R131G have not been functionally studied but have been reported in cancer and predicted to be pathogenic. They are annotated as candidate disease variants based on their similarity with OGG1 R46Q and OGG1 R131Q, respectively.
OGG1 S326C, a frequent variant in European and Asian populations, is susceptible to oxidation, which diminishes catalytic activity under conditions of oxidative stress (Dherin et al. 1999, Yamane et al. 2004, Kershaw and Hodges 2012, Moritz et al. 2014).
The following OGG1 mutants show at least a partial loss of their ability to remove FapyG:
OGG1 R46Q (Audebert, Radicella et al. 2000);
OGG1 R154H (Audebert, Radicella et al. 2000).
OGG1 R46L has not been functionally studied but has been reported in cancer and predicted to be pathogenic. It is annotated as a candidate disease variant for FapyG excision, based on its similarity with OGG1 R46Q.
R-HSA-5578998 Defective OPLAH causes OPLAHD The gamma-glutamyl cycle is a six-enzyme cycle that represents the primary pathway for glutathione synthesis and degradation. One step is the cleavage of 5-oxo-L-proline (OPRO) to form L-glutamate, coupled to the hydrolysis of ATP. This is catalysed by 5-oxoprolinase (OPLAH) is a homodimeric, cytosolic protein. Defects in OPLAH can cause 5-oxoprolinase deficiency (OPLAHD; MIM:260005), an extremely rare disorder of the gamma-glutamyl cycle about which debate continues as to whether it is a disorder or just a biochemical condition with no adverse clinical effects apart from 5-oxoprolinuria (Calpena et al. 2013, Almaghlouth et al. 2012, Aoyama & Nakaki 2013).
R-HSA-3560796 Defective PAPSS2 causes SEMD-PA Defects in PAPSS2 cause spondyloepimetaphyseal dysplasia Pakistani type (SEMD-PA; MIM:612847), a bone disease characterized by epiphyseal dysplasia with mild metaphyseal abnormalities. Clinical features include short stature from birth, short and bowed lower limbs, mild brachydactyly, kyphoscoliosis, abnormal gait and enlarged knee joints. Some patients may manifest premature pubarche and hyperandrogenism (Ahmed et al. 1998, Noordam et al. 2009, Miyake et al. 2012).
R-HSA-5609974 Defective PGM1 causes PGM1-CDG Phosphoglucomutases 1 and 2 (PGM1, 2) are involved in the cytosolic biosynthesis of nucleotide sugars needed for glycan biosynthesis, specifically, the isomerisation of glucose-6-phosphate (G6P) into glucose-1-phosphate (G1P). Defects in PGM1 can cause congenital disorder of glycosylation 1t (CDG1t, now known as PGM1-CDG; MIM:614921), a broad spectrum disorder characterised by under-glycosylated serum glycoproteins (Timal et al. 2012, Tegtmeyer et al. 2014). CDGs result in a wide variety of clinical features such as defects in nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency.
R-HSA-4043911 Defective PMM2 causes PMM2-CDG Phosphomannomutase 2 (PMM2) normally catalyses the isomerisation of mannose 6-phosphate (Man6P) to mannose 1-phosphate (Man1P) in the cytosol of cells. Man1P is a precursor in the synthesis of GDP-mannose and dolichol-phosphate-mannose, required for critical mannosyl transfer reactions in the N-glycosylation of proteins. Mutations in the PMM2 gene are one of the causes of Jaeken syndrome, a congenital disorder of glycosylation type 1a (PMM2-CDG, previously CDG-1a) (Matthijs et al. 1997). PMM2-CDG was first described in Belgian identical twin sisters, characterized by psychomotor retardation and multiple serum glycoprotein abnormalities. Serum and CSF transferrin were found to be deficient in sialic acid (Jaeken et al. 1984). PMM2-CDG is the most common CDG disease subtype.
R-HSA-9735763 Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine Normally in humans, PNP (purine nucleotide phosphorylase) catalyzes the conversion of (deoxy)guanosine and (deoxy)inosine to guanine and hypoxanthine, respectively. In the absence of PNP activity, however, these purine nucleosides accumulate, disrupting lymphoid cell function and leading to severe immunodeficiency (Aust et al. 1992; Williams et al. 1987).
R-HSA-5083628 Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (POMGNT1; CAZy family GT61; MIM:606822) mediates the transfer of N-acetylglucosaminyl (GlcNAc) residues to mannosylated proteins such as mannose-O-serine-dystroglycan (man-O-Ser-DAG1). DAG1 is a cell surface protein that plays an important role in the assembly of the extracellular matrix in muscle, brain, and peripheral nerves by linking the basal lamina to cytoskeletal proteins. Defects in POMGNT1 (MIM:606822) result in disrupted glycosylation of DAG1 and can cause severe congenital muscular dystrophy-dystroglycanopathies ranging from a severe type A3 (MDDGA3; MIM:253280), through a less severe type B3 (MDDGB3; MIM:613151) to a milder type C3 (MDDGC3; MIM:613157) (Bertini et al. 2011, Wells 2013).
R-HSA-5083633 Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 Co-expression of both protein O-mannosyl-transferases 1 and 2 (POMT1 and POMT2; CAZy family GT39) is necessary for enzyme activity, that is mediating the transfer of mannosyl residues to the hydroxyl group of serine or threonine residues of proteins such as alpha-dystroglycan (DAG1; MIM:128239). DAG1 is a cell surface protein that plays an important role in the assembly of the extracellular matrix in muscle, brain, and peripheral nerves by linking the basal lamina to cytoskeletal proteins. Defects in POMT1 (MIM:607423) results in defective glycosylation of DAG1 and can cause severe congenital muscular dystrophy-dystroglycanopathies ranging from a severe type A, MDDGA1 (brain and eye abnormalities; MIM:236670), through a less severe type B, MDDGB1 (congenital form with mental retardation; MIM:613155) to a milder type C, MDDGC1 (limb girdle form; MIM:609308) (Bertini et al. 2011, Wells 2013).
R-HSA-5083629 Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 Co-expression of both protein O-mannosyl-transferases 1 and 2 (POMT1 and POMT2; CAZy family GT39) is necessary for enzyme activity, that is mediating the transfer of mannosyl residues to the hydroxyl group of serine or threonine residues of proteins such as alpha-dystroglycan (DAG1; MIM:128239). DAG1 is a cell surface protein that plays an important role in the assembly of the extracellular matrix in muscle, brain, and peripheral nerves by linking the basal lamina to cytoskeletal proteins. Defects in POMT2 (MIM:607439) results in defective glycosylation of DAG1 and can cause severe congenital muscular dystrophy dystroglycanopathies ranging from a severe type A, MDDGA2 (brain and eye abnormalities; MIM:613150), through a less severe type B, MDDGB2 (congenital form with mental retardation; MIM:613156) to a milder type C, MDDGC2 (limb girdle form; MIM:603158) (Bertini et al. 2011, Wells 2013).
R-HSA-4570571 Defective RFT1 causes CDG-1n The N-glycan precursor is flipped across the ER membrane, moving it from the cytosolic side to the ER lumenal side. The exact mechanism of this translocation is not well understood but protein RFT1 homolog (RFT1) is known to be involved (Helenius et al. 2002). Defects in RFT1 are associated with congenital disorder of glycosylation 1n (RFT1-CDG, CDG-1n). The disease is a multi-system disorder characterised by under-glycosylated serum glycoproteins. Early-onset developmental retardation, dysmorphic features, hypotonia, coagulation disorders and immunodeficiency are reported features of this disorder (Haeuptle et al. 2008).
R-HSA-5619042 Defective RHAG causes regulator type Rh-null hemolytic anemia (RHN) Rhesus (Rh) blood group antigens consist of several membrane-associated polypeptides including RHAG, which is required for cell-surface expression of the complex. The Rh(null) phenotype arises from missing or severely deficient Rh antigens and sufferers present a clinical syndrome of varying severity characterised by abnormalities of red cell shape, cation transport and membrane phospholipid organisation. The human gene RHAG encodes a Rhesus blood group family type A glycoprotein (belonging to the SLC42 solute transporter family) which is expressed specifically in erythroid cells. A transport function for RHAG is suggested to mediate ammonium (NH4+) export from these cells and prevent toxic build-up of NH3/NH4+ (Westhoff et al. 2002, Ripoche et al. 2004). Defects in RHAG are the cause of regulator type Rh-null hemolytic anemia (RHN, Rh-deficiency syndrome). RHN is a form of chronic hemolytic anemia (Huang & Ye 2010).
R-HSA-9693928 Defective RIPK1-mediated regulated necrosis Receptor Interacting Serine/Threonine Kinase 1 (RIPK1)-mediated regulated necrosis also called necroptosis is an important type of programmed cell death in addition to apoptosis. Necroptosis eventually leads to cell lysis and release of cytoplasmic content into the extracellular region. Necroptosis must be tightly controlled. Disregulated or defective necroptotic cell death is often associated with a tissue damage resulting in an intense inflammatory response. Defects of necroptosis may contribute to various pathological processes, including autoimmune disease, neurodegeneration, multiple cancers, and kidney injury.
R-HSA-9657689 Defective SERPING1 causes hereditary angioedema The reciprocal activation is initiated when zymogen factor XII (F12 or FXII) binds to a negatively charged surface, which induces FXII autoactivation. Activated FXII (FXIIa) converts prekallikrein (PK) to kallikrein, which proteolytically liberates bradykinin from high molecular weight kininogen (HK) (Renne T 2012; Renne T et al. 2012; Maas C et al. 2011). Kallikrein also activates FXII to produce more FXIIa (initially). FXIIa and kallikrein reciprocally activate their zymogens and thus generate a positive feedback loop. In the presence of sufficient amounts of active enzyme, FXIIa also generates active factor XI (FXIa) to potentiate the intrinsic coagulation pathway. All of these enzymatic steps are normally inhibited by C1-esterase inhibitor (C1-INH, encoded by the SERPING1 gene).
Binding of the proinflammatory peptide hormone bradykinin to the bradykinin B2 receptor (B2R) activates various proinflammatory signaling pathways that increase vascular permeability and fluid efflux. An excessive formation of bradykinin due to uncontrolled activation of the coagulation factor XII (FXII)-dependent kallikrein-kinin system causes increased vascular permeability at the level of the postcapillary venule and results in hereditary angioedema (HAE) (Bossi F et al. 2009; Kaplan AP 2010; Suffritti C et al. 2014: Zuraw BL & Christiansen SC 2016). HAE is a rare life-threatening inherited edema disorder that is characterized by recurrent episodes of localized edema of the skin or of the mucosa of the gastrointestinal tract or upper airway. Angioedema initiated by bradykinin is usually associated with SERPING1 (C1-INH) deficiency. Thus, a major role of SERPING1 (C1-INH) is to prevent the development of excessive vascular permeability. More rarely, HAE occurs in individuals with normal SERPING1 activity, linked to mutations in other proteins, including FXII, plasminogen, and angiopoietin (Magerl M et al. 2017; Zuraw BL 2018; Ivanov I et al. 2019). Patients with HAE are heterozygous for deficiency of SERPING1.The disease, therefore, has an autosomal dominant inheritance and may result from lack of expression of SERPING1 from one allele (type 1 HAE) or from expression of a nonfunctional SERPING1 protein (type 2 HAE). This classification has however been challenged by observations of intermediary HAE types, that can arise, when small amounts of dysfunctional SERPING1 is present in the blood stream (Eldering E et al. 1995; Verpy E et al. 1995; Madsen DE et al. 2014).
R-HSA-5687868 Defective SFTPA2 causes IPF One function of the pulmonary collectins, surfactant proteins A1, A2, A3 and D (SFTPAs, D), is that they influence surfactant homeostasis, contributing to the physical structures of lipids in the alveoli and to the regulation of surfactant function and metabolism. They are directly secreted from alveolar type II cells into the airway to function as part of the surfactant. The mechanism of secretion is unknown. Mutations in SFTPA2 disrupt protein structure and the defective protein is retained in the ER membrane causing idiopathic pulmonary fibrosis (IPF; MIM:178500). IPF is one of a family of idiopathic pneumonias sharing clinical features of shortness of breath, formation of scar tissue and varying degrees of inflammation and/or fibrosis on lung biopsy. IPF is typically progressive, leading to death from respiratory failure within 2-5 years of diagnosis in the majority of instances (Meltzer & Noble 2008, Noble & Barkauskas 2012).
R-HSA-5619048 Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) The primary site for absorption of dietary iron is the duodenum. Ferrous iron (Fe2+) is taken up from the gut lumen across the apical membranes of enterocytes and released into the portal vein circulation across basolateral membranes. The human gene SLC11A2 encodes the divalent cation transporter DCT1 (NRAMP2, Natural resistance-associated macrophage protein 2). DCT1 resides on the apical membrane of enterocytes and mediates the uptake of many metal ions, particularly ferrous iron, into these cells. Defects in SLC11A2 can cause hypochromic microcytic anemia, with iron overload 1 (AHMIO1; MIM:206100), a blood disorder characterised by high serum iron, large hepatic iron deposition, abnormal haemoglobin content in erythrocytes which are reduced in size and absence of sideroblasts and stainable bone marrow iron store (Shawki et al. 2012, Iolascon & De Falco 2009).
R-HSA-5619104 Defective SLC12A1 causes Bartter syndrome 1 (BS1) The solute carrier family 12 member 1 (SLC12A1, NKCC2) is a kidney-specific, membrane-bound protein that cotransports two Cl- ions electroneutrally into cells with a Na+ ion and a K+ ion and plays a vital role in the regulation of ionic balance and cell volume. Defects in SLC12A1 can cause Bartter’s syndrome (BS1; MIM:601678), an autosomal-recessive disease salt-wasting disorder characterised by renal tubular hypokalaemia, metabolic alkalosis and hypercalciuria. Clinical features present in infancy and include muscle weakness, anorexia, polydipsia, polyuria, failure to thrive and mental and growth retardation (Favero et al. 2011, Gagnon & Delpire 2013).
R-HSA-5619087 Defective SLC12A3 causes Gitelman syndrome (GS) The SLC12A3 gene encodes for the Thiazide-sensitive sodium-chloride cotransporter (TSC). TSC mediates sodium and chloride removal from the distal convoluted tubule of the kidney. Defects in SLC12A3 are the cause of Gitelman syndrome (GS aka familial hypokalemic hypomagnesemia; MIM:263800). GS is an autosomal recessive disorder characterised by hypokalemic metabolic alkalosis, hypomagnesemia, and hypocalciuria. Patients can present with periods of muscular weakness and tetany, usually accompanied by abdominal pain, vomiting and fever. GS has overlapping features with Bartter syndrome (caused by defects in SLC12A1). This cotransporter is the major target for thiazide-type diuretics, used in the treatment of hypertension, extracellular fluid overload and renal stone disease (Nakhoul et al. 2012).
R-HSA-5619039 Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) K+/Cl- cotransport is implicated not only in regulatory volume decrease, but also in transepithelial salt absorption, renal K+ secretion, myocardial K+ loss during ischemia and regulation of neuronal Cl- concentration. Four genes (SLC12A4-7) encode the K+/Cl- cotransporters KCC1-4 respectively. Cotransport of K+ and Cl- is electroneutral with a 1:1 stoichiometry. These cotransporters function as homomultimers or heteromultimers with other K+/Cl- cotransporters. SLC12A6 encodes KCC3 which is highly expressed in heart, brain, spinal cord, kidney, muscle, pancreas and placenta. Defects in SLC12A6 are a cause of agenesis of the corpus callosum with peripheral neuropathy (ACCPN; MIM:218000), a autosomal recessive disease characterised by severe progressive sensorimotor neuropathy, mental retardation, dysmorphic features and variable degree of agenesis of the corpus callosum (Howard et al. 2002, Dupre et al. 2003, Salin-Cantegrel et al. 2011).
R-HSA-5619070 Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) Four members of the SLC16A gene family encode classical monocarboxylate transporters MCT1-4. Widely expressed, they all function as proton-dependent transporters of monocarboxylic acids such as lactate and pyruvate and ketone bodies such as acetacetate and beta-hydroxybutyrate. These processes are crucial in the regulation of energy metabolism and acid-base homeostasis.
SLC16A1 encodes MCT1, a ubiquitiously expressed protein. Heterozygous defects in SLC16A1 were found in patients with symptomatic deficiency in lactate transport (SDLT aka erythrocyte lactate transporter defect; MIM:245340), resulting in an acidic intracellular environment and muscle degeneration with the release of myoglobin and creatine kinase (Merezhinskaya et al. 2000). This defect could compromise extreme performance in otherwise healthy individuals.
SLC16A1 is essential for lactate transport in muscle cells. It is also highly enriched in astrocytes and oligodendroglia, neuroglia that support, insulate and provide energy metabolites to axons. Oligodendroglia dysfunction can lead to axon degeneration in several diseases. The cause is unknown but disruption of SLC16A1 transporter produces axon damage and neuron loss in animal and cell culture models. In humans, this transporter is reduced in patients with amyotrophic lateral sclerosis (Lee et al. 2012).
In cancer cells, a common change is the upregulation of glycolysis. The anti-cancer drug candidate 3-bromopyruvate (3-BrPA) can inhibit glycolysis through its uptake into cancer cells via SLC16A1 so it is the main determinant of 3-BrPA sensitivity in these cells (Birsoy et al. 2013).
R-HSA-5619035 Defective SLC17A5 causes Salla disease (SD) and ISSD SLC17A5 encodes a lysosomal sialic acid transporter, sialin (AST, membrane glycoprotein HP59) which exports sialic acid (N-acetylneuraminic acid, Neu5Ac) derived from the degradation of glycoconjugates from lysosomes. This export is dependent on the proton electrochemical gradient across the lysosomal membrane. SLC17A5 is present in the pathological tumor vasculature of the lung, breast, colon, and ovary, but not in the normal vasculature, suggesting that the protein may be critical to pathological angiogenesis. Sialin is not expressed in a variety of normal tissues, but is significantly expressed in human fetal lung. Defects in SLC17A5 cause Salla disease (SD) and infantile sialic acid storage disorder (ISSD aka N-acetylneuraminic acid storage disease, NSD). These diseases belong to the sialic acid storage diseases (SASDs) and are autosomal recessive neurodegenerative disorders characterised by hypotonia, cerebellar ataxia and mental retardation with patients excreting large amounts of free Neu5Ac in urine. ISSD is a severe infantile form of SASD with a more severe clinical course than SD (Verheijen et al. 1999, Aula et al. 2000).
R-HSA-5619076 Defective SLC17A8 causes autosomal dominant deafness 25 (DFNA25) There are two classes of glutamate transporters; the excitatory amino acid transporters (EAATs) which depend on an electrochemical gradient of Na+ ions and vesicular glutamate transporters (VGLUTs) which are proton-dependent. Together, these transporters uptake and release glutamate to mediate this neurotransmitter's excitatory signal and are part of the glutamate-glutamine cycle. Three members of the SLC17A gene family (7, 6 and 8) encode VGLUTs 1-3 respectively. This uptake is thought to be coupled to the proton electrochemical gradient generated by the vacuolar type H+-ATPase. They are all expressed in the CNS in neuron-rich areas but SLC17A8 (VGLUT3) is also expressed on astrocytes and in the liver and kidney. Defects in SLC17A8 can cause autosomal dominant deafness 25 (DFNA25; MIM:605583), a form of non-syndromic sensorineural hearing loss. The cochlea expresses SLC17A8 and in mice which lack this transporter are congenitally deaf. Hearing loss is due to the lack of glutamate release by inner hair cells therefore a loss of synaptic transmission at the IHC-afferent nerve synapse. Successful restoration of hearing by gene replacement in mice could be a significant advance toward gene therapy of human deafness (Ruel et al. 2008, Akil et al. 2012).
R-HSA-5619067 Defective SLC1A1 is implicated in schizophrenia 18 (SCZD18) and dicarboxylic aminoaciduria (DCBXA) There are two classes of glutamate transporters; the excitatory amino acid transporters (EAATs) which depend on an electrochemical gradient of Na+ ions and vesicular glutamate transporters (VGLUTs) which are proton-dependent. Together, these transporters uptake and release glutamate to mediate this neurotransmitter's excitatory signal and are part of the glutamate-glutamine cycle.
The SLC1 gene family includes five high-affinity glutamate transporters encoded by SLC1, 2, 3, 6 and 7. These transporters can mediate transport of L-Glutamate (L-Glu), L-Aspartate (L-Asp) and D-Aspartate (D-Asp) with cotransport of 3 Na+ ions and H+ and antiport of a K+ ion. This mechanism allows glutamate into cells against a concentration gradient. This is a crucial factor in the protection of neurons against glutamate excitotoxicity (the excitation of nerve cells to their death) in the CNS (Zhou & Danbolt 2014).
SLC1A1 encodes an excitatory amino-acid carrier 1 (EAAC1, also called EAAT3) and is abundant particularly in brain but also in kidney, liver, muscle, ovary, testis and in retinoblastoma cell lines. In the kidney, SLC1A1 is present at apical membranes of proximal tubes where it serves as a major route of glutamate and aspartate reuptake from urine. Defects in SLC1A1 are the cause of dicarboxylic aminoaciduria (DCBXA; MIM:222730), an autosomal recessive glutamate-aspartate transport defect in the kidney and intestine (Bailey et al. 2011). Mutations that can cause DCBXA are R445W and I395del (Bailey et al. 2011).
A defect in SLC1A1 is also implicated in schizophrenia 18 (SCZD18; MIM:615232). Schizophrenia (SCZD; MIM:181500) is a complex, multifactorial psychotic disorder characterised by disturbances in the form and content of thought, in mood, in sense of self and relationship to the external world and in behaviour. It ranks amongst the world's top 10 causes of long-term disability. At the neuropathological level, SCZD appears to be characterised by synaptic deficits, alterations in glutamate and dopamine neurotransmission and hypofrontality (a state of decreased cerebral blood flow (CBF) in the prefrontal cortex of the brain). Variations in the SLC1A1 gene can confer susceptibility to SCZD18 (Harris et al. 2013). In the remote Pacific island of Palau, the risk of SCZD is 2-3 times the worldwide rate. In a 5-generation Palauan family, an 84kb deletion was carried by psychosis patients and proposed to increase the disease risk more than 18-fold for family members (Myles-Worsley et al. 2013).
R-HSA-5619062 Defective SLC1A3 causes episodic ataxia 6 (EA6) There are two classes of glutamate transporters; the excitatory amino acid transporters (EAATs) which depend on an electrochemical gradient of Na+ ions and vesicular glutamate transporters (VGLUTs) which are proton-dependent. Together, these transporters uptake and release glutamate to mediate this neurotransmitter's excitatory signal and are part of the glutamate-gluatamine cycle.
The SLC1 gene family includes five high-affinity glutamate transporters encoded by SLC1, 2, 3, 6 and 7. These transporters can mediate transport of L-Glutamate (L-Glu), L-Aspartate (L-Asp) and D-Aspartate (D-Asp) with cotransport of 3 Na+ ions and H+ and antiport of a K+ ion. This mechanism allows glutamate into cells against a concentration gradient. This is a crucial factor in the protection of neurons against glutamate excitotoxicity (the excitation of nerve cells to their death) in the CNS (Zhou & Danbolt 2014).
SLC1A3 is highly expressed in the cerebellum but also found in the frontal cortex, hippocampus and basal ganglia. Defects in SLC1A3 have been shown to cause episodic ataxia type 6 (EA6; MIM:612656) where mutations in SLC1A3 can lead to decreased glutamate uptake, thus contributing to neuronal hyperexcitability to cause seizures, hemiplegia and episodic ataxia (Jen et al. 2005, de Vries et al. 2009).
R-HSA-5619111 Defective SLC20A2 causes idiopathic basal ganglia calcification 1 (IBGC1) The genes SLC20A1 and SLC20A2 encode for phosphate transporters 1 and 2 (PiT1 and PiT2 respectively). They both have a broad tissue distribution and may play a general housekeeping role in phosphate transport such as absorbing phosphate from interstitial fluid and in extracellular matrix and cartilage calcification as well as in vascular calcification.
They possess Na+-coupled phosphate (Pi) cotransporter function with a stoichiometry of 2:1 (Na+:Pi). Defects in SLC20A2 can cause idiopathic basal ganglia calcification 1 (IBGC1; MIM:213600), an autosomal dominant disorder characterised by vascular and pericapillary calcification by calcium phosphate in the basal ganglia and other brain regions. Affected individuals can either be asymptomatic or show a wide spectrum of neuropsychiatric symptoms including parkinsonism and dementia (Wang et al. 2012, Hsu et al. 2013, Ashtari et al. 2013, Forster et al. 2013).
R-HSA-5619071 Defective SLC22A12 causes renal hypouricemia 1 (RHUC1) Urate is a naturally occurring product of purine metabolism and is a scavenger of biological oxidants. Uric acid readily precipitates out of aqueous solutions causing gout and kidney stones. Due to this ability, changes in urate levels are implicated in numerous disease processes. The human gene SLC22A12 encodes urate transporter 1 (URAT1), predominantly expressed in the kidney and is involved in the regulation of blood urate levels. This transport can be trans-stimulated by organic anions such as L-lactate (LACT). Defects in SLC22A12 result in idiopathic renal hypouricaemia 1 (RHUC1; MIM:220150), a disorder characterised by impaired urate reabsorption at the apical membrane of proximal renal tubule cells and high urinary urate excretion (Wakida et al. 2005, Esparza Martin & Garcia Nieto 2011).
R-HSA-5619066 Defective SLC22A18 causes lung cancer (LNCR) and embryonal rhabdomyosarcoma 1 (RMSE1) The human gene SLC22A18 (aka TSSC5) encodes organic cation transporter-like protein 2 (ORCTL2). It is expressed at high levels in kidney, liver and colon and at lower levels in heart, brain and lung. ORCTL2 can transport organic cations such as chloroquine and quinidine with the antiport of protons.
The human chromosome region 11p15.5 is linked with Beckwith-Wiedemann syndrome (associated with susceptibility to Wilms' tumor, rhabdomyosarcoma and hepatoblastoma). SLC22A18 is located in this region (Cooper et al. 1998, Lee et al. 1998). Mutations and/or reduced expression of SLC22A18 have been found in certain tumors such as lung cancer (LNCR; MIM:211980) (Lee et al. 1998) and embryonal rhabdomyosarcoma 1 (RMSE1; MIM:268210) (Schwienbacher et al. 1998). How SLC22A18 might be involved in growth regulation is poorly understood. There is speculation that it may be involved in resistance to chemotherapy drugs and/or in the export of genotoxic substances whose retention may increase the risk of tumor formation.
R-HSA-5619053 Defective SLC22A5 causes systemic primary carnitine deficiency (CDSP) The human SLC22A5,15 and 16 genes encode for sodium-dependent, high affinity carnitine cotransporters which maintain systemic and tissue concentrations of carnitine. Carnitine is essential for beta-oxidation of long-chain fatty acids to produce ATP. SLC22A5 encodes the organic cation/carnitine transporter 2 (OCTN2). SLC22A5 is strongly expressed in the kidney, skeletal muscle, heart and placenta. Defects in SLC22A5 are the cause of systemic primary carnitine deficiency (CDSP; MIM:212140), an autosomal recessive disorder of fatty-acid oxidation caused by defective carnitine transport resulting in cardiac, skeletal, or metabolic symptoms. If diagnosed early, all clinical symptoms can be completely reversed with a carnitine supplement. However, if left untreated, patients will develop lethal heart failure (Shibbani et al. 2014, Tamai 2013).
R-HSA-5619077 Defective SLC24A1 causes congenital stationary night blindness 1D (CSNB1D) Five members of the NCKX (SLC24) family are all able to exchange one Ca2+ and one K+ for four Na+. SLC24A1 encodes an exchanger protein NCKX1 which is the most extensively studied member and is highly expressed in the eye. The light-induced lowering of calcium by efflux via this protein plays a key role in the process of light adaptation (Schnetkamp 2013). Defects in SLC24A1 can cause congenital stationary night blindness 1D (CSNB1D), an autosomal recessive, non-progressive retinal disorder characterised by impaired night vision and characterised by a Riggs-type of electroretinogram (Riazuddin et al. 2010).
R-HSA-5619055 Defective SLC24A4 causes hypomineralized amelogenesis imperfecta (AI) The five members of the NCKX (SLC24) family are all able to exchange one Ca2+ and one K+ for four Na+. SLC24A4 encodes an exchanger protein NCKX4 which may play a role in calcium transport during amelogenesis (the process of formation of tooth enamel). SLC24A4 is upregulated in ameloblasts during the maturation stage of amelogenesis (Hu et al. 2012). Defects in SLC24A4 can cause hypomineralised amelogenesis imperfecta (AI), an autosomal recessive disorder in which tooth enamel formation fails. Screening of AI families identified mutations which severely diminish or abolish transport function of SLC24A4 (Parry et al. 2013, Wang et al. 2014).
Genetic variants in SLC24A4 define the skin/hair/eye pigmentation variation locus 6 (SHEP6; MIM:210750). In a genomewide association scan of thousands of Icelanders and Dutch, Sulem et al. found a strong association between the T allele of a SNP in the SLC24A4 gene and blond versus brown hair and blue versus green eyes (Sulem et al. 2007).
R-HSA-5619036 Defective SLC24A5 causes oculocutaneous albinism 6 (OCA6) Five members of the NCKX (SLC24) family are all able to exchange one Ca2+ and one K+ for four Na+. SLC24A5 (NCKX5, located on the trans-Golgi membrane) is the prediminant K+-dependent Na+/Ca2+ exchanger in melanocytes and is one of a handful of genes thought to play a role in determining human skin colour (Wilson et al. 2013). Defects in SLC24A5 can cause oculocutaneous albinism 6 (OCA6; MIM:113750), a disorder characterised by a reduction or complete loss of melanin in the skin, hair and eyes. Patients with this condition show accompanied eye symptoms (Kamaraj & Purohit 2014, Morice-Picard et al. 2014).
R-HSA-3560792 Defective SLC26A2 causes chondrodysplasias The SLC26A1 and 2 genes encode sulfate transporter proteins that facilitate sulfate uptake into cells, critical in cartilage for sulfation of proteoglycans and extracellular matrix organization. Defects in SLC26A2 result in impaired SO4(2-) transport leading to insufficient sulfation of cartilage proteoglycans. Defective SLC26A2 is implicated in the pathogenesis of a spectrum of autosomal recessive human chondrodysplasias. Severity of symptoms range from mild (diastrophic dysplasia; MIM:222600), intermediate (atelosteogenesis type II; MIM256050) to severe (achondrogenesis type 1B; MIM:600972) (Superti-Furga et al. 1996, Dwyer et al. 2010, Dawson & Markovich 2005).
R-HSA-5619085 Defective SLC26A3 causes congenital secretory chloride diarrhea 1 (DIAR1) Solute carrier (SLC) genes that code chloride (Cl-)/bicarbonate (HCO3-) exchanger proteins are the SLC4 and SLC26 families. The chloride anion exchanger SLC26A3 (aka down-regulated in adenoma, DRA) mediates electrolyte and fluid absorption in the colon. It is also localised to the midpiece tail membrane of sperm where it plays a role in Cl-/HCO3- homeostasis during sperm epididymal maturation. Defects in SLC26A3 cause congenital chloride diarrhea 1 (DIAR1), a disease characterised by watery stools containing an excess of chloride resulting in dehydration, hypokalemia, and metabolic alkalosis (Alper & Sharma 2013, Wedenoja et al. 2011).
R-HSA-5619046 Defective SLC26A4 causes Pendred syndrome (PDS) Solute carrier (SLC) genes that code chloride (Cl-)/bicarbonate (HCO3-) exchanger proteins are in the SLC4 and SLC26 families. SLC26A4 (pendrin) is thought to act as a chloride/anion exchanger but in the thyroid and inner ear, it also contributes to the conditioning of the endolymphatic fluid by mediating iodide (I-) transport. Defects in SLC26A4 can cause Pendred syndrome (PDS; MIM:274600), an autosomal recessive disorder characterised by congenital sensorineural hearing loss in association with thyroid goiter (Choi et al. 2011, Pesce & Kopp 2014).
R-HSA-5619108 Defective SLC27A4 causes ichthyosis prematurity syndrome (IPS) The SLC27 gene family code for fatty acid transport proteins (FATPs). Long chain fatty acids (LCFAs) are critical for many physiological and cellular processes as a primary energy source. Of the six FATPs characterised, three have been shown to mediate the influx of LCFAs into cells; FATP1, 4 and 6. SLC27A4 (FATP4) is the major intestinal LCFA transporter but is also expressed at lower levels in brain, kidney, liver and heart. SLC27A4 is also expressed in skin, where it has been shown to play a major role in epidermal development, being highly expressed in neonatal keratinocytes. Defects in SLC27A4 can cause ichthyosis prematurity syndrome (IPS; MIM:604194), a keratinisation disorder which is characterised by thickened epidermis and respiratory complications. Patients suffer from a lifelong non-scaly ichthyosis (Anderson & Stahl 2013).
R-HSA-5619063 Defective SLC29A3 causes histiocytosis-lymphadenopathy plus syndrome (HLAS) The human gene SLC29A3 encodes the equilibrative nucleoside transporter 3 (ENT3). It is abundant in many tissues, especially the placenta and is localized intracellularly on the lysosomal membrane. SLC29A3 mediates the reversible transport of nucleosides as well as anticancer and antiviral agents such as cladribine, cordycepin, tubercidin and AZT. Defects in SLC29A3 can cause histiocytosis-lymphadenopathy plus syndrome (HLAS; MIM:602782), an autosomal recessive disorder characterised by combined features from 2 or more of four histiocytic disorders (Morgan et al. 2010, Colmenero et al. 2012, Young et al. 2013).
R-HSA-5619043 Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1) Members of the SLC2A family encode glucose transporter (GLUT) proteins that mediate the facilitated diffusion of glucose between the extracellular space and the cytosol. While the monomeric protein can form a channel and transport glucose, kinetic studies suggest that the functional form of the protein is a homotetramer. SLC2A1 (GLUT1) is expressed by many cell types, notably endothelial cells, red blood cells and cells of the brain. Its low Km for glucose (~1 mM) relative to normal blood glucose concentration (~5 mM) allows these cells to take up glucose independent of changes in blood glucose levels. Defects in SLC2A1 can cause neurological disorders with wide phenotypic variability. The most severe 'classic' phenotype, GLUT1 deficiency syndrome 1 (GLUT1DS1; MIM:606777), comprises infantile-onset epileptic encephalopathy associated with delayed development, acquired microcephaly, motor incoordination and spasticity (Brockmann 2009, De Giorgis & Veggiotti 2013).
R-HSA-5619068 Defective SLC2A10 causes arterial tortuosity syndrome (ATS) Four class III facilitative transporters can transport glucose; SLC2A6, 8, 10 and 12 (encoding GLUT6, 8, 10 and 12 respectively). SLC2A10 (located in the Type 2 diabetes-linked region of human chromosome 20q12-13.1) encodes GLUT10, a transporter with high affinity for glucose. GLUT10 is highly expressed in liver and pancreas but is present at lower levels in most tissues. Defects in SLC2A10 are the cause of arterial tortuosity syndrome (ATS), an autosomal recessive disorder of connective tissue characterised by tortuosity and elongation of major arteries, often resulting in death at a young age (Coucke et al. 2006, Callewaert et al. 2008).
R-HSA-5619098 Defective SLC2A2 causes Fanconi-Bickel syndrome (FBS) The reversible facilitated diffusion of fructose, galactose, and glucose from the cytosol to the extracellular space is mediated by the SLC2A2 (GLUT2) transporter in the plasma membrane. In the epithelial cells of the small intestine, the basolateral localisation of SLC2A2 enables hexose sugars derived from the diet (and taken up by SLC5A1 and SLC2A5 transporters into cells) to be released into the circulation. SLC2A2 is a low affinity glucose transporter expressed mainly in the kidney, liver and pancreatic beta-cells. In beta-cells, it functions as a glucose-sensor for insulin secretion and in the liver, it allows for bi-directional glucose transport. Defects in SLC2A2 can cause Fanconi-Bickel syndrome (FBS; MIM:227810), a rare but well-defined disorder characterised by glycogen accumulation, proximal renal tubular dysfunction, and impaired utilisation of glucose and galactose (Leturque et al. 2009, Douard & Ferraris 2013).
R-HSA-5619047 Defective SLC2A9 causes hypouricemia renal 2 (RHUC2) The human SLC2A9 gene encodes the class II facilitative glucose transporter 9 (GLUT9). SLC2A9 is expressed mainly in kidney (proximal tubules of epithelial cells) and liver. SLC2A9 is a bona fide urate transporter (uric acid), but also the uptake of fructose (Fru) and glucose (Glc) at a low rate. Uric acid is the end product of purine metabolism in humans and great apes. Defects in SLC2A9 can cause renal hypouricemia 2 (RHUC2), a common inherited disorder characterised by impaired renal urate reabsorption and resultant low serum urate levels. Some patients present with severe complications, such as exercise-induced acute kidney injury (EIAKI) and nephrolithiasis (Esparza Martin & Garcia Nieto 2011, Sebesta 2012, Shen et al. 2014).
R-HSA-5619061 Defective SLC33A1 causes spastic paraplegia 42 (SPG42) The human gene SLC33A1 encodes acetyl-CoA transporter AT1. SLC33A1 transports cytosolic acetyl-CoA (Ac-CoA) to the Golgi apparatus lumen, where it serves as the substrate for acetyltransferases that O-acetylates sialyl residues of gangliosides and glycoproteins (Hirabayashi et al. 2013). Defects in SLC33A1 are the cause of spastic paraplegia autosomal dominant type 42 (SPG42; MIM:612539), a neurodegenerative disorder characterised by a variable speed of (but progressive) weakness and spasticity of the lower limbs (Lin et al. 2008, Hirabayashi et al. 2013). Defects in SLC33A1 can also cause congenital cataracts, hearing loss, and neurodegeneration (CCHLND; MIM:614482), an autosomal recessive disorder characterised by congenital cataracts, severe psychomotor retardation, and hearing loss, together with decreased serum ceruloplasmin and copper (Huppke et al. 2012).
R-HSA-5619040 Defective SLC34A1 causes hypophosphatemic nephrolithiasis/osteoporosis 1 (NPHLOP1) SLC34A1 and 2 encode Na+/Pi cotransporters, which cotransport divalent phosphate (PO4(2-), Pi) with 3 Na+ ions. SLC34A1 is an important Pi transporter mainly expressed in renal proximal tubules where it plays a major role in Pi homeostasis. Defects in SLC34A1 are the cause of hypophosphatemic nephrolithiasis/osteoporosis type 1 (NPHLOP1; MIM:612286), disease characterised by decreased renal phosphate absorption, hypophosphatemia, hyperphosphaturia, hypercalciuria, nephrolithiasis and implicated in the formation of renal calcium stones and/or bone demineralisation (Prie et al. 2002, Prie et al. 2004, Choi 2008, Boskey et al. 2013, Forster et al. 2013).
R-HSA-5687583 Defective SLC34A2 causes PALM The human gene SLC34A2 encodes NaPi-2b which is abundantly expressed in lung and to a lesser degree in epithelia of other tissues including small intestine, pancreas, prostate, and kidney. In the lung, SLC34A2 is expressed only in alveolar type II cells, which are responsible for surfactant production, so it is proposed that it uptakes liberated phosphate from the alveolar fluid for surfactant production. SLC34A2 cotransports divalent phosphate (HPO4(2-)) with three Na+ ions (electrogenic transport) from the extracellular region into alveolar type II cells. Defects in SLC34A2 can cause pulmonary alveolar microlithiasis (PALM; MIM:265100), a rare disease characterised by the deposition of calcium phosphate microliths (tiny, roundish corpuscles) throughout the lung. Most patients remain asymptomatic for years or decades, the disease following a long-term, progressive course resulting in slow deterioration of lung functions. PALM can result in a potentially lethal disease (Yin et al. 2013, Ferreira Francisco et al. 2013, Whitsett et al. 2015).
R-HSA-5619045 Defective SLC34A2 causes pulmonary alveolar microlithiasis (PALM) SLC34A1 and 2 encode Na+/Pi cotransporters, which cotransport divalent phosphate (PO4(2-), Pi) with 3 Na+ ions. SLC34A2 is abundantly expressed in lung and to a lesser extent in tissues of epithelial origin including small intestine, pancreas, prostate, and kidney. Defects in SLC34A2 are a cause of pulmonary alveolar microlithiasis (PALM; MIM:265100), a rare disease characterised by the deposition of calcium phosphate microliths throughout the lungs. The disease follows a long-term progressive course, resulting in a slow deterioration of lung function (Corut et al. 2006, Forster et al. 2013).
R-HSA-5619097 Defective SLC34A3 causes Hereditary hypophosphatemic rickets with hypercalciuria (HHRH) SLC34A3 is almost exclusively expressed at the apical membranes of kidney proximal tubules and encodes a Na+/Pi cotransporter. It cotransports 2 Na+ ions with every phosphate (Pi) (electroneutral transport). Defects in SLC34A3 are the cause of hereditary hypophosphatemic rickets with hypercalciuria (HHRH; MIM:241530), an autosomal recessive form of hypophosphatemia characterised by reduced renal phosphate reabsorption and rickets (Bergwitz et al. 2006, Segawa et al. 2013, Forster et al. 2013).
R-HSA-5619037 Defective SLC35A1 causes congenital disorder of glycosylation 2F (CDG2F) The human gene SLC35A1 encodes the CMP-sialic acid transporter which mediates the antiport of CMP-sialic acid (CMP-Neu5Ac) into the Golgi lumen in exchange for CMP (Ishida et al. 1996). Defects in SLC35A1 are the cause of congenital disorder of glycosylation type 2F (CDG2F; MIM:603585), characterised by under-glycosylated serum proteins. CDGs are a family of severe inherited diseases caused by a defect in protein N-glycosylation. These multisystem disorders present with a wide spectrum of phenotypes such as disorders of nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders and immunodeficiency (Martinez-Duncker et al. 2005, Song 2013).
R-HSA-5663020 Defective SLC35A1 causes congenital disorder of glycosylation 2F (CDG2F) The human gene SLC35A1 encodes the CMP-sialic acid transporter which mediates the antiport of CMP-sialic acid (CMP-Neu5Ac) into the Golgi lumen in exchange for CMP (Ishida et al. 1996). Defects in SLC35A1 are the cause of congenital disorder of glycosylation type 2F (CDG2F; MIM:603585), characterised by under-glycosylated serum proteins. CDGs are a family of severe inherited diseases caused by a defect in protein N-glycosylation. These multisystem disorders present with a wide spectrum of phenotypes such as disorders of nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders and immunodeficiency (Martinez-Duncker et al. 2005, Song 2013).
R-HSA-5619072 Defective SLC35A2 causes congenital disorder of glycosylation 2M (CDG2M) The human gene SLC35A2 encodes the UDP-galactose transporter. It is located on the Golgi membrane and mediates the antiport of UDP-Gal into the Golgi lumen in exchange for UMP. Nucleotide sugars such as UDP-Gal are used in protein glycosylation in the Golgi lumen. This transporter is also known to transport UDP-N-acetylgalactosamine (UDP-GalNAc) by the same antiport mechanism. Defects in SLC35A2 limit Golgi-localised pools of UDP-Gal, resulting in truncated beta-GlcNAc-terminated N-glycans and alpha-GalNAc-terminated O-glycans. Defects in SLC35A2 can cause congenital disorder of glycosylation 2M (CDG2M; MIM:300896), a disorder characterised by developmental delay, hypotonia, ocular defects and brain malformations (Ng et al. 2013). Congenital disorders of glycosylation (CDGs) are generally characterised by under-glycosylated serum glycoproteins and a wide spectrum of clinical features. Defects in SLC35A2 can also cause early infantile epileptic encephalopathy 22 (EIEE22; MIM:300896), a severe form of epilepsy characterised by by frequent tonic seizures or spasms beginning in infancy and accompanied by developmental problems (Kodera et al. 2013).
R-HSA-5619083 Defective SLC35A3 causes arthrogryposis, mental retardation, and seizures (AMRS) The human gene SLC35A3 encodes a UDP-GlcNAc transporter. It is ubiquitously expressed and resides on the Golgi membrane where it transports UDP- N-acetylglucosamine (UDP-GlcNAc) into the Golgi lumen in exchange for UMP. UDP-GlcNAc is a substrate required by Golgi-resident glycosyltransferases that generate branching of N-glycosylated proteins. Defects in SLC35A3 can cause arthrogryposis, mental retardation, and seizures (AMRS; MIM:615553) (Edvardson et al. 2013). Patient cells show a large reduction of tetraantennary N-glycans with an accumulation of abnormal lower-branched glycoproteins, although the serum N-glycome was normal.
R-HSA-5619078 Defective SLC35C1 causes congenital disorder of glycosylation 2C (CDG2C) The human gene SLC35C1 encodes a GDP-fucose transporter that resides on the Golgi membrane and mediates the transport of GDP-fucose into the Golgi lumen. Defects in SLC35C1 cause the congenital disorder of glycosylation type 2C (CDG2C aka leukocyte adhesion deficiency type II, LAD2), an autosomal recessive disorder characterised by moderate to severe psychomotor retardation, mild dysmorphism and impaired neutrophil motility (Lubke et al. 2001, Liu & Hirschberg 2013).
R-HSA-5579020 Defective SLC35D1 causes SCHBCKD The UDP-glucuronic acid/UDP-N-acetylgalactosamine transporter (SLC35D1) is an ER membrane-spanning protein that transports nucleotide-sugars from the cytosol into the ER lumen. SLC35D1 transports UDP-GlcUA and UDP-GalNAc, which are substrates for the synthesis of chondroitin sulfate disaccharide repeats, suggesting a role in chondroitin sulfate biosynthesis. Mutations in SLC35D1 can cause Schneckenbecken dysplasia (SCHBCKD; MIM:269250), a rare, autosomal recessive, lethal short-limbed skeletal dysplasia affecting cartilage and skeletal development (Liu et al. 2010, Liu & Hirschberg 2013).
R-HSA-5619041 Defective SLC36A2 causes iminoglycinuria (IG) and hyperglycinuria (HG) SLC36A2 encodes proton-coupled amino acid transporter 2 (PAT2), a high-affinity cotransporter of glycine and proline coupled with the uptake of a proton in kidney and muscles (Schweikhard & Ziegler 2012). Defects in SLC36A2 can cause iminoglycinuria (IG; MIM:242600), an autosomal recessive abnormality of renal transport of glycine and the imino acids proline and hydroxyproline. Defects can also cause hyperglycinuria (HG; MIM:138500), a related disorder to IG which is characterised by excess glycine in the urine (Broer et al. 2008). Polymorphisms in the modifiers SLC6A18, 19 and 20, contribute to these phenotypes.
R-HSA-5619088 Defective SLC39A4 causes acrodermatitis enteropathica, zinc-deficiency type (AEZ) SLC39A4 encodes the human zinc transporter hZIP4 which plays an important role in cellular zinc homeostasis. Defects in SLC39A4 result in the inherited condition acrodermatitis enteropathica, zinc deficiency type (AEZ; MIM:201100), caused by the inability to absorb dietary zinc from the duodenum and jejunum. Clinical features include growth retardation, immune system dysfunction, severe dermatitis and mental disorders (Schmitt et al. 2009).
R-HSA-5619113 Defective SLC3A1 causes cystinuria (CSNU) Neutral and basic amino acid transport protein rBAT (SLC3A1) and b(0,+)-type amino acid transporter 1 (SLC7A9) are linked by a disulfide bridge to form system b(0,+)-like activity in the high affinity transport of neutral and dibasic amino acids and cystine. The SLC7A9:SLC3A1 heterodimer mediates the electrogenic exchange of extracellular amino acids such as L-arginine (L-Arg) and L-lysine (L-lys) and cystine (CySS-, the oxidised form of L-cysteine) for intracellular neutral amino acids such as L-leucine (L-Leu). These solute carriers are mainly expressed in the kidney and small intestine where they remove dibasic amino acids and cystine from the renal tubular and intestinal lumen respectively (Schweikhard & Ziegler 2012). Defects in SLC3A1 (or SLC7A9) can cause cystinuria (CSNU; MIM:220100), an autosomal recessive disorder characterised by impaired epithelial cell transport of cystine and dibasic amino acids in the proximal renal tubule and GI tract. The build-up and low solubility of cystine causes the formation of calculi in the urinary tract, resulting in obstructive uropathy, pyelonephritis and in severe cases, renal failure (Palacin et al. 2001, Mattoo & Goldfarb 2008, Fotiadis et al. 2013, Saravakos et al. 2014). Cystinuria is subcategorized as type A (mutations on SLC3A1) and type B (mutations on SLC7A9).
R-HSA-5655799 Defective SLC40A1 causes hemochromatosis 4 (HFE4) (duodenum) The primary site for absorption of dietary iron is the duodenum. Ferrous iron (Fe2+) is taken up from the gut lumen across the apical membranes of enterocytes and released into the portal vein circulation across basolateral membranes. The human gene SLC40A1 encodes the metal transporter protein MTP1 (aka ferroportin or IREG1). This protein resides on the basolateral membrane of enterocytes and mediates ferrous iron efflux into the portal vein. SLC40A1 colocalises with hephaestin (HEPH) which stablises it and is necessary for the efflux reaction to occur.
Defects in SLC40A1 can cause hemochromatosis 4 (HFE4; MIM:606069), a disorder of iron metabolism characterised by iron overload. Excess iron is deposited in a variety of organs leading to their failure, resulting in serious illnesses including cirrhosis, hepatomas, diabetes, cardiomyopathy, arthritis and hypogonadotropic hypogonadism. Severe effects of the disease don't usually appear until after decades of progressive iron overloading (De Domenico et al. 2005, 2006, 2011, Kaplan et al. 2011).
R-HSA-5619049 Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) SLC40A1 (MTP1 aka ferroportin or IREG1) is highly expressed on macrophages where it mediates iron efflux from the breakdown of haem. SLC40A1 colocalises with ceruloplasmin (CP) which stablizes SLC40A1 and is necessary for the efflux reaction to occur. Six copper ions are required by ceruloplasmin as a cofactor.
Defects in SLC40A1 can cause hemochromatosis 4 (HFE4; MIM:606069), a disorder of iron metabolism characterised by iron overload. Excess iron is deposited in a variety of organs leading to their failure, resulting in serious illnesses including cirrhosis, hepatomas, diabetes, cardiomyopathy, arthritis and hypogonadotropic hypogonadism. Severe effects of the disease don't usually appear until after decades of progressive iron overloading (De Domenico et al. 2005, 2006, 2011, Kaplan et al. 2011).
R-HSA-5619050 Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA) The proteins responsible for the exchange of Cl- with HCO3- are members of the SLC4 (1-3) and SLC26 (3, 4, 6, 7 and 9) transporter families. SLC4A1 (Band 3, AE1, anion exchanger 1) was the first bicarbonate transporter gene to be cloned and sequenced. It is ubiquitous throughout vertebrates and in humans, is the major glycoprotein present on erythrocytes and the basolateral surfaces of kidney cells. Variations in erythroid SLC4A1 determine the Diego blood group system. Mutations in the erythrocyte form of SLC4A1 can cause hereditary spherocytosis type 4 (HSP4; MIM:612653), a disorder leading to haemolytic anaemia (HA). Some mutations in SLC4A1 can cause distal (type1) renal tubular acidosis (dRTA; MIM:179800) (an inability to acidify urine) and dRTA-HA (dRTA with hemolytic anemia) (MIM:611590) (Tanner 2002, Romero et al. 2013).
R-HSA-5619054 Defective SLC4A4 causes renal tubular acidosis, proximal, with ocular abnormalities and mental retardation (pRTA-OA) Members 4, 5, 7 and 9 of the SLC4A family couple the transport of bicarbonate (HCO3-) with sodium ions (Na+). SLC4A4 (aka NBCe1) is an electrogenic Na+/HCO3- cotransporter with a stoichiometry of 1:3. SLC4A4 is expressed in the kidney and pancreas, with lesser expression in many other tissues. Mutations in SLC4A4 can cause permanent isolated proximal renal tubular acidosis with ocular abnormalities and mental retardation (pRTA-OA), a rare autosomal recessive syndrome characterised by short stature, proximal renal tubular acidosis, mental retardation, bilateral glaucoma, cataracts and bandkeratopathy. pRTA results from the failure of the proximal tubular cells to reabsorb filtered HCO3- from urine, leading to urinary HCO3- wasting and subsequent acidemia. HCO3- also needs to move out of cells in the eye, thus failure to do so can affect ocular pressure homeostasis (Horita et al. 2005, Kurtz & Zhu 2013, Kurtz & Zhu 2013b, Seki et al. 2013).
R-HSA-5656364 Defective SLC5A1 causes congenital glucose/galactose malabsorption (GGM) Sodium/glucose cotransporter 1 (SLC5A1 aka SGLT1) actively and reversibly transports glucose (Glc) into cells by Na+ cotransport with a Na+ to glucose coupling ratio of 2:1. SLC5A1 is mainly expressed in the microvilli of intestine and kidney and responsible for the absorption of sugars. Overexpressed SLC5A1 has been found in various cancers, possibly playing a role in preventing autophagic cell death by maintaining intracellular glucose levels. Defects in SLC5A1 can cause congenital glucose/galactose malabsorption (GGM; MIM:606824), an autosomal recessive disorder manifesting itself in newborns characterised by severe, life-threatening diarrhea which is usually fatal unless glucose and galactose are removed from the diet (Wright et al. 2002, Bergeron et al. 2008, Wright et al. 2007, Wright 2013).
R-HSA-5658208 Defective SLC5A2 causes renal glucosuria (GLYS1) The human gene SLC5A2 encodes a sodium-dependent glucose transporter (SGLT2), expressed in many tissues but primarily in the kidney, specifically S1 and S2 proximal tubule segments. It is a low affinity, high capacity transporter of glucose across the apical membrane, with co-transport of Na+ ions in a 1:1 ratio and is the main transporter of glucose in the kidney, responsible for approximately 98% of glucose reabsorption (reaminder by SGLT1). Defects in SLC5A2 are the cause of renal glucosuria (GLYS1; MIM:233100), an autosomal recessive renal tubular disorder characterised by glucosuria in the absence of both hyperglycemia and generalized proximal tubular dysfunction. Establishing definite genotype–phenotype correlations for GLYS1 is made difficult by variable expression of SLC5A2 and because other genes may have an impact on overall renal glucose resorption. Drugs that inhibit SLC5A2 are used to treat type 2 diabetes (T2D). The strategy to reduce hyperglycemia in T2D is to target renal glucose reabsorption by inhibiting SLC5A2 (Santer & Calado 2010, Calado et al. 2011).
R-HSA-5619096 Defective SLC5A5 causes thyroid dyshormonogenesis 1 (TDH1) Human SLC5A5 encodes the Na+/I- symporter NIS which is localised in the basolateral membrane of thyrocytes facing the bloodstream where it mediates iodide accumulation into these cells. Defects in SLC5A5 can cause hyroid dyshormonogenesis 1 (TDH1; MIM:274400), a disorder characterised by the inability of the thyroid to maintain a concentration difference of readily exchangeable iodine between the plasma and the thyroid gland (termed iodine trapping) leading to congenital hypothyroidism (Spitzweg & Morris 2010, Grasberger & Refetoff 2011).
R-HSA-5658471 Defective SLC5A7 causes distal hereditary motor neuronopathy 7A (HMN7A) The human SLC5A7 gene encodes a sodium- and chloride-dependent, high affinity choline transporter (CHT) transports choline (Cho) from the extracellular space into neuronal cells. Cho uptake is the rate-limiting step in acetylcholine synthesis, a neurotransmitter released at the neuromuscular junction (NMJ). Defects in SLC5A7 can cause distal hereditary motor neuronopathy 7A (HMN7A; MIM:158580). Distal hereditary motor neuronopathies are a group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The clinical picture consists of a progressive distal muscle wasting and weakness in the legs without clinical sensory loss (Barwick et al. 2012).
R-HSA-5619114 Defective SLC5A7 causes distal hereditary motor neuronopathy 7A (HMN7A) The human SLC5A7 gene encodes a sodium- and chloride-dependent, high affinity choline transporter (CHT) transports choline (Cho) from the extracellular space into neuronal cells. Cho uptake is the rate-limiting step in acetylcholine synthesis, a neurotransmitter released at the neuromuscular junction (NMJ). Defects in SLC5A7 can cause distal hereditary motor neuronopathy 7A (HMN7A; MIM:158580). Distal hereditary motor neuronopathies are a group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The clinical picture consists of a progressive distal muscle wasting and weakness in the legs without clinical sensory loss (Barwick et al. 2012).
R-HSA-5659729 Defective SLC6A18 may confer susceptibility to iminoglycinuria and/or hyperglycinuria SLC6A18 encodes a neutral amino acid transporter B(0)AT3 which has preference for the amino acid glycine. It is abundantly expressed in the kidney, specifically the S2/3 segments of the kidney proximal tubule (Broer & Gether 2012, Schweikhard & Ziegler 2012). Iminoglycinuria (IG; MIM:242600) or hyperglycinuria (HG; MIM:138500) can arise from defects in SLC36A2, encoding a proton-coupled amino acid transporter 2 (PAT2), a high-affinity cotransporter of glycine and proline. Mutation in SLC6A18 may contribute to both IG and HG (Broer et al. 2008).
R-HSA-5619079 Defective SLC6A18 may confer susceptibility to iminoglycinuria and/or hyperglycinuria SLC6A18 encodes a neutral amino acid transporter B(0)AT3 which has preference for the amino acid glycine. It is abundantly expressed in the kidney, specifically the S2/3 segments of the kidney proximal tubule (Broer & Gether 2012, Schweikhard & Ziegler 2012). Iminoglycinuria (IG; MIM:242600) or hyperglycinuria (HG; MIM:138500) can arise from defects in SLC36A2, encoding a proton-coupled amino acid transporter 2 (PAT2), a high-affinity cotransporter of glycine and proline. Mutation in SLC6A18 may contribute to both IG and HG (Broer et al. 2008).
R-HSA-5659735 Defective SLC6A19 causes Hartnup disorder (HND) SLC6A19 encodes the sodium-dependent neutral amino acid transporter B(0)AT1 and mediates the uptake of neutral amino acids across the plasma membrane accompanied by uptake of a sodium ion. The protein is abundantly expressed in the small intestine and kidney (Broer & Gether 2012, Schweikhard & Ziegler 2012). Defects in SLC6A19 can cause Hartnup disorder (HND; MIM:234500), an autosomal recessive abnormality of renal and gastrointestinal neutral amino acid transport characterised by increased urinary and intestinal excretion of neutral amino acids. Symptoms include transient manifestations of rashes, cerebellar ataxia and psychotic behaviour (Broer 2009, Cheon et al. 2010). Some mutations in SLC6A19 are thought to contribute to the phenotypes iminoglycinuria (IG; MIM:242600) and hyperglycinuria (HG; MIM:138500) (Broer et al. 2008).
R-HSA-5619044 Defective SLC6A19 causes Hartnup disorder (HND) SLC6A19 encodes the sodium-dependent neutral amino acid transporter B(0)AT1 and mediates the uptake of neutral amino acids across the plasma membrane accompanied by uptake of a sodium ion. The protein is abundantly expressed in the small intestine and kidney (Broer & Gether 2012, Schweikhard & Ziegler 2012). Defects in SLC6A19 can cause Hartnup disorder (HND; MIM:234500), an autosomal recessive abnormality of renal and gastrointestinal neutral amino acid transport characterised by increased urinary and intestinal excretion of neutral amino acids. Symptoms include transient manifestations of rashes, cerebellar ataxia and psychotic behaviour (Broer 2009, Cheon et al. 2010). Some mutations in SLC6A19 are thought to contribute to the phenotypes iminoglycinuria (IG; MIM:242600) and hyperglycinuria (HG; MIM:138500) (Broer et al. 2008).
R-HSA-5619109 Defective SLC6A2 causes orthostatic intolerance (OI) SLC6A2 encodes the sodium-dependent noradrenaline transporter NAT1 which terminates the action of the neurotransmitter noradrenaline by transporting it from the synapse back to its vesicles for storage and reuse (Broer & Gether 2012, Schweikhard & Ziegler 2012). SLC6A2 is expressed in the CNS and adrenal glands. Defects in SLC6A2 can cause orthostatic intolerance (OI; MIM:604715), a syndrome characterised by lightheadedness, fatigue and development of symptoms during upright standing, relieved by sitting back down again. Plasma norepinephrine concentration is abnormally high (Lambert & Lambert 2014).
R-HSA-5660724 Defective SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) The human gene SLC6A3 encodes the sodium-dependent dopamine transporter DAT which mediates the Na-dependent re-uptake of dopamine (DA) from the synaptic cleft back into cells, thereby terminating the action of DA (Broer & Gether 2012, Schweikhard & Ziegler 2012). Defects in SLC6A3 can cause Parkinsonism-dystonia infantile (PKDYS; MIM:613135), a neurodegenerative disorder characterised by infantile onset of parkinsonism and dystonia (Kurian et al. 2011).
R-HSA-5619081 Defective SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) The human gene SLC6A3 encodes the sodium-dependent dopamine transporter DAT which mediates the Na-dependent re-uptake of dopamine (DA) from the synaptic cleft back into cells, thereby terminating the action of DA (Broer & Gether 2012, Schweikhard & Ziegler 2012). Defects in SLC6A3 can cause Parkinsonism-dystonia infantile (PKDYS; MIM:613135), a neurodegenerative disorder characterised by infantile onset of parkinsonism and dystonia (Kurian et al. 2011).
R-HSA-5619089 Defective SLC6A5 causes hyperekplexia 3 (HKPX3) The amino acid glycine (Gly) plays an important role in neurotransmission. Its action is terminated by rapid re-uptake into the pre-synaptic terminal or surrounding glial cells. This re-uptake is mediated by the sodium- and chloride-dependent glycine transporters 1 and 2 (GLYT1 and GLYT2 respectively) (Broer & Gether 2012, Schweikhard & Ziegler 2012). GLYT2 is encoded by the human gene SLC6A5 and is predominantly expressed in the medulla. Defects in SLC6A5 cause startle disease (STHE or hyperekplexia (HKPX3; MIM:614618)), a neurologic disorder characterised by neonatal hypertonia, an exaggerated startle response to tactile or acoustic stimuli, and life-threatening neonatal apnea. Sometimes symptoms resolve in the first year of life (Bode & Lynch 2014, James et al. 2012).
R-HSA-5660862 Defective SLC7A7 causes lysinuric protein intolerance (LPI) SLC7A7 encodes the y+L amino acid transporter 1 (y+LAT1). As a heterodimer with SLC3A2 in the plasma membrane, SLC7A7 mediates the exchange of arginine (L-Arg) for leucine (L-Leu) and a sodium ion (Na+). The physiological concentrations of arginine and leucine are expected to favor arginine export (Schweikhard & Ziegler 2012). Defects in SLC7A7 can cause Lysinuric protein intolerance (LPI; MIM:222700), a metabolic disorder characterised by decreased cationic amino acid (CAA) transport at the basolateral membrane of epithelial cells in the intestine and kidney, increased renal excretion of CAA and orotic aciduria. There is extreme variability clinically but typical symptoms include refusal to feed, vomiting and consequent failure to thrive. Hepatosplenomegaly, hematological anomalies and neurological involvement are recurrent clinical features (Sperandeo et al. 2008, Sebastio et al. 2011).
R-HSA-5660883 Defective SLC7A9 causes cystinuria (CSNU) SLC7A9 encodes the b(0,+)-type amino acid transporter 1 BAT1. As a heterodimer with SLC3A1 in the plasma membrane, SLC7A9 mediates the high-affinity, sodium-independent transport of cystine (CySS-, the oxidised form of L-cysteine) and dibasic amino acids in exchange for neutral amino acids and is thought to be responsible for the reabsorption of CySS- and dibasic amino acids in the kidney tubule (Schweikhard & Ziegler 2012). Defects in SLC7A9 (or SLC3A1) can cause cystinuria (CSNU; MIM:220100), an autosomal disorder characterised by impaired renal reabsorption of cystine and dibasic amino acids. The low solubility of cystine causes the formation of calculi in the urinary tract resulting in obstructive uropathy, pyelonephritis, and, rarely, renal failure (Palacin et al. 2001, Mattoo & Goldfarb 2008, Fotiadis et al. 2013, Saravakos et al. 2014, Barbosa et al. 2012). Cystinuria is subcategorised as type A (mutations on SLC3A1) and type B (mutations on SLC7A9).
R-HSA-5619092 Defective SLC9A6 causes X-linked, syndromic mental retardation,, Christianson type (MRXSCH) SLC9A6 encodes the sodium/hydrogen exchanger 6 NHE6, a protein ubiquitously expressed but most abundant in mitochondria-rich tissues such as brain, skeletal muscle and heart. It is located on endosomal membranes and thought to play a housekeeping role in pH homeostasis in early endosomes. It mediates the electroneutral exchange of protons for Na+ and K+ across the early and recycling endosome membranes. Defects in SLC9A6 can cause mental retardation, X-linked, syndromic, Christianson type (MRXSCH; MIM:300243), a syndrome characterised by profound mental retardation, epilepsy, ataxia and microcephaly. MRXSCH shows phenotypic overlap with Angelman syndrome (Gilfillan et al. 2008, Schroer et al. 2010, Kondapalli et al. 2014).
R-HSA-5619052 Defective SLC9A9 causes autism 16 (AUTS16) SLC9A9 encodes the sodium/hydrogen exchanger 9 NHE9 which is expressed ubiquitously and thought to play a housekeeping role in pH homeostasis in the late endosome membrane. A defect in SLC9A9 can contribute to susceptibility to autism 16 (AUTS16; MIM:613410). Autism, the prototypic pervasive developmental disorder (PDD), is a complex, multifactorial disorder characterised by reciprocal social interaction and communication impairment, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by age 3 (Morrow et al. 2008, Kondapalli et al. 2014).
R-HSA-5619110 Defective SLCO1B1 causes hyperbilirubinemia, Rotor type (HBLRR) The solute carrier organic anion transporter family member 1B1 (SLCO1B1) is expressed on the basolateral surfaces of hepatocytes and mediates the uptake of bilirubin (BIL), a breakdown product of heme degradation, to the liver where it is conjugated and excreted from the body. Defects in SLCO1B1 can cause hyperbilirubinemia, Rotor type (HBLRR; MIM:237450), an autosomal recessive form of primary conjugated hyperbilirubinemia. Mild jaundice, not associated with hemolysis, develops shortly after birth or in childhood (van de Steeg et al. 2012, Sticova & Jirsa 2013, Keppler 2014).
R-HSA-5619058 Defective SLCO1B3 causes hyperbilirubinemia, Rotor type (HBLRR) In the body, solute carrier organic anion transporter family member 1B3 (SLCO1B3) is expressed on the basolateral surfaces of hepatocytes and may play a role in the uptake of bilirubin (BIL), a breakdown product of heme that requires conjugation and excretion from the body. Defects in SLCO1B3 can cause hyperbilirubinemia, Rotor type (HBLRR; MIM:237450), an autosomal recessive form of primary conjugated hyperbilirubinemia. Mild jaundice, not associated with hemolysis, develops shortly after birth or in childhood (van de Steeg et al. 2012, Sticova & Jirsa 2013, Keppler 2014).
R-HSA-5619095 Defective SLCO2A1 causes primary, autosomal recessive hypertrophic osteoarthropathy 2 (PHOAR2) The human gene SLCO2A1 encodes prostaglandin transporter PGT. It is ubiquitously expressed and can transport the protaglandins PGD2, PGE1, PGE2 and PGF2A. This transport may be important for release of newly-formed prostaglandins (PGs) and/or their clearance of prostaglandins from the circulation. Defects in SLCO2A1 can cause hypertrophic osteoarthropathy, primary, autosomal recessive, 2 (PHOAR2; MIM:614441), a rare genodermatosis characterised by pachydermia, digital clubbing, periostosis and affecting more males than females (Castori et al. 2005, Seifert et al. 2012, Diggle et al. 2012, Madruga Dias et al. 2014).
R-HSA-4755579 Defective SRD5A3 causes SRD5A3-CDG, KHRZ Polyprenol reductase (SRD5A3), resident on the endoplasmic reticulum membrane, normally mediates the reduction of the alpha-isoprene unit of polyprenol (pPNOL) to form dolichol (DCHOL) in a NADPH-dependent manner (Cantagrel et al. 2010). DCHOLs are substrates required for the synthesis of the lipid-linked oligosaccharide (LLO) precursor used for N-glycosylation. Defects in SRD5A3 cause congenital disorder of glycosylation 1q (SRD5A3-CDG, CDG1q; MIM:612379), a neurodevelopmental disorder characterised by under-glycosylated serum glycoproteins resulting in nervous system development, psychomotor retardation, hypotonia, coagulation disorders and immunodeficiency (Cantagrel et al. 2010, Kasapkara et al. 2012). Defects in SRD5A3 can also cause Kahrizi syndrome (KHRZ; MIM:612713), a neurodevelopmental disorder characterised by mental retardation, cataracts, holes in eye structures, pathological curvature of the spine, and coarse facial features (Kahrizi et al. 2011).
R-HSA-3656243 Defective ST3GAL3 causes MCT12 and EIEE15 CMP-N-acetylneuraminate-beta-1,4-galactoside alpha-2,3-sialyltransferase (ST3GAL3) mediates the transfer of sialic acid from CMP-sialic acid to galactose-containing glycoproteins and forms the sialyl Lewis a epitope on proteins which are required for attaining and/or maintaining higher cognitive functions. Some defects in ST3GAL3 result in mental retardation, autosomal recessive 12 (MRT12; MIM:611090), a disorder characterised by below average general intellectual function and impaired adaptive behaviour (Najmabadi et al. 2007, Hu et al. 2011). Another defect of ST3GAL3 can cause early infantile epileptic encephalopathy-15 (EIEE15: MIM:615006), resulting in severe mental retardation (Edvardson et al. 2012).
R-HSA-5579032 Defective TBXAS1 causes GHDD Thromboxane-A synthase (TBXAS1), an enzyme of the arachidonic acid cascade, produces thromboxane A2 (TXA2) from prostaglandin H2 (PGH2). Together with prostacyclin (PGI2), TXA2 plays a key role in the maintenance of haemostasis. It is also a constrictor of vascular and respiratory smooth muscle and implicated in the induction of osteoclast differentiation and activation. Defects in TBXAS1 can cause Ghosal hematodiaphyseal dysplasia (GHDD; MIM:231095), a rare autosomal recessive disorder characterised by increased bone density with predominant diaphyseal involvement and aregenerative anemia, a bone marrow failure where functional marrow cells are regenerated slowly or not at all (Genevieve et al. 2008).
R-HSA-3359454 Defective TCN2 causes TCN2 deficiency Defective transcobalamin II (produced by the TCN2 gene) results in TCN2 deficiency (MIM:275350), an autosomal recessive disorder with early-onset in infancy characterized by failure to thrive, megaloblastic anemia, and pancytopenia. If left untreated, the disorder can result in mental retardation and neurologic abnormalities (Haberle et al. 2009).
R-HSA-5578995 Defective TPMT causes TPMT deficiency Methylation is a major biotransformation route of thiopurine drugs such as 6-mercaptopurine (6MP), used in the treatment of inflammatory diseases such as rheumatoid arthritis and childhood acute lymphoblastic leukemia. 6MP and its thioguanine nucleotide metabolites are principally inactivated by thiopurine methyltransferase (TPMT)-catalysed S-methylation.
Defects in TPMT can cause thiopurine S-methyltransferase deficiency (TPMT deficiency; MIM:610460). Patients with intermediate or no TPMT activity are at risk of toxicity such as myelosuppression after receiving standard doses of thiopurine drugs. Inter individual differences in response to these drugs are largely determined by genetic variation at the TPMT locus. TPMT exhibits an autosomal co dominant phenotype: About one in 300 people in Caucasian, African, African-American, and Asian populations are TPMT deficient. Approximately 6-10% of people in these populations inherit intermediate TPMT activity and are heterozygous at the TPMT locus. The rest are homozygous for the wild type allele and have high levels of TPMT activity. (Remy 1963, Weinshilboum et al. 1999, Couldhard & Hogarth 2005, Al Hadithy et al. 2005, Azimi et al. 2014).
R-HSA-5619107 Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) The nuclear pore complex (NPC) trafficks cargo across the nuclear membrane. Nucleoprotein TPR functions as a scaffolding element in the nuclear phase of the NPC essential for normal nucleocytoplasmic transport of proteins and mRNAs. The complex glucokinase (GCK1) and glucokinase regulatory protein (GKRP) can be translocated to the nucleus via the NPC. Defects in TPR may confer susceptibility towards thyroid papillary carcinona (TPC; MIM:18850), a common tumor of the thyroid that typically arises as an irregular, solid or cystic mass from otherwise normal thyroid tissue (Vriens et al. 2009, Bonora et al. 2010).
R-HSA-5579002 Defective UGT1A1 causes hyperbilirubinemia UDP-glucuronosyltransferases (UGTs) play a major role in the conjugation and therefore elimination of potentially toxic xenobiotics and endogenous compounds. The 1-1 isoform UGT1A1 is able to act upon lipophilic bilirubin, the end product of heme breakdown. Defects in UGT1A1 can cause hyperbilirubinemia syndromes ranging from mild forms such as Gilbert syndrome (GILBS; MIM:143500) and transient familial neonatal hyperbilirubinemia (HBLRTFN; MIM:237900) to the more severe Crigler-Najjar syndromes 1 and 2 (CN1, CN2; MIM:218800 and MIM:606785) (Sticova & Jirsa 2013, Strassburg 2010, Udomuksorn et al. 2007, Costa 2006, Maruo et al. 2000).
R-HSA-5579016 Defective UGT1A4 causes hyperbilirubinemia UDP-glucuronosyltransferases (UGTs) play a major role in the conjugation and therefore elimination of potentially toxic xenobiotics and endogenous compounds. The 1-4 isoform UGT1A4 is able to act upon lipophilic bilirubin, the end product of heme breakdown. Defects in UGT1A4 can cause hyperbilirubinemia syndromes ranging from mild forms such as Gilbert syndrome (GILBS; MIM:143500) to the more severe Crigler-Najjar syndromes 1 and 2 (CN1, CN2; MIM:218800 and MIM:606785) (Sticova & Jirsa 2013, Strassburg 2010, Udomuksorn et al. 2007, Costa 2006, Maruo et al. 2000).
R-HSA-9845622 Defective VWF binding to collagen type I Upon vascular injury, circulating von Willebrand factor (VWF) binds to exposed vascular collagen. This Reactome event shows defective binding of VWF to collagen type I caused by loss-of-function mutations in the A3 domain of VWF found in patients with von Willebrand disease (VWD) type 2M, which is characterized by defects in platelet adhesion and/or collagen binding with normal or subnormal VWF multimer distribution.
R-HSA-9845621 Defective VWF cleavage by ADAMTS13 variant Under normal physiological conditions, a disintegrin and metalloproteinase with thrombospondin type 1 repeats 13 (ADAMTS13) downregulates VWF procoagulant activity by cleaving the peptide bond between Tyr1605 and Met1606 within the A2 domain of VWF in a shear-dependent manner. Deficiencies in ADAMTS13 activity results in defective cleavage of ultra large VWF multimer in the plasma and are associated with excessive thrombi formation in the microvasculature in patients with thrombotic thrombocytopenic purpura (TTP) (Zheng XL 2015; Sukumar S et al. 2021). TTP is caused either by inherited mutations in the ADAMTS13 gene or by acquired inhibitory autoantibodies directed against the ADAMTS13 protein. This Reactome event describes defective cleavage of VWF by TTP-causing loss-of-function ADAMTS13 variants, A250V, P475S, Q449*, which showed normal or slightly reduced secretion (Kokame K et al., 2002; Uchida T et al., 2004; Markham-Lee Z et al., 2022).
R-HSA-9661069 Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) This pathway describes impaired binding of RB1 pocket domain mutants to activating E2Fs, E2F1, E2F2 and E2F3 (Templeton et al. 1991, Helin et al. 1993, Otterson et al. 1997, Ji et al. 2004).
R-HSA-9846298 Defective binding of VWF variant to GPIb:IX:V This Reactome event describes von Willebrand disease (VWD)-associated missense mutations in the A1 domain of VWF, namely VWF S1358N, S1387I, S1394F and Q1402P, that compromise the clot formation due to reduced binding to GPIb (Larsen DM et al., 2013).
R-HSA-9672396 Defective cofactor function of FVIIIa variant Factor VIII (FVIII) in its activated form, FVIIIa, acts as a cofactor to the serine protease FIXa, in the conversion of the zymogen FX to the active enzyme (FXa). Missense mutations within the S577-Q584 region of FVIII have been associated with mild/moderate hemophilia A (HA) (Amano K et al. 1998; Celie PH et al. 1999; Jenkins PV et al. 2002). A functional assay demonstrated that the mutations S577F, V578A, D579A, and Q584R interfere with FVIIIa:FIXa-mediated stimulation of FX activation thus the effect of the mutations is to reduce the cofactor potential of FVIII in FXa generation. The Reactome event describes failed generation of FXa as the functional consequence of the FIXa interaction with HA-associated FVIIIa variants due to reduced ability of defective FVIII to act as a cofactor for FIXa within the intrinsic tenase complex.
R-HSA-9668250 Defective factor IX causes hemophilia B The F9 gene encodes coagulation factor IX (FIX), a vitamin K-dependent plasma protease that participates in the intrinsic blood coagulation pathway. FIX circulates as a zymogen, and is proteolytically activated to FIXa by activated FXIa or tissue factor-bound FVIIa. After being activated, FIXa forms a complex with Ca2+ ions, membrane phospholipids and coagulation factor VIIIa to activate coagulation factor X. Mutations within F9 gene that lead to quantitative and/or qualitative deficiencies in the circulating FIX protein are associated with hemophilia B (HB), a rare X-linked, recessively transmitted bleeding disorder (White GC et al. 2001; Rallapalli PM et al. 2013; Goodeve AC 2015). The disease severity in hemophilia is classified according to the plasma procoagulant levels of FIX activity. The severe form is defined as a factor level <1% of normal, the moderate form as a factor level of 1-5%, and the mild form with a factor level >5 and <40%. Patients with severe hemophilia frequently develop hemorrhages into joints, muscles or soft tissues without any apparent cause. They can also suffer from life-threatening bleeding episodes such as intracranial hemorrhages. Persons with mild and moderate factor deficiency rarely experience spontaneous hemorrhages, and excessive bleeding mostly occurs only following trauma or in association with invasive procedures.
A wide range of different genetic alterations are spread throughout the F9 gene, including single nucleotide substitutions, small and large deletions (Rallapalli PM et al. 2013). However functional consequences of most F9 mutations are poorly studied. The Reactome event describes altered functions of HB-associated FIX variants such as reduced FIX protein secretion due to defective expression and/or processing, failed proteolysis of factor X to Xa by defective FIX and failed formation of a membrane complex in the presence of Ca2+ ions, phospholipid, and cofactor VIIIa. The annotated HB-associated FIX variants are supported with data from functional studies (Usharani P et al. 1985; Spitzer SG et al. 1990; Ludwig M et a. 1992; Kurachi S et al. 1997; Branchini A et al. 2013). R-HSA-9672383 Defective factor IX causes thrombophilia In healthy individuals factor IXa (FIXa), in a complex with factor VIIIa on the surfaces of activated platelets, catalyzes the formation of activated factor X with high efficiency. A substitution of leucine for arginine at residue 384 in FIX (FIX R384L, also know as FIX Padua) is a gain-of-function mutation that resulted in elevated FIX clotting activity in a patient with venous thrombosis (Simioni P et al. 2009). R-HSA-9662001 Defective factor VIII causes hemophilia A Hemophilia A is an X‐chromosome‐linked recessive bleeding disorder defined by a qualitative and/or quantitative factor VIII (FVIII, F8) deficiency (Salen P & Babiker HM 2019). Patients affected by the mild form of the disease (FVIII activity 0.05–0.4 IU/mL) suffer from bleedings occurring after trauma or surgery. In severe hemophilia A patients (FVIII activity<0.01 IU/mL) bleedings occur spontaneously, whereas moderate hemophilia A patients (FVIII activity 0.01–0.05 IU/mL present with an intermediate bleeding phenotype (White GC 2nd et al. 2001). In healthy individuals, FVIII is synthesized as an ∼ 300-kDa glycoprotein by hepatocytes, liver sinusoidal endothelial cells, and certain types of endothelial cells (Wion KL et al. 1995; Jacquemin M et al. 2006; Shahani T et al. 2009; Turner NA & Moake JL 2015). The FVIII protein contains a domain sequence A1-A2-B-ap-A3-C1-C2 and circulates as an A1-A2-B:ap-A3-C1-C2 heterodimer bound noncovalently to the von Willebrand factor (vWF) protein. vWF protects FVIII from rapid clearance (Lenting PJ et al. 2007). During the activation of FVIII by thrombin to FVIIIa, the B domain and an activation peptide (ap) are released, and cleavage between the A1 and A2 domains produces an A1:A2:A3-C1-C2 heterotrimer (Lollar P & Parker ET 1991; Nogami K et al. 2005; Newell JL & Fay PJ 2007; 2009). Once activated, FVIIIa dissociates from vWF and binds to the membrane of activated platelets to assemble with activated factor IX (FIXa) (Gilbert GE & Arena AA 1996; Ahmad SS et al. 2003; Panteleev MA et al. 2004; Ngo JC et al. 2008). At physiologic concentrations, the A2 subunit spontaneously dissociates, leading to loss of FVIIIa cofactor activity (Lollar P & Parker CG 1990).
Hemophilia A results from a broad spectrum of mutations that occur along the entire length of the F8 gene causing diverse molecular phenotypes that result in similar disease states (Peyvandi F et al. 2016). Together with missense mutations being the most common type of mutations in hemophilia A, a relatively frequent cause is ascribable to nonsense and splice site mutations, deletions/insertions and promoter mutations (Hakeos WH et al. 2002; Wei W et al. 2017; Jacquemin M et al. 2000; Amano K et al. 1998; Gilbert GE et al. 2012; Pahl S et al. 2014; Peyvandi F et al. 2016). In addition, the inversion of intron 1 or 22 in the F8 gene is responsible for approximately half of severely affected hemophilia A patients (Antonarakis SE et al. 1995). Although specific FVIII missense mutations correlate with defects including decreased secretion or stability and specific functional impairment of FVIII, the mechanisms of the majority of missense mutations are poorly understood (Hakeos WH et al. 2002; Wei W et al. 2017, 2018; Jacquemin M et al. 2000; Amano K et al. 1998; Gilbert GE et al. 2012; Pahl S et al. 2014). The Reactome module describes several molecular mechanisms underlying hemophilia A which include:(1) low-level secretion of defective FVIII molecule as a result of impaired FVIII folding and intracellular processing, (2) reduced ability of FVIII variants to bind to von Willebrand factor (VWF) that leads to instability of FVIII variants in the plasma, (3) abnormal interaction of defective FVIII with FIXa. Defects in FVIII activity may also result in potentially slowing down FVIII activation by thrombin or altering stability of activated FVIIIa.
R-HSA-9657688 Defective factor XII causes hereditary angioedema Hereditary angioedema (HAE) is a rare life-threatening inherited edema disorder that is characterized by recurrent episodes of localized edema of the skin or of the mucosa of the gastrointestinal tract or upper airway. The edema formation in patients with HAE is primarily caused by a transient increased bradykinin release from high molecular weight kininogen (HK) due to uncontrolled activation of the coagulation factor XII (FXII)-dependent kallikrein kinin system (KKS) (Bossi F et al. 2009; Kaplan AP 2010; Suffritti C et al. 2014: Zuraw BL & Christiansen SC 2016). Angioedema initiated by bradykinin is usually associated with SERPING1 (C1-INH) deficiency. SERPING1 is the major regulator of the contact system. More rarely, HAE occurs in individuals with normal SERPING1 activity, and has been linked to mutations in other proteins, including FXII, plasminogen, and angiopoietin (Magerl M et al. 2017; Zuraw BL 2018; Ivanov I et al. 2019). Substitution of threonine 328 by either a lysine or an arginine residue (T328K or T328R) in the FXII proline-rich region has been identified in several families with HAE and normal SERPING1. FXII T328K or T328R variants change protein glycosylation and introduce a new site that is sensitive to enzymatic cleavage by fibrinolytic and coagulation proteases such as plasmin, thrombin, or FXIa (de Maat S et al. 2016; Ivanov I et al. 2019). The intrinsic capacity of the truncated form of FXII (329-615) (also known as δFXII) to convert prekallikrein to kallikrein is greater than that of FXII leading to more kallikrein generated early during reciprocal activation (Ivanov I et al. 2019). Second, FXII (329-615) is a better kallikrein substrate than is FXII. The accelerated kallikrein/FXII activation with truncated FXII (329-615) appears to overwhelm the regulatory function of SERPING1 at normal plasma levels leading to uncontrolled bradykinin formation (de Maat S et al. 2016; Ivanov I et al. 2019). Binding of the proinflammatory peptide hormone bradykinin to the bradykinin B2 receptor (B2R) activates various proinflammatory signaling pathways that increase vascular permeability and fluid efflux. An excessive formation of bradykinin due to uncontrolled activation of FXII-dependent KKS causes increased vascular permeability at the level of the postcapillary venule and results in HAE (Zuraw BL & Christiansen SC 2016; de Maat S et al. 2016; Ivanov I et al. 2019).
R-HSA-9673240 Defective gamma-carboxylation of F9 Naturally occurring hemophilia B (HB)-associated point mutations in the FIX propeptide sequence reduce affinity to gamma-glutamyl carboxylase (GGCX) resulting in reduced γ-carboxylation and aberrant propeptide processing (Bentley AK et al. 1986; Rabiet MJ et al. 1987; Diuguid DL et al. 1986; Ware J et al. 1989; de la Salle C et al. 1993). Unprocessed FIX variants such as F9 N43Q/L or F9 N46S, circulate with the attached propeptide and show delayed FIX activation (Bentley AK et al. 1986; Diuguid DL et al. 1986; Ware J et al. 1989; de la Salle C et al. 1993).
R-HSA-9701192 Defective homologous recombination repair (HRR) due to BRCA1 loss of function In addition to its role in DNA double-strand break (DSB) signaling, BRCA1 plays an important role in homologous recombination repair (HRR) of DSBs by directly promoting recruitment of PALB2 and indirectly BRCA2 to DSB repair sites. In addition, BRCA1 increases the speed and processivity of DNA end resection which consists of 5′–3′ nucleolytic degradation of DSBs (Cruz-Garcia et al. 2014). The direct BRCA1 interaction with PALB2 helps to fine-tune the localization of BRCA2 and RAD51 at DSBs (Zhang et al. 2009, Sy et al. 2009). PALB2 simultaneously interacts with RAD51, BRCA2 and RAD51AP1 (Modesti et al. 2007, Wiese et al. 2007, Buisson et al. 2010, Dray et al. 2010). PALB2 and RAD51AP1 synergistically stimulate RAD51 recombinase activity, thus enhancing RAD51-mediated strand exchange (branch migration) and promoting the formation of D-loop structures (synaptic complex assembly). A D-loop structure is formed when complementary duplex DNA (sister chromatid arm) is progressively invaded by the RAD51 nucleoprotein filament, with base pairing of the invading ssDNA and the complementary sister chromatid DNA strand (Sung et al. 2003).
The N-terminal region of BRCA1 contains the RING domain (residues 7-98), required for the heterodimerization of BRCA1 with BARD1. BRCA1:BARD1 heterodimer has E3 ubiquitin ligase activity which is important for DNA repair (Drost et al. 2011). Several missense mutations within the RING domain have been linked to increased risks of developing breast/ovarian cancers (Bouwman et al. 2013; Starita et al. 2018). BRCA1 mutant proteins impaired in BARD1 binding are annotated in the pathway "Defective DNA double strand break response due to BRCA1 loss of function".
The C-terminal region of BRCA1 which contains two coiled coil domains (residues 1397-1424) and two BRCT domains (residues 1642-1736 for BRCT 1; residues 1756-1855 for BRCT 2) is involved in PALB2 binding, with the second coiled coil domain being essential (Sy et al. 2009). Several cancer-associated BRCA1 missense mutants that affect the C-terminal region were shown to have reduced ability to bind PALB2 (Sy et al. 2009). In addition, many nonsense and frameshift mutations in BRCA1 reported in cancer result in truncated proteins that lack the PALB2-binding domain.
R-HSA-9701190 Defective homologous recombination repair (HRR) due to BRCA2 loss of function BRCA2 (FANCD1) is a tumor suppressor gene located on chromosomal arm 13q. BRCA2 protein is a mediator of the core mechanism of homologous recombination repair (HRR), essential for the recruitment of RAD51 recombinase to resected DNA double-strand breaks (DSBs). Monoallelic pathogenic germline mutations in BRCA2 are one of the underlying causes of the hereditary breast and ovarian cancer (HBOC) syndrome, with carriers having close to 50% lifetime risk for development of breast cancer and about 15% lifetime risk for development of ovarian cancer. In addition, BRCA2 germline mutation carriers are predisposed to cancers of the fallopian tube, pancreas, stomach, larynx and prostate. Biallelic germline mutations in BRCA2 cause Fanconi anemia subtype characterized by brain and soft tissue tumors, including medulloblastoma and Wilms tumor. BRCA2-deficient cells are defective in the formation of RAD51 foci upon treatment with DSB-inducing DNA damaging agents and accumulate chromatid breaks and radial chromosomes.
Besides its crucial role in HRR, BRCA2 is also implicated in protection of replication forks, centrosome duplication, spindle assembly checkpoint and cytokinesis. Recently published studies show the involvement of BRCA2 in the turnover of R-loops (hybrids between RNA and single strand DNA that are generated as intermediates of gene transcription). Unscheduled accumulated R-loops may be processed into DSBs, leading to genomic instability. Finally, BRCA2 is involved in pathway choice of DSB repair by inhibiting DNA polymerase theta-mediated end-joining (TMEJ) until M-phase (reviewed in Petropoulos and Halazonetis 2021, and Llorens-Agost et al. 2021). TMEJ is the predominant pathway for microhomology-mediated end joining MMEJ/alternative-nonhomologous end joining (alt-NHEJ, a-EJ) in mammals (reviewed in Ramsden et al. 2022).
BRCA2 haploinsufficiency is frequently observed in cancers, with close to 50% of BRCA2-mutant breast cancers retaining one wild type allele, suggesting that in some tissues at least heterozygous loss of BRCA2 function is sufficient for carcinogenesis. Promoter hypermethylation is not an obvious contributor to BRCA2 gene inactivation and no pathogenic mutations in the promoter region have been identified so far.
For review, please refer to Roy et al. 2011, Nalepa and Clapp 2018, Santana dos Santos et al. 2018, Venkitaraman 2019, Le et al. 2021, and Llorens-Agost et al. 2021.
R-HSA-9701193 Defective homologous recombination repair (HRR) due to PALB2 loss of function Biallelic loss-of-function mutations in PALB2 results in Fanconi anemia subtype N (FA-N), which is phenotypically very similar to Fanconi anemia subtype D1, caused by biallelic loss-of-function of BRCA2 (Reid et al. 2007). FA-D1 and FA-N are characterized by developmental abnormalities, bone marrow failure and childhood cancer susceptibility, especially childhood solid tumors, such as Wilms tumor and medulloblastoma. Monoallelic PALB2 loss-of-function is an underlying cause of hereditary breast cancer in particular, but inactivating PALB2 mutations are also to a lesser extent found in some other cancer types, including pancreatic cancer (Erkko et al. 2007, Erkko et al. 2008, Antoniou et al. 2014, Yang et al. 2020). Germline PALB2 mutations are somewhat less frequent than those occurring in BRCA1 and BRCA2, but cause a comparably high risk of developing breast cancer. Therefore, PALB2 is a high-risk breast cancer predisposing gene (Nepomuceno et al. 2021).
PALB2 interacts with both BRCA1 and BRCA2, and serves as a bridge that connects BRCA2 with BRCA1 at sites of DNA double-strand break repair (DSBR). PALB2 also interacts directly with DNA and takes part in the regulation of RAD51-mediated homologous recombination (Buisson et al. 2010; Dray et al. 2010). PALB2 loss-of-function mutations can affect its interaction with BRCA1 when they affect the N-terminal coiled-coil domain that is necessary for BRCA1 binding (Sy et al. 2009, Foo et al. 2017). Mutations in the coiled-coil domain can also affect PALB2 self-interaction, recruitment to double-strand break sites, homologous recombination repair and RAD51 foci formation (Buisson and Masson 2012). PALB2 missense mutants that do not bind to BRCA1 can still be recruited to DSBR sites, probably through interaction with other proteins involved in DSBR, but they are unable to restore efficient gene conversion in PALB2-deficient cells and they render cells hypersensitive to the DNA damaging agent mitomycin C (Sy et al. 2009), with some variants also presenting sensitivity to PARP inhibitors (Foo et al. 2017).
Mutations evaluated so far in the central region of PALB2, which contains the ChAM motif and the MRG15-binding region, have shown no functional impact on the protein.
Mutations affecting the C-terminal WD40 domain of PALB2 impair its ability to interact with BRCA2, RAD51 and/or RAD51C (Erkko et al. 2007, Park et al. 2014, Simhadri et al. 2019). In addition, disruption of the WD40 domain can lead to the exposure of a nuclear export signal (NES), leading to cytoplasmic translocation of PALB2 (Pauty et al. 2017). Mutations affecting the C-terminal domain of PALB2 are more frequent than mutations that affect the N-terminus and have been observed, as germline mutations, in familial breast cancer and in Fanconi anemia, but somatic mutations also occur in sporadic cancers. Cells that express PALB2 mutants defective in BRCA2, RAD51 and/or RAD51C binding show reduced ability to perform DSBR via homologous recombination repair, form fewer RAD51 foci at DSBR sites, and are sensitive to DNA crosslinking agents such as mitomycin C (Erkko et al. 2007, Parker et al. 2014).
For review, please refer to Tischkowitz and Xia 2010, Pauty et al. 2014, Park et al. 2014, Nepomuceno et al. 2017, Ducy et al. 2019, Wu et al. 2020, Nepomuceno et al. 2021.
R-HSA-5688031 Defective pro-SFTPB causes SMDP1 and RDS Pulmonary surfactant-associated protein B (SFTPB), amongst other roles, is a component of surfactant, a surface-active film that helps reduce surface tension in alveoli. Defects in the SFTPB gene result in loss-of-function SFTPB proteins and accumulation of partially-processed , inactive pro-SFTPC in alveoli. Defects in SFTPB can cause pulmonary surfactant metabolism dysfunction 1 (SMDP1; MIM:265120), a rare lung disorder due to impaired surfactant homeostasis characterised by alveoli filling with floccular material. Excessive lipoprotein accumulation in the alveoli results in a form of respiratory distress syndrome in premature infants (RDS; MIM:267450) (Vorbroker et al. 1995, Li et al. 2004, Wert et al. 2009, Whitsett et al. 2015).
R-HSA-5688354 Defective pro-SFTPC causes SMDP2 and RDS Pulmonary surfactant-associated protein C (SFTPC), amongst other roles, is a component of surfactant, a surface-active film that helps reduce surface tension in alveoli. Defects in the SFTPC gene result in protein misfolding, misrouting and/or misprocessing resulting in accumulation of partially-processed, inactive pro-SFTPC in alveoli causing cell toxicity. Defects in SFTPC can cause pulmonary surfactant metabolism dysfunction 2 (SMDP2; MIM:610913), a rare lung disorder due to impaired surfactant homeostasis characterised by alveoli filling with floccular material. Cellular responses to the misfolded pro-SFTPC products include ER stress, the activation of reactive oxygen species and autophagy. Excessive lipoprotein accumulation in the alveoli results in a form of respiratory distress syndrome in premature infants (RDS; MIM:267450) (Thomas et al. 2002, Mulugeta et al. 2005, Thurm et al. 2013, Whitsett et al. 2015).
R-HSA-9710421 Defective pyroptosis Pyroptosis is a form of lytic inflammatory programmed cell death that is mediated by the pore‑forming gasdermins (GSDMs) (Shi J et al. 2017) to stimulate immune responses through the release of pro‑inflammatory interleukin (IL)‑1β, IL‑18 (mainly in GSDMD-mediated pyroptosis) as well as danger signals such as adenosine triphosphate (ATP) or high mobility group protein B1 (HMGB1) (reviewed in Shi J et al. 2017; Man SM et al. 2017; Tang D et al. 2019; Lieberman J et al. 2019). Pyroptosis protects the host from microbial infection but can also lead to pathological inflammation if overactivated or dysregulated (reviewed in Orning P et al. 2019; Tang L et al. 2020). During infections, the excessive production of cytokines can lead to a cytokine storm, which is associated with acute respiratory distress syndrome (ARDS) and systemic inflammatory response syndrome (SIRS) (reviewed in Tisoncik JR et al. 2012; Karki R et al. 2020; Ragab D et al. 2020). Pyroptosis has a close but complicated relationship to tumorigenesis, affected by tissue type and genetic background. Pyroptosis can trigger potent antitumor immune responses or serve as an effector mechanism in antitumor immunity (Wang Q et al. 2020; Zhou Z et al. 2020; Zhang Z et al. 2020), while in other cases, as a type of proinflammatory death, pyroptosis can contribute to the formation of a microenvironment suitable for tumor cell growth (reviewed in Xia X et al. 2019; Jiang M et al. 2020; Zhang Z et al. 2021).
This Reactome module describes the defective GSDME function caused by cancer‑related GSDME mutations (Zhang Z et al. 2020). It also shows epigenetic inactivation of GSDME due to hypermethylation of the GSDME promoter region (Akino K et al. 2007; Kim MS et al. 2008a,b; Croes L et al. 2017, 2018; Ibrahim J et al. 2019). Aberrant promoter methylation is considered to be a hallmark of cancer (Ehrlich M et al. 2002; Dong Y et al. 2014; Lam K et al. 2016; Croes L et al. 2018). Treatment with the DNA methyltransferase inhibitor decitabine (5‑aza‑2'‑deoxycytidine or DAC) may elevate GSDME expression in certain cancer cells (Akino K et al. 2007; Fujikane T et al. 2009; Wang Y et al. 2017). R-HSA-9824856 Defective regulation of TLR7 by endogenous ligand Activation of innate immune receptors including Toll-like receptors (TLRs) by pathogen-associated molecular patterns (PAMPs) is crucial in the host defense against microbial infections. On the other hand, these receptors are also activated by diverse molecules of host-cell origin. These molecules are known as damage-associated molecular patterns (DAMPs). This Reactome module describes defects in activation of TLRs by the endogenous ligands.
DAMPs are released from necrotic cells or secreted from activated cells in response to tissue damage to mediate tissue repair by promoting inflammatory responses (reviewed by Piccinini AM et al., 2010; Gong T et al., 2020; Zindel LJ et al., 2020). However, DAMPs have also been implicated in the pathogenesis of many inflammatory and autoimmune diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and atherosclerosis (Duffy L & O’Reilly SC 2016; Fukuda D et al., 2019; Gong T et al., 2020; Liu J et al., 2022). There is a correlation between high level of endogenous TLR ligands and different chronic inflammatory conditions in human subjects and mouse models (Duvvuri B & Lood C et al., 2019; Negishi H et al., 2019; Punnanitinont A et al., 2022). The mechanism underlying the switch from DAMPs that initiate controlled tissue repair, to those that mediate chronic, uncontrolled inflammation is still unclear. Studies suggest that an abnormal increase in protein citrullination is involved in disease pathophysiology (Anzilotti C et al., 2010; Sanchez-Pernaute O et al., 2013; Sokolove J et al., 2011; Sharma P et al., 2012; Olsen I et al., 2018). Moreover, gene polymorphisms within TLRs may predispose to the abnormal inflammatory responses associated with chronic diseases including autoimmune diseases (Devarapu SK & Anders HJ 2018; Zhang Y et al., 2021). For example, polymorphisms that increase expression of TLR7 are associated with a higher risk of SLE (reviewed in Fillatreau S et al., 2021). Further, inherited genetic variations can promote autoimmune responses. For example, TLR7 Y264H was identified as a gain-of-function mutation in a patient with SLE (Brown GJ et al., 2022). TLR7 Y264H exhibited enhanced affinity to endogenous guanosine-containing ligands (Brown GJ et al., 2022).
R-HSA-9661070 Defective translocation of RB1 mutants to the nucleus This pathway describes impaired nuclear localization of RB1 mutants that lack the nuclear localization signal (NLS) (Zacksenhaus et al. 1993, Bremner et al. 1997).
R-HSA-9918454 Defective visual phototransduction due to ABCA4 loss of function ATP-binding cassette protein A4 (ABCA4, ABCR), expressed exclusively in retinal photoreceptors, is thought to be involved in the clearance of toxic by-products of the retinoid cycle. Defects in ABCA4 cause a diverse range of human diseases. One such disease is Stargardt's disease type 1 (STGD1, MIM:248200) (Allikmets et al. 1997), an autosomal recessive form of juvenile macular degeneration leading to progressive irreversible loss of central vision and delayed dark adaptation. STGD1 was first identified by Stargardt in 1909 (Stargardt, Arch. Klin. Exp. Ophthal. 71: 534-549, 1909), has an approximate prevalence of 1 in 10,000 (see reviews Paskowitz et al. 2006, Walia & Fishman 2009) and is usually diagnosed within the first two decades of life.
R-HSA-9918442 Defective visual phototransduction due to LRAT loss of function Normally functioning lecithin retinol acyltransferase (LRAT) mediates the transfer of an acyl group onto all-trans-retinol (atROL), forming retinyl esters (REs), the storage form of retinoids. Defects in LRAT cause Leber congenital amaurosis type 14 (LCA14, MIM:613341), an autosomal recessive juvenile-onset retinal dystrophy affecting rod and cone photoreceptors. Leber congenital amaurosis (LCA) comprises a group of early-onset retinal dystrophies characterized by vision loss, nystagmus, and severe retinal dysfunction (Chung & Traboulsi 2009).
R-HSA-9918450 Defective visual phototransduction due to OPN1LW loss of function Blue cone monochromatism (BCM) is a rare X-linked congenital cone dysfunction characterized by the absence of functional long wavelength-sensitive (red) and medium wavelength-sensitive (green) cones in the retina. Colour discrimination is severely impaired from birth, and vision is derived from the preserved short wavelength-sensitive (blue) cones and rod photoreceptors. BCM typically presents with reduced visual acuity, pendular nystagmus, photophobia and patients often have myopia. BCM affects approximately 1 in 100,000 individuals and can be caused by loss-of-function mutations in the OPN1LW gene (see review Gardner et al. 2009).
Defects in OPN1LW also cause partial colorblindness, protan series (CBP, protanopia; MIM:303900) due to non-functional red cones (Ueyama et al. 2002).
R-HSA-9918436 Defective visual phototransduction due to OPN1MW loss of function Normal human colour vision is trichromatic, based on 3 types of cones that are maximally sensitive to light at approximately 420 nm (blue cones), 530 nm (green cones), and 560 nm (red cones). Neural circuits compare light absorbed by these 3 cone types to perceive those primary colours and combinations of them. Colour vision deficiencies result from genetic mutations that affect the expression of the full complement of cone photoreceptors and are classified by severity of deficiency (see reviews Deeb 2005, Simunovic 2010).
Deutan colourblindness (DCB, deuteranopia, partial colorblindness, green colourblindness; MIM:303800) is caused by mutations in the OPN1MW gene which encodes green cones. In European populations, red-green colourblindness is prevelant in 8% of males and 0.5% of females. This frequency is lower in non-European populations (Deeb 2005).
Defects in OPN1MW also cause X-linked cone dystrophy type 5 (COD5; MIM:303700), a retinal dystrophy characterized by progressive degeneration of cone photoreceptors but with preserved rod function.
R-HSA-9918443 Defective visual phototransduction due to OPN1SW loss of function Normal human colour vision is trichromatic, based on 3 types of cones that are maximally sensitive to light at approximately 420 nm (blue cones), 530 nm (green cones), and 560 nm (red cones). Neural circuits compare light absorbed by these 3 cone types to perceive those primary colours and combinations of them. Colour vision deficiencies result from genetic mutations that affect the expression of the full complement of cone photoreceptors and are classified by severity of deficiency (see reviews Deeb 2005, Simunovic 2010).
Tritan (blue-yellow, blue colourblindness, tritanopia; MIM:190900) deficiencies are rare (1 in 500) (Went & Pronk 1985) compared to those involving green- and red-cone deficiencies. The first report of tritan defects was in 1952 (Wright 1952). Tritan deficiencies are inherited as autosomal dominant traits (Kalmus 1955) and are a result of missense mutations in the blue-cone photopigment gene OPN1SW, leading to amino-acid substitutions in the protein sequence. Tritan defects are characterized by a selective deficiency of blue spectral sensitivity (Weitz et al. 1992).
R-HSA-9918440 Defective visual phototransduction due to RDH12 loss of function Retinol dehydrogenase RDH12 mediates the reversible, NADP(H)-dependent reduction of all-trans-retinal (atRAL) or 11-cis-retinal (11cRAL) to all-trans-retinol (atROL) or 11-cis-retinol (11cROL) respectively in photoreceptor cells.
Defects in RDH12 cause Leber congenital amaurosis type 13 (LCA13; MIM:612712). LCA defects are early-onset and severe retinal degenerations that are responsible for the most common cause of congenital blindness in infants and children (Janecke et al. 2004; Perrault et al. 2004).
Defects in RDH12 cause retinitis pigmentosa type 53 (RP53; MIM:612712), an autosomal recessive retinal dystrophy characterised by retinal pigment deposits and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptor cells (Benayoun et al. 2009).
R-HSA-9918438 Defective visual phototransduction due to RDH5 loss of function 11-cis-retinol dehydrogenase (RDH5) can reversibly catalyse the oxidation of all-trans-retinol (atROL, bound to RLBP1) to all-trans-retinal (atRAL) in retinal pigment epithelium (RPE) cells using NAD+ as cofactor. Defective RDH5 causes retinitis punctata albescens (RPA, also called fundus albipunctatus, FA; MIM:136880). RPA (an autosomal recessive disorder) is a form of stationary congenital night blindness characterised by a reduced regeneration rate of rod and cone photoreceptors and yellow-white lesions within the retina or the RPE. For review, please refer to Zeitz et al. 2015.
R-HSA-9918449 Defective visual phototransduction due to STRA6 loss of function Defects in STRA6 cause microphthalmia syndromic type 9 (MCOPS9, Matthew-Wood syndrome or Spear syndrome; MIM:601186) (Chassaing et al. 2009). Mutiple systems are affected by this fatal syndrome including occular and cardiac abnormalities. Microphthalmia (also called microphthalmos, nanophthalmia or nanophthalmos) is a developmental disorder of the eye that literally means small eye and in most cases results in blindness.
R-HSA-3323169 Defects in biotin (Btn) metabolism Biotin (Btn, vitamin B7, vitamin H, coenzyme R) is an essential cofactor for five biotin-dependent carboxylase enzymes, involved in the synthesis of fatty acids, isoleucine, valine and in gluconeogenesis. Thus, Btn is necessary for cell growth, fatty acid synthesis and the metabolism of fats and amino acids. Inherited metabolic disorders characterized by deficient activities of all five biotin dependent carboxylases are termed multiple carboxylase deficiencies. Two congenital defects in biotin metabolism leading to multiple carboxylase deficiency are known, holocarboxylase synthetase deficiency (MIM 609018) and biotinidase deficiency (MIM 253260). In both scenarios symptoms include ketolactic acidosis, organic aciduria, hyperammonemia, skin rashes, hypotonia, seizures, developmental delay, alopecia, and coma. As humans are auxotrophic for Btn, the micronutrient must be obtained from external soures such as intestinal microflora and dietary forms. Accordingly, severe malnutrition can also give rise to biotin deficiency and multiple carboxylase deficiency. Biotin deficiency can also be induced by the excessive consumption of raw egg white that contains the biotin-binding protein avidin. Holocarboxylase synthetase deficiency arises when all five biotin-dependent enzymes are not biotinylated leading to their reduced activities. The defective genes causing these conditions are described here (Pendini et al. 2008, Suzuki et al. 2005). Biotinidase deficiency is caused by defects in the recycling of Btn. General symptoms include decreased appetite and growth, dermatitis and perosis. The defective genes causing these conditions are described here (Procter et al. 2013).
R-HSA-3296469 Defects in cobalamin (B12) metabolism Cobalamin (Cbl, vitamin B12) is a nutrient essential for normal functioning of the brain and nervous system and for the formation of blood. Cbl-dependent methionine synthase (MTR) is required for conversion of 5-methyltetrahydrofolate (metTHF) to tetrahydrofolate (THF), in addition to its role in conversion of homocysteine to methionine. In Cbl deficiency, and in inborn errors of Cbl metabolism that affect function of methionine synthase, inability to regenerate THF from metTHF results in decreased function of folate-dependent reactions that are involved in 2 steps of purine biosynthesis and thymidylate synthesis. Cbl deficiency results in hyperhomocysteinemia (due to defects in the conversion of homocysteine to methionine which requires Cbl as a cofactor) and increased levels of methylmalonic acid (MMA). Methionine is used in myelin production, protein, neurotransmitter, fatty acid and phospholipid production and DNA methylation. Symptoms of Cbl deficiency are bone marrow promegaloblastosis (megaloblastic anemia) due to the inhibition of DNA synthesis (specifically purines and thymidine) and neurological symptoms. The defective genes involved in Cbl deficiencies are described below (Froese & Gravel 2010, Nielsen et al. 2012, Whitehead 2006, Watkins & Rosenblatt 2011, Fowler 1998).
R-HSA-3296482 Defects in vitamin and cofactor metabolism Vitamins are essential nutrients, required in small amounts from the diet for the normal growth and development of a multicellular organism. Where there is vitamin deficiency, either by poor diet or a defect in metabolic conversion, diseases called Avitaminoses occur. Currently, cobalamin (Cbl, vitamin B12) metabolic defects are described below (Chapter 155 in The Metabolic and Molecular Bases of Inherited Disease, 8th ed, Scriver et al. 2001)
R-HSA-9651496 Defects of contact activation system (CAS) and kallikrein/kinin system (KKS) The contact activation system (CAS) is a plasma protease cascade initiated by factor XII (FXII) that activates the pro-inflammatory kallikrein‐kinin system (KKS) and the pro-coagulant intrinsic coagulation pathway (Renne T 2012; Renne T et al. 2012; Maas C et al. 2011; Schmaier AH 2016; Long AT et al. 2016). The CAS is initiated by the auto‐activation of factor XII (FXII) on charged or neutral surfaces with conversion of plasma prekallikrein (PK) to plasma kallikrein (Samuel M et al. 1992; Ivanov I et al. 2017). These events are followed by reciprocal activation of FXII by kallikrein and amplification of each other's activation. Two branches of the CAS have been identified: (i) the inflammatory branch activates contact factors FXII and PK on the surface of endothelial cells resulting in release of the peptide bradykinin (BK) and (ii) the plasma coagulation branch activates FXII and FXI on the surface of platelets. The CAS is thought to be central to crosstalk between coagulation and inflammation and the underlying cause for various disorders affecting the cardiovascular system (Wu Y 2015; Long AT et al. 2016). Physiologically, a fine balance is normally maintained between blood flow and blood clotting, the dysfunction of which yields either hemorrhage or thrombosis. Defects in the intrinsic pathway coagulation factors (FVIII, FIX, and FXI) are associated with a significant bleeding tendency. The X-linked recessive disorders, hemophilia A (FVIII deficiency) and B (FIX deficiency), are associated with spontaneous and excessive hemorrhage, especially hemarthroses and muscle hematomas (Bowen DJ 2002; Goodeve AC 2015). A deficiency in FXI, which is encoded by a gene on chromosome 4, generally results in a less severe, but still significant, bleeding tendency (James P et al. 2014; Puy C et al. 2016). Although PK and FXIIa are recognized as upstream triggers for the intrinsic coagulation system, the clinical significance of these factors on thrombosis and hemorrhage is not fully understood. The CAS blockade results in prolonged coagulation times in the activated partial thromboplastin time (aPTT) assay. However, the absence of thrombotic and hemostatic abnormalities in individuals with genetic deficiencies of PK or FXII has suggested that the CAS plays a minimal role in physiological coagulation (Müller F et al. 2011). At the same time, excessive formation of bradykinin due to abnormal FXII-dependent KKS activation causes increased vascular permeability at the level of the post capillary venule and results in hereditary angioedema (HAE). HAE initiated by bradykinin is usually associated with SERPING1 (C1-INH) deficiency (Suffritti C et al. 2014). More rarely, HAE occurs in individuals with normal SERPING1 activity, and has been linked to mutations in other proteins, including FXII, plasminogen, and angiopoietin (Cichon S et al. 2006; Magerl M et al. 2017; Zuraw BL 2016; Ivanov I et al. 2019). This Reactome module describes abnormal FXII-dependent KKS activation that leads to an excessive formation of bradykinin causing increased vascular permeability at the level of the post capillary venule and results in hereditary angioedema (HAE). HAE caused by defective function of SERPING1 is also covered here. The module also includes disorders that can cause abnormal bleeding due to a shortage (deficiency) of coagulation factor proteins, which are involved in blood clotting. This module also describes elevation of FIX activity associated with thrombophilia. Genetic variants are named following Human Genome Variation Society (HGVS) nomenclature with sequence numbering starting from the first methionine of the protein as +1.(Goodeve AC et al.2011).
R-HSA-9823587 Defects of platelet adhesion to exposed collagen This Reactome module describes dysfunctions in platelet adhesion caused by mutations in different genes, including VWF, ADAMTS13 and GP1BA.
R-HSA-1461973 Defensins The defensins are a family of antimicrobial cationic peptide molecules which in mammals have a characteristic beta-sheet-rich fold and framework of six disulphide-linked cysteines (Selsted & Ouellette 2005, Ganz 2003). Human defensin peptides have two subfamilies, alpha- and beta-defensins, differing in the length of peptide chain between the six cysteines and the order of disulphide bond pairing between them. A third subfamily, the theta defensins, is derived from alpha-defensins prematurely truncated by a stop codon between the third and fourth cysteine residues. The translated products are shortened to nonapeptides, covalently dimerized by disulfide linkages, and cyclized via new peptide bonds between the first and ninth residues. Humans have one pseudogene but no translated representatives of the theta class.
In solution most alpha and beta defensins are monomers but can form dimers and higher order structures.
The primary cellular sources of defensins are neutrophils, epithelial cells and intestinal Paneth cells.Those expressed in neutrophils and the gut are predominantly constitutive, while those in epithelial tissues such as skin are often inducible by proinflammatory stimuli such as LPS or TNF-alpha.
Defensins are translated as precursor polypeptides that include a typical signal peptide or prepiece that is cleaved in the Golgi body, and a propiece, cleaved by differing mechanisms to produce the mature defensin. Mature defensin peptides can be further processed by removal of individual N-terminal residues (Yang et al. 2004). This may be a mechanism to broaden the activity profile of defensins (Ghosh et al. 2002).
Defensins have direct antimicrobial effects and kill a wide range of Gram-positive and negative bacteria, fungi and some viruses. The primary antimicrobial action of defensins is permeabilization of microbial target membranes but several additional mechanisms have been suggested (Brogden 2005, Wilmes et al. 2011). Defensins and related antimicrobial peptides such as cathelicidin bridge the innate and acquired immune responses. In addition to their antimicrobial properties, cathelicidin and several defensins show receptor-mediated chemotactic activity for immune cells such as monocytes, T cells or immature DCs, induce cytokine production by monocytes and epithelial cells, modulate angiogenesis and stimulate wound healing (Yang et al. 1999, 2000, 2004, Rehaume & Hancock 2008, Yeung et al. 2011).
R-HSA-4641257 Degradation of AXIN AXIN is present in low concentrations in the cell and is considered to be the limiting component of the beta-catenin destruction complex in Xenopus; this may not be the case in mammalian cells, however (Lee et al, 2003; Tan et al, 2012). Cellular levels of AXIN are regulated in part through ubiquitin-mediated turnover. E3 ligases SMURF2 and RNF146 have both been shown to play a role in promoting the degradation of AXIN by the 26S proteasome (Kim and Jho, 2010; Callow et al, 2011; Zhang et al, 2011).
R-HSA-4641258 Degradation of DVL DVL protein levels are regulated by both proteasomal and lysosomal degradation (reviewed in Gao and Chen, 2010). The E3 ligases HECF1, ITCH and KLHL12:CUL3 have all been shown to contribute to the polyubiquitination and subsequent degradation of DVL (Angers et al, 2006; Miyazaki et al, 2004; Wei et al, 2012). DVL stability is also regulated by its interaction with DACT1, which promotes degradation of DVL in the lysosome (Cheyette et al, 2002; Zhang et al, 2006).
R-HSA-916853 Degradation of GABA GABA is metabolized in the mitochondrial matrix to succinate by the serial action of two enzymes, 4-aminobutyrate aminotransferase and suucinate semialdehyde dehydrogenase. Failure of the second reaction is associated with a rare human genetic disorder (Malaspina et al. 2016; Pearl et al. 2009).
R-HSA-5610780 Degradation of GLI1 by the proteasome GLI1 is the most divergent of the 3 mammalian GLI transcription factors and lacks a transcriptional repressor domain. Although GLI1 is dispensible for development, the gene is an early transcriptional target of Hh signaling and the protein contributes a minor activation function in mammals (Dai et al, 1999; Bai et al, 2002; Park et al, 2000).
In the absence of Hh signaling, GLI1 is completely degraded by the proteasome, in contrast to the partial processing that occurs with GLI3. This differential response reflects the absence in GLI1 of two of the three elements identified in GLI3 that promote partial proteolysis; these are the zinc finger region, present in all GLI proteins, and an adjacent linker sequence and the degron, neither of which are found in the GLI1 protein (Schrader et al, 2011; Pan and Wang, 2007).
R-HSA-5610783 Degradation of GLI2 by the proteasome The primary role of the GLI2 protein is as an activator of Hh-dependent signaling upon pathway stimulation; in the absence of Hh ligand, a small fraction of GLI2 appears to be processed to a repressor form, but the bulk of the protein is completely degraded by the proteasome (reviewed in Briscoe and Therond, 2013). Both the processing and the degradation of GLI2 is dependent upon sequential phosphorylation of multiple serine residues by PKA, CK1 and GSK3, analagous to the requirement for these kinases in the processing of GLI3 (Pan et al, 2009; Pan et al, 2006; Pan and Wang, 2007). The differential processing of GLI2 and GLI3 depends on the processing determinant domain (PDD) in the C-terminal of the proteins, which directs the partial proteolysis of GLI3 in the absence of Hh signal. Substitution of 2 amino-acids from GLI3 into the GLI2 protein is sufficient to promote efficient processing of GLI2 to the repressor form (Pan and Wang, 2007).
R-HSA-195253 Degradation of beta-catenin by the destruction complex The beta-catenin destruction complex plays a key role in the canonical Wnt signaling pathway. In the absence of Wnt signaling, this complex controls the levels of cytoplamic beta-catenin. Beta-catenin associates with and is phosphorylated by the destruction complex. Phosphorylated beta-catenin is recognized and ubiquitinated by the SCF-beta TrCP ubiquitin ligase complex and is subsequently degraded by the proteasome (reviewed in Kimelman and Xu, 2006).
R-HSA-1614558 Degradation of cysteine and homocysteine While in humans excess methionine is converted to homocysteine, homocysteine and its transsulfuration product cysteine can be degraded to several end products, two of which, taurine and hydrogen sulfide, have uses in other biological processes (Stipanuk & Ueki 2011).
R-HSA-1474228 Degradation of the extracellular matrix Matrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the metzincin family. They contain a characteristic zinc-binding motif HEXXHXXGXXH (Stocker & Bode 1995) and a conserved Methionine which forms a Met-turn. Humans have 24 MMP genes giving rise to 23 MMP proteins, as MMP23 is encoded by two identical genes. All MMPs contain an N-terminal secretory signal peptide and a prodomain with a conserved PRCGXPD motif that in the inactive enzyme is localized with the catalytic site, the cysteine acting as a fourth unpaired ligand for the catalytic zinc atom. Activation involves delocalization of the domain containing this cysteine by a conformational change or proteolytic cleavage, a mechanism referred to as the cysteine-switch (Van Wart & Birkedal-Hansen 1990). Most MMPs are secreted but the membrane type MT-MMPs are membrane anchored and some MMPs may act on intracellular proteins. Various domains determine substrate specificity, cell localization and activation (Hadler-Olsen et al. 2011). MMPs are regulated by transcription, cellular location (most are not activated until secreted), activating proteinases that can be other MMPs, and by metalloproteinase inhibitors such as the tissue inhibitors of metalloproteinases (TIMPs). MMPs are best known for their role in the degradation and removal of ECM molecules. In addition, cleavage of the ECM and other cell surface molecules can release ECM-bound growth factors, and a number of non-ECM proteins are substrates of MMPs (Nagase et al. 2006). MMPs can be divided into subgroups based on domain structure and substrate specificity but it is clear that these are somewhat artificial, many MMPs belong to more than one functional group (Vise & Nagase 2003, Somerville et al. 2003).
R-HSA-5467343 Deletions in the AMER1 gene destabilize the destruction complex Genomic deletions of the entire AMER1/WTX gene occur in about 12% of Wilms tumors, a pediatric kidney cancer. Nonsense and missense mutations have also been identified (Ruteshouser et al, 2008; Wegert et al, 2009). AMER1 is a known component of the destruction complex and interacts directly with beta-catenin through the C-terminal half (Major et al, 2007). siRNA depletion of AMER1 in mammalian cells stabilizes cellular beta-catenin levels and increases the expression of a beta-catenin-dependent reporter gene, suggesting that AMER1 is a tumor suppressor gene (Major et al, 2007; reviewed in Huff, 2011).
R-HSA-5467345 Deletions in the AXIN1 gene destabilize the destruction complex Deletions in the AXIN1 gene have been identified in 2 hepatocellular carcinoma cell lines. These deletions, which remove the N-terminal exons of the gene, compromise AXIN1 expression and result in elevated expression of a TCF-dependent reporter (Satoh et al, 2000, reviewed in Salahshor and Woodgett, 2005).
R-HSA-4419969 Depolymerization of the Nuclear Lamina The nuclear envelope breakdown in mitotic prophase involves depolymerization of lamin filaments, the main constituents of the nuclear lamina. The nuclear lamina is located at the nuclear face of the inner nuclear membrane and plays and important role in the structure and function of the nuclear envelope (reviewed by Burke and Stewart 2012). Depolymerization of lamin filaments, which consist of lamin homodimers associated through electrostatic interactions in head-to-tail molecular strings, is triggered by phosphorylation of lamins. While CDK1 phosphorylates the N-termini of lamins (Heald and McKeon 1990, Peter et al. 1990, Ward and Kirschner 1990, Mall et al. 2012), PKCs (PRKCA and PRKCB) phosphorylate the C-termini of lamins (Hocevar et al. 1993, Goss et al. 1994, Mall et al. 2012). PKCs are activated by lipid-mediated signaling, where lipins, activated by CTDNEP1:CNEP1R1 serine/threonine protein phosphatase complex, catalyze the formation of DAG (Gorjanacz et al. 2009, Golden et al. 2009, Wu et al. 2011, Han et al. 2012, Mall et al. 2012).
R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere Eukaryotic centromeres are marked by a unique form of histone H3, designated CENPA in humans. In human cells newly synthesized CENPA is deposited in nucleosomes at the centromere during late telophase/early G1 phase of the cell cycle. Once deposited, nucleosomes containing CENPA remain stably associated with the centromere and are partitioned equally to daughter centromeres during S phase. A current model proposes that pre-existing CENPA at the centromere drives recruitment of new CENPA, however this has not been proved.
The deposition process requires at least 3 complexes: the Mis18 complex, HJURP complex, and the RSF complex. HJURP binds newly synthesized CENPA-H4 tetramers before deposition and brings them to the centromere for deposition in new CENPA-containing nucleosomes. The exact mechanism of deposition remains unknown.
R-HSA-73927 Depurination Depurination of a damaged nucleotide is mediated by a purine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, generating a free base and an abasic i.e. apurinic/apyrimidinic (AP) site (Slupphaug et al. 1996, Parikh et al. 1998).
R-HSA-73928 Depyrimidination Depyrimidination of a damaged nucleotide in DNA is mediated by a pyrimidine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar generating a free base and an abasic i.e. apurinic/apyrimidinic (AP) site (Lindahl and Wood 1999).
R-HSA-8862803 Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models Post-mitotic neurons do not have an active cell cycle. However, deregulation of Cyclin Dependent Kinase-5 (CDK5) activity in these neurons can aberrantly activate various components of cell cycle leading to neuronal death (Chang et al. 2012). Random activation of cell cycle proteins has been shown to play a key role in the pathogenesis of several neurodegenerative disorders (Yang et al. 2003, Lopes et al. 2009). CDK5 is not activated by the canonical cyclins, but binds to its own specific partners, CDK5R1 and CDK5R2 (aka p35 and p39, respectively) (Tsai et al. 1994, Tang et al. 1995). Expression of p35 is nearly ubiquitous, whereas p39 is largely expressed in the central nervous system. A variety of neurotoxic insults such as beta-amyloid (A-beta), ischemia, excitotoxicity and oxidative stress disrupt the intracellular calcium homeostasis in neurons, thereby leading to the activation of calpain, which cleaves p35 into p25 and p10 (Lee et al. 2000). p25 has a six-fold longer half-life compared to p35 and lacks the membrane anchoring signal, which results in its constitutive activation and mislocalization of the CDK5:p25 complex to the cytoplasm and the nucleus. There, CDK5:p25 is able to access and phosphorylate a variety of atypical targets, triggering a cascade of neurotoxic pathways that culminate in neuronal death. One such neurotoxic pathway involves CDK5-mediated random activation of cell cycle proteins which culminate in neuronal death. Exposure of primary cortical neurons to oligomeric beta-amyloid (1-42) hyper-activates CDK5 due to p25 formation, which in turn phosphorylates CDC25A, CDC25B and CDC25C. CDK5 phosphorylates CDC25A at S40, S116 and S261; CDC25B at S50, T69, S160, S321 and S470; and CDC25C at T48, T67, S122, T130, S168 and S214. CDK5-mediated phosphorylation of CDC25A, CDC25B and CDC25C not only increases their phosphatase activities but also facilitates their release from 14-3-3 inhibitory binding. CDC25A, CDC25B and CDC25C in turn activate CDK1, CDK2 and CDK4 kinases causing neuronal death. Consistent with this mechanism, higher CDC25A, CDC25B and CDC25C activities were observed in human Alzheimer's disease (AD) clinical samples, as compared to age-matched controls. Inhibition of CDC25 isoforms confers neuroprotection to beta-amyloid toxicity, which underscores the contribution of this pathway to AD pathogenesis
R-HSA-2022923 Dermatan sulfate biosynthesis Dermatan sulfate (DS) consists of N-acetylgalactosamine (GalNAc) residues alternating in glycosidic linkages with glucuronic acid (GlcA) or iduronic acid (IdoA) residues. As with CS, GalNAc residues can be sulfated in CS chains but also the uronic acid
residues may be substituted with sulfate at the 2- and 4- positions. The steps below outline the synthesis of a simple DS chain (Silbert & Sugumaran 2002).
R-HSA-3299685 Detoxification of Reactive Oxygen Species Reactive oxygen species such as superoxide (O2.-), peroxides (ROOR), singlet oxygen, peroxynitrite (ONOO-), and hydroxyl radical (OH.) are generated by cellular processes such as respiration (reviewed in Murphy 2009, Brand 2010) and redox enzymes and are required for signaling yet they are damaging due to their high reactivity (reviewed in Imlay 2008, Buettner 2011, Kavdia 2011, Birben et al. 2012, Ray et al. 2012). Aerobic cells have defenses that detoxify reactive oxygen species by converting them to less reactive products. Superoxide dismutases convert superoxide to hydrogen peroxide and oxygen (reviewed in Fukai and Ushio-Fukai 2011). Catalase and peroxidases then convert hydrogen peroxide to water.
Humans contain 3 superoxide dismutases: SOD1 is located in the cytosol and mitochondrial intermembrane space, SOD2 is located in the mitochondrial matrix, and SOD3 is located in the extracellular region. Superoxide, a negative ion, is unable to easily cross membranes and tends to remain in the compartment where it was produced. Hydrogen peroxide, one of the products of superoxide dismutase, is able to diffuse across membranes and pass through aquaporin channels. In most cells the primary source of hydrogen peroxide is mitochondria and, once in the cytosol, hydrogen peroxide serves as a signaling molecule to regulate redox-sensitive proteins such as transcription factors, kinases, phosphatases, ion channels, and others (reviewed in Veal and Day 2011, Ray et al. 2012). Hydrogen peroxide is decomposed to water by catalase, decomposed to water plus oxidized thioredoxin by peroxiredoxins, and decomposed to water plus oxidized glutathione by glutathione peroxidases (Presnell et al. 2013).
R-HSA-5688426 Deubiquitination Ubiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S proteasome. Ub conjugates linked via lysine 48 (K48) target substrates to the proteasome, whereas those linked via any of the six other Ub lysines can alter the function of the modified protein without leading to degradation. Deubiquitination, the reversal of this modification, regulates the function of ubiquitin-conjugated proteins. Deubiquitinating enzymes (DUBs) catalyze the removal of Ub and regulate Ub-mediated pathways.
Given that Ub is covalently-linked to proteins destined to be degraded, it is a surprisingly long-lived protein in vivo (Haas & Bright 1987). This is due to the removal of Ub from its conjugates by DUBs prior to proteolysis. This may represent a quality control mechanism that prevents the degradation of proteins that were inappropriately tagged for degradation (Lam et al. 1997). DUBs are responsible for processing inactive Ub precursors and for keeping the 26S proteasome free of unanchored Ub chains that compete for Ub-binding sites.
DUBs can be grouped into five families based on their conserved catalytic domains (Amerik & Hochstrasser 2004). Four of these families are thiol proteases and comprise the bulk of DUBs, while the fifth family is a small group of Ub specific metalloproteases.
Thiol protease DUBs contain a Cys-His-Asp/Asn catalytic triad in which the Asp/Asn functions to polarize and orient the His, while the His serves as a general acid/base by both priming the catalytic Cys for nucleophilic attack on the (iso)peptide carbonyl carbon and by donating a proton to the lysine epsilon-amino leaving group. The nucleophilic attack of the catalytic Cys on the carbonyl carbon produces a negatively charged transition state that is stabilized by an oxyanion hole composed of hydrogen bond donors. A Cys-carbonyl acyl intermediate ensues and is then hydrolyzed by nucleophilic attack of a water molecule to liberate a protein C-terminal carboxylate and regenerate the enzyme. Ub binding often causes structural rearrangements necessary for catalysis. Many DUBs are inactivated by oxidation of the catalytic cysteine to sulphenic acid (single bond SOH) (Cotto-Rios et al. 2012, Lee et al. 2013). This can be reversed by reduction with DTT or glutathione. The sulphenic acid can be irreversibly oxidized to sulphinic acid (single bond SO2H) or sulphonic acid (single bond SO3H).
Thiol proteases are reversibly inhibited by Ub C-terminal aldehyde, forming a thio-hemiacetal between the aldehyde group and the active site thiol.
R-HSA-1266738 Developmental Biology Developmental biology seeks to understand the array of processes by which a fertilized egg gives rise to the diverse tissues of the adult body. Examples of several developmental processes have been annotated here. In the early embryo, transcriptional regulation of pluripotent stem cells, gastrulation (including NODAL signaling), and activation of HOX genes during differentiation are annotated. Annotations of later, more specialized processes include nervous system development, cardiogenesis, aspects of the roles of cell adhesion molecules in axonal guidance and myogenesis, transcriptional regulation in pancreatic beta cells, adipogenesis, transcriptional regulation of granulopoeisis, transcriptional regulation of testis differentiation, LGI-ADAM interactions, and keratinization.
Transitions between cell types and cell states in developmental and differentiation processes are annotated as developmental cell lineages.
R-HSA-9734767 Developmental Cell Lineages Our bodies are built of >30 trillion cells specialized to fulfill diverse roles within our tissues, organs, and organ systems. All these cells originate from a single cell, a zygote formed at conception. From zygote to fetus, and throughout childhood, adolescence, and adulthood, cells divide and commit to different fates in order for the organism to develop, sustain and regenerate. The series of steps that lead from an undifferentiated progenitor cell, such as a stem cell, to one of its several possible specialized descendants constitutes a cell lineage path (Burgess et al. 2018). Cell lineage paths are organized by organ systems. Each cell lineage path cross-references a Gene Ontology (GO) biological process (The Gene Ontology Consortium 2019), and consists of a series of causally connected cell development steps. Cell development steps describe the transition between cell states during development or differentiation and are characterized by regulators (molecules promoting or inhibiting the step) and, when established, “required input components” (cell state biomarkers required for the action of regulators). Each cell state is characterized by a cell type defined in Cell Ontology (Sarntivijai et al. 2014; Osumi-Sutherland 2017), anatomical location from UBERON (Haendel et al. 2014), and a unique combination of protein and/or RNA markers with references, when available, to CellMarker (Hu et al. 2023) and PanglaoDB (Franzen et al. 2019). For a more detailed data model description, please refer to Milacic et al. 2024. Recent technological advances have allowed researchers to harvest high-throughput omics data from single cells of multicellular organisms and use it to track and manipulate cell fates (Burgess 2018; Saelens et al. 2019). This opens the door to the possibility of deciphering cell lineage paths at single-cell resolution, a critical requirement for the advancement of regenerative medicine and cancer medicine.
The cell lineage path “Differentiation of keratinocytes in interfollicular epidermis in mammalian skin” describes the differentiation of keratinocytes from stem cells to corneocytes in the interfollicular epidermis, the skin surface layer in between the adnexa (hair follicles, sweat glands, and sebaceous glands).
R-HSA-9925561 Developmental Lineage of Pancreatic Acinar Cells
The exocrine pancreas, which comprises more than 95% of the pancreas mass, consists of lobules formed by tubuloacinar glands that are built by two cell types: acinar cells and ductal cells. A third, centroacinar cells type has been identified in murine studies, but their existence and functional role is under debate. Acinar cells are large pyramidal secretory epithelial cells, with apical-basal polarization, that surround the lumen of the acinus. Acinar cells have prominent endoplasmic reticulum and Golgi networks, and their cytoplasm contains a large number of secretory zymogen granules, filled with various digestive enzymes, that are clustered in the vicinity of the apical surface. At the surface of the lumen, acinar cells are attached to each other by apical tight junctions, while their basal surfaces are associated with the basal lamina. For overview, please refer to Liggitt and Dintzis; "Pancreas"; Comparative Anatomy and Histology; a Mouse, Rat, and Human Atlas; edited by Treuting, Dintzis, and Montine, Elsevier Inc., 2018, 241-250. For review, please refer to Tritschler et al. 2017.
Pancreatic acinar cells originate from definitive endoderm cells that form during gastrulation, and then undergo patterning along anterior/posterior, dorsal/ventral, and median/lateral axes, producing, among other embryonal cell types, endoderm cells of dorsal and ventral foregut, which, after transitioning through an intermediary duodeno-pancreatic endoderm cell state for dorsal foregut endoderm and possibly a hepato-pancreatic or pancreato-biliary intermediary state for ventral foregut endoderm, give rise to multipotent pancreatic progenitor cells (MPCs) that form dorsal and ventral pancreatic buds (Yu et al. 2019, reviewed in Jennings et al. 2015). Developing pancreas undergoes branching morphogenesis, which results in the apical-basal polarity that is critical for establishing the acinar-ductal functional unit (Darrigrand et al. 2024). Both dorsal and ventral MPCs located at the tips of the developing, branching pancreas, start committing to the acinar cell fate from Carnegie stage 19 (45-47 days post conception) of human embryonic development and around embryonic day E12 during mouse development, initially becoming distinct tip progenitors, and then pro-acinar and acinar cells (Yu et al. 2019, reviewed in Jennings et al. 2015).
R-HSA-9725554 Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin The interfollicular epidermis is the skin surface layer in between the adnexa (hair follicles, sweat glands, and sebaceous glands). Going from the dermal epidermal junction, the interfollicular epidermis strata include the basal layer (stratum basale), spinous layer (stratum spinosum), granular layer (stratum granulosum), and the cornified layer (stratum corneum). The basal layer consists of keratinocyte stem cells and transit amplifying cells. The spinous, granular, and cornified layers consist of spinous keratinocytes, granular keratinocytes, and corneocytes, respectively. Interfollicular epidermis has a high cell turnover rate. Keratinocyte stem cells self renew throughout adulthood and give rise to transit amplifying cells. Transit amplifying cells undergo several cell cycles before committing to differentiation, first into spinous layer keratinocytes, then into granular layer keratinocytes, and finally into corneocytes. Corneocytes lose their nuclei and cytoplasmic organelles, forming flattened squames that provide a physical barrier against the invasion of pathogens and loss of bodily fluids. For a detailed review, please refer to Zijl et al. 2022, and for the single cell transcriptomic and spatial transcriptomic studies that provide a higher resolution view of human interfollicular epidermis, please refer to Cheng et al. 2018, Wang et al. 2020, Aragona et al. 2020, Haensel et al. 2020, Negri et al. 2023, and Ganier et al. 2024).The first group encompasses the infectious diseases such as influenza, tuberculosis and HIV infection. The second group involves human proteins modified either by a mutation or by an abnormal post-translational event that produces an aberrant protein with a novel function. Examples include somatic mutations of EGFR and FGFR (epidermal and fibroblast growth factor receptor) genes, which encode constitutively active receptors that signal even in the absence of their ligands, or the somatic mutation of IDH1 (isocitrate dehydrogenase 1) that leads to an enzyme active on 2-oxoglutarate rather than isocitrate, or the abnormal protein aggregations of amyloidosis which lead to diseases such as Alzheimer's.
Infectious diseases are represented in Reactome as microbial-human protein interactions and the consequent events. The existence of variant proteins and their association with disease-specific biological processes is represented by inclusion of the modified protein in a new or variant reaction, an extension to the 'normal' pathway. Diseases which result from proteins performing their normal functions but at abnormal rates can also be captured, though less directly. Many mutant alleles encode proteins that retain their normal functions but have abnormal stabilities or catalytic efficiencies, leading to normal reactions that proceed to abnormal extents. The phenotypes of such diseases can be revealed when pathway annotations are combined with expression or rate data from other sources.
Depending on the biological pathway/process immediately affected by disease-causing gene variants, non-infectious diseases in Reactome are organized into diseases of signal transduction by growth factore receptors and second messengers, diseases of mitotic cell cycle, diseases of cellular response to stress, diseases of programmed cell death, diseases of DNA repair, disorders of transmembrane transporters, diseases of metabolism, diseases of immune system, diseases of neuronal system, disorders of developmental biology, disorders of extracellular matrix organization, and diseases of hemostatis.
R-HSA-3781860 Diseases associated with N-glycosylation of proteins Congenital disorders of glycosylation (CDGs) are a group of autosomal recessive disorders caused by enzymatic defects in the synthesis and processing of asparagine (N)-linked glycans or oligosaccharides on glycoproteins. These glycoconjugates play critical roles in processes such as metabolism, cell recognition and adhesion, cell migration, protease resistance, host defense, and antigenicity. CDGs are divided into 2 main groups: type I CDGs comprise defects in the assembly of the dolichol lipid-linked oligosaccharide (LLO) chain and its transfer to the nascent protein, whereas type II CDGs comprise defects in the trimming and processing of protein-bound glycans (Marquardt & Denecke 2003, Grunewald et al. 2002, Hennet 2012, Cylwik et al. 2013).
R-HSA-3906995 Diseases associated with O-glycosylation of proteins Glycosylation is the most abundant modification of proteins, variations of which occur in all living cells. Glycosylation can be further categorized into N-linked (where the oligosaccharide is conjugated to Asparagine residues) and O-linked glycosylation (where the oligosaccharide is conjugated to Serine, Threonine and possibly Tyrosine residues). Within the family of O-linked glycosylation, the oligosaccharides attached can be further categorized according to their reducing end residue: GalNAc (often described as mucin-type, due to the abundance of this type of glycosylation on mucins), Mannose and Fucose. This section reviews currently known congenital disorders of glycosylation associated with defects of protein O-glycosylation (Cylwik et al. 2013, Freeze et al. 2014).
R-HSA-3560782 Diseases associated with glycosaminoglycan metabolism A number of genetic disorders are caused by mutations in the genes encoding glycosyltransferases and sulfotransferases, enzymes responsible for the synthesis of glycosaminoglycans (GAGs) as well as hexosaminidase degradation of GAGs (Mizumoto et al. 2013).
R-HSA-5609975 Diseases associated with glycosylation precursor biosynthesis Glycosylation diseases associated with the enzymes that mediate the biosynthesis of glycosylation precursors are curated in this section (Jaeken & Matthijs 2007, Freeze et al. 2015).
R-HSA-5687613 Diseases associated with surfactant metabolism The reactions annotated here describe genetic defects in genes regulating surfactant homeostasis which are associated with severe acute and chronic lung diseases in newborns and older infants (Whitsett et al. 2015).
R-HSA-5602358 Diseases associated with the TLR signaling cascade Toll like receptors (TLRs) are sensors of the innate immune system that detect danger signals derived from pathogens (pathogen-associated molecular patterns - PAMP) or damaged cells (damage-associated molecular patterns - DAMP) (Pasare C and Medzhitov R 2005; Barton GM and Kagan JC 2009; Kawai T and Akira S 2010). Signaling by these sensors promotes the activation and nuclear translocation of transcription factors (IRFs, NFkB and AP1). The transcription factors induce secretion of inflammatory cytokines such as IL-6, TNF and pro-IL1beta that direct the adaptive immune response. Inherited or acquired abnormalities in TLR-mediated processes may lead to increased susceptibility to infection, excessive inflammation, autoimmunity and malignancy (Picard C et al. 2010; Netea MG et al. 2012; Varettoni M et al. 2013). Here we describe four primary immunodeficiency (PID) disorders associated with defective TLR-mediated responses. First, MyD88 or IRAK4 deficiency is characterized with a greater susceptibility to pyogenic bacteria in affected patients (Picard C et al. 2003; von Bernuth H et al. 2008). Second, defects in the TLR3 signaling pathway are associated with a greater susceptibility to herpes simplex virus encephalitis (Zhang SY et al. 2013). Third, imunodeficiencies due to defects in NFkB signaling components are linked to impaired TLR-mediated responses (Courtois G et al. 2003; Fusco F et al. 2004). Finally, events are annotated showing constitutive activation of a somatically mutated MyD88 gene which results in malignancy (Varettoni M et al. 2013).
R-HSA-2474795 Diseases associated with visual transduction The process of vision involves two stages; the retinoid cycle which supplies and regenerates the visual chromophore required for vision and phototransduction which propagates the light signal. Defects in the genes involved in the retinoid cycle cause degenerative retinal diseases. These defective genes are described here (for reviews see Travis et al. 2007, Palczewski 2010, Fletcher et al. 2011, den Hollander et al. 2008).
R-HSA-9605308 Diseases of Base Excision Repair Germline mutations, single nucleotide polymorphisms (SNPs) and somatic mutations in several genes involved in base excision repair (BER), a DNA repair pathway where a damaged DNA base is excised and replaced with a correct base, are involved in the development of cancer and several other oxidative stress-related diseases. For review, please refer to Fu et al. 2012, Fletcher and Houlston 2010, Brenerman et al. 2014, Patrono et al. 2014, and D'Errico et al. 2017.
R-HSA-9630747 Diseases of Cellular Senescence Cellular senescence plays an important role in normal aging, as well as in age-related diseases. Impaired cellular senescence contributes to malignant transformation and cancer development. Presence of an excessive number of senescent cells that are not cleared by the immune system, however, promotes tissue inflammation and creates a microenvironment suitable for growth of neighboring malignant cells. Besides cancer, senescence is also involved in atherosclerosis, osteoarthritis and diabetes (Childs et al. 2015, He and Sharpless 2017).
Evasion of oncogene-induced senescence, at least in cell culture, can occur due to loss-of-function (LOF) mutation in the CDKN2A gene product p16INK4A that acts as a cyclin-dependent kinase inhibitor (reviewed in Sharpless and Sherr 2015). LOF mutations in the CDKN2A gene that affect its other protein product, p14ARF, involved in stabilization of TP53 protein (p53), can contribute to evasion of oncogene-induced senescence (reviewed in Fontana et al. 2019).
LOF mutations in p16INK4A and p14ARF also contribute to evasion of oxidative stress-induced senescence (reviewed in Sharpless and Sherr 2015, and Fontana et al. 2019, respectively).
R-HSA-9675136 Diseases of DNA Double-Strand Break Repair Diseases of DNA double-strand break repair (DSBR) are caused by mutations in genes involved in repair of double strand breaks (DSBs), one of the most cytotoxic types of DNA damage. Unrepaired DSBs can lead to cell death, cellular senescence, or malignant transformation.
Germline mutations in DSBR genes are responsible for several developmental disorders associated with increased predisposition to cancer:
Ataxia telangiectasia, characterized by cerebellar neurodegeneration, hematologic malignancies and immunodeficiency, is usually caused by germline mutations in the ATM gene;
Nijmegen breakage syndrome 1, characterized by microcephaly, short stature and recurrent infections, is caused by germline mutations in the NBN (NBS1) gene;
Seckel syndrome, characterized by short stature, skeletal deformities and microcephaly, is caused by germline mutations in the ATR or RBBP8 (CtIP) genes.
Heterozygous germline mutations in BRCA1, BRCA2 or PALB2 cause the hereditary breast and ovarian cancer syndrome (HBOC), while homozygous germline mutations in BRCA2 and PALB2 cause Fanconi anemia, a developmental disorder characterized by short stature, microcephaly, skeletal defects, bone marrow failure, and predisposition to cancer.
Somatic mutations in DSBR genes are also frequently found in sporadic cancers.
The pathways "Defective DNA double strand break response due to BRCA1 loss of function" describes defects in DSB response caused by loss-of-function mutations in BRCA1 which prevent the formation of the BRCA1:BARD1 complex.
The pathway "Defective DNA double strand break response due to BARD1 loss of function" describes defects in DSB response caused by loss-of-function mutations in BARD1, the heterodimerization partner of BRCA1, which prevent the formation of the BRCA1:BARD1 complex.
The pathway "Defective homologous recombination repair (HRR) due to BRCA1 loss of function" describes defects in HRR caused by loss-of-function mutations in BRCA1 that impair its association with PALB2.
The pathway "Defective homologous recombination repair (HRR) due to BRCA2 loss of function" describes defects in HRR caused by loss-of-function mutations in BRCA2 that impair either it association with SEM1 (DSS1), its translocation to the nucleus, its binding to RAD51, or its binding to PALB2.
The pathway "Defective homologous recombination repair (HRR) due to PALB2 loss of function" describes defects in HRR caused by loss-of-function mutations in PALB2 that impair its association with BRCA2/RAD51/RAD51C.
For review, please refer to McKinnon and Caldecott 2007, Keijzers et al. 2017, and Jachimowicz et al. 2019.
R-HSA-9675135 Diseases of DNA repair Germline and somatic defects in genes that encode proteins that participate in DNA repair give rise to genetic instability that can lead to malignant transformation or trigger cellular senescence or apoptosis. Germline defects in DNA repair genes are an underlying cause of familial cancer syndromes and premature ageing syndromes. Somatic defects in DNA repair genes are frequently found in tumors. For review, please refer to Tiwari and Wilson 2019.
We have so far annotated diseases of mismatch repair, diseases of base excision repair and diseases of DNA double-strand break repair.
Defects in mammalian DNA mismatch repair (MMR) genes (MLH1, PMS2, MSH2, and MSH6) result in microsatellite instability (MSI) and reduced fidelity during replication and repair steps. Defective variants of MMR genes are associated with sporadic cancers with hypermutation phenotypes as well as hereditary cancer syndromes such as Lynch syndrome (hereditary non-polyposis colorectal cancer) and constitutional mismatch repair deficiency syndrome (CMMRD). MSI is an important predictor of sensitivity to cancer immunotherapy as the high mutational burden renders MSI tumors immunogenic and sensitive to programmed cell death-1 (PD-1) immune checkpoint inhibitors (Mandal et al. 2019). For review, please refer to Pena-Diaz and Rasmussen 2016, Sijmons and Hofstra 2016, Tabori et al. 2017, Baretti and Le 2018.
Germline mutations, single nucleotide polymorphisms (SNPs) and somatic mutations in several genes involved in base excision repair (BER), a DNA repair pathway where a damaged DNA base is excised and replaced with a correct base, are involved in the development of cancer and several oxidative stress-related diseases. For review, please refer to Fu et al. 2012, Fletcher and Houlston 2010, Brenerman et al. 2014, Patrono et al. 2014, and D'Errico et al. 2017.
Germline mutations in genes involved in repair of DNA double-strand breaks (DSBs) are the underlying cause of several cancer predisposition syndromes, some of which also encompass developmental disorders associated with immune dysfunction, radiosensitivity and neurodegeneration. Somatic mutations in genes involved in DSB repair also occur in sporadic cancers. For review, please refer to McKinnon and Caldecott 2007, Keijzers et al. 2017, and Jachimowicz et al. 2019.
R-HSA-5260271 Diseases of Immune System The immune system is a complex network of the biological processes that provide defense mechanisms during infection or in response to an intrinsic danger signal. Compromised immune response may present itself as either overactivity or underactivity of the immune system leading to a broad spectrum of clinical phenotypes that can be categorized into four main groups - autoimmunity, immunodeficiency (ID) with a greater susceptibility to infectious diseases, hypersensitivity to compounds that are usually not harmful and malignancy. Several host conditions may cause the dysfunctional immunity. Among them are inherited and somatic mutations found in the components of immune signaling pathways. In addition to genetic defects, infection with pathogen such as human immunodeficiency virus (HIV), or interaction of immune cells with immunosuppressive drugs result in non-genetic immunodeficiencies. Age-associated alterations in immunity may also contribute to pathogenesis of immunodeficiency .
The Reactome module represents selected defects of the immune system and provides a short description of their clinical phenotypes. The module also describes functional features of defective molecules by both providing a published source for experimental functional analysis data and linking to the corresponding normal process within the Reactome database.
R-HSA-5423599 Diseases of Mismatch Repair (MMR) Defects in mammalian DNA mismatch repair (MMR) genes (MLH1, PMS2, MSH2, and MSH6) are characterized by microsatellite instability and reduced fidelity during replication and repair steps. The MMR proteins interact with each other to execute steps within the mismatch repair pathway. Defective variants of these proteins are associated with nonpolyposis colorectal cancer. The MutS proteins are thought to directly contact double-stranded DNA, scanning along the genomic DNA for mismatches analogous to a "sliding clamp" until they encounter a base pair containing a mismatch. The MutS proteins interact with multiple proteins including other MLH and MutL, the later have significant amino acid identify and structural similarity to the MLH proteins, as well as RPA, EXO1, RFC, possibly HMGB1, and other less well-characterized proteins.
With respect to the mutator function, the MSH2/MutSaplha heterodimer is thought primarily to repair single-base substitutions and 1 bp insertiondeletion mutations, while MSH2/MutSbeta is thought primarily to repair 1-4 bp insertiondeletion mutations. The MLH and MutL heterodimer proteins interact with heterodimers of MutS proteins to help catalyze different functions. MLH1:MutLalpha is the primary complex that interacts with both MutS alpha and beta complex in mechanisms thought to be relevant to cancer prevention. Recent studies suggest that MLH1:MLH3 may also contributes to some of these processes as well, but in all mechanisms tested to a lesser degree than MLH1:PMS2.
Heterozygous mutations in the MLH1 gene result in hereditary nonpolyposis colorectal cancer-2 (Papadopoulos et al., 1994).
Variants of the MSH2 gene are associated with hereditary nonpolyposis colorectal cancer. Alteration of MSH2 is also involved in Muir-Torre syndrome and mismatch repair cancer syndrome (Fishel et al. 1993).
Defects in the MSH3 gene are a cause of susceptibility to endometrial cancer (Risinger et al. 1996).
Defects in the MSH6 gene are less common than MLH1 and MSH2 defects. They have been mostly observed in atypical HNPCC families and are characterized by a weaker family history of tumor development, higher age at disease onset, and low degrees of microsatellite instability (MSI) (Lucci-Cordisco et al. 2001).
Mutations in the PMS2 gene are associated with hereditary nonpolyposis colorectal cancer, Turcot syndrome, and are a cause of supratentorial primitive neuroectodermal tumors. Heterozygous truncating mutations in PMS2 play a role in a small subset of hereditary nonpolyposis colorectal carcinoma (Lynch syndrome, HNPCC-like) families. PMS2 mutations lead to microsatellite instability with carriers showing a microsatellite instability high phenotype and loss of PMS2 protein expression in all tumors (Hamilton et al. 1995, Hendriks et al. 2006).
R-HSA-9673013 Diseases of Telomere Maintenance Somatic mutations or rearrangements in genes involved in telomere maintenance enable immortalization of cancer cells either through upregulation of telomerase activity or through activation of alternative lengthening of telomeres (ALT) (Killela et al. 2013, reviewed by Gocha et al. 2013, Pickett and Reddel 2015, Amorim et al. 2016, Yuan et al. 2019). Germline mutations in telomere maintenance genes lead to telomere syndromes, such as dyskeratosis congenita (DC) and Hoyeraal-Hreidarsson (HH) syndrome, characterized by impaired ability to maintain telomere lengths during growth and development, leading to abnormally short telomere lengths and genomic instability that affects multiple organs and is associated with increased risk of certain cancers (reviewed by Sarek et al. 2015).
R-HSA-9865118 Diseases of branched-chain amino acid catabolism Mutations in the genes that encode enzymes responsible for the catabolism of the branched-chain amino acids leucine, isoleucine and valine give rise to a number of inborn errors of metabolism (IEMs). Although IEMs are individually rare, collectively they are relatively common with an estimated overall prevalence of ~1:800 live births (Mak et al, 2013). The frequency of particular IEMs is also highly variable across different populations, a result in part of founder effects in closed populations. For instance, although the overall frequency of Maple Syrup Urine disease is 1:185,000 live births (Strauss et al, 2020), the frequency rises to 1:380 in some Old Order Mennonite communities (Fisher et al, 1991).
Accumulation of toxic intermediary metabolites causes a range of clinical phenotypes in patients with IEMs including metabolic acidosis, vomiting, seizures, psychomotor and developmental delays and death (reviewed in Schrier Vergano et al, 2022; Holoček, 2018; Neinast et al, 2019).
R-HSA-5663084 Diseases of carbohydrate metabolism The processes by which dietary carbohydrate is digested to monosaccharides and these are taken up from the gut lumen into cells where they are oxidized to yield energy or consumed in biosynthetic processes are a central part of human metabolism and defects in them can lead to serious disease. Defects annotated here affect saccharide digestion in the gut lumen, fructose metabolism, and the pentose phosphate pathway. In addition, the defect in glucuronate catabolism that leads to essential pentosuria, a benign phenotype that is one of Garrod's original four inborn errors of metabolism, is annotated.
R-HSA-9675132 Diseases of cellular response to stress Cells are subject to external and internal stressors, such as foreign molecules that perturb metabolic or signaling processes, cellular respiration-generated reactive oxygen species that can cause DNA damage, oxygen and nutrient deprivation, and changes in temperature or pH. The ability of cells and tissues to respond to stress is essential to the maintenance of tissue homeostasis (Kultz 2005) and dysregulation of cellular response to stress is involved in disease.
So far, we have captured diseases of cellular senescence.
Impaired cellular senescence contributes to malignant transformation and cancer development by enabling continuous proliferation of damaged cells. On the other hand, presence of an excessive number of senescent cells that are not cleared by the immune system promotes tissue inflammation and creates a microenvironment suitable for growth of neighboring malignant cells. In addition to cancer, senescence is also involved in other age-related diseases such as atherosclerosis, osteoarthritis, chronic obstructive lung disease, and diabetes (Childs et al. 2015, He and Sharpless 2017, Hamsanathan et al. 2019, Faget et al. 2019, Gorgoulis et al. 2019, Rhinn et al. 2019). Senotherapy is a new field of pharmacology that aims to therapeutically target senescence to improve healthy aging and age-related diseases (Schmitt 2017, Gorgoulis et al. 2019).
R-HSA-3781865 Diseases of glycosylation Diseases of glycosylation, usually referred to as congenital disorders of glycosylation (CDG), are rare inherited disorders ascribing defects of nucleotide-sugar biosynthesis and transport, glycosyl transfer events and vesicular transport. Most CDGs cause neurological impairment ranging from severe psychomotor retardation to mild intellectual disability. Defects in N-glycosylation are the main cause of CDGs (Marquardt & Denecke 2003, Grunewald et al. 2002, Hennet 2012, Goreta et al. 2012) and can be identified by a characteristic abnormal isoelectric focusing profile of plasma transferrin (Jaeken et al. 1984, Stibler & Jaeken 1990). Disorders of O-glycosylation, glycosaminoglycan and glycolipid metabolism have recently been discovered and, together with N-glycosylation, represent the major pathways affected by glycan biosynthetic disorders (Freeze 2006, Jaeken 2011). In addition, glycosylation diseases associated with the enzymes that mediate the biosynthesis of glycosylation precursors are described in this section. As the number of these disorders has increased, nomenclature has been simplified so that now, the name of the mutant gene is followed by the abbreviation CDG (Jaeken et al. 2009). Effective therapies for most types of CDGs are so far not available (Thiel & Korner 2013).
R-HSA-9671793 Diseases of hemostasis Hemostasis is a complex process that leads to the formation of a blood clot at the site of vessel injury. Three phases can be distinguished: primary hemostasis or formation of a platelet plug, secondary hemostasis, or coagulation and fibrinolysis (Kriz N et al. 2009). Defects in hemostasis cause an imbalance between the coagulation and fibrinolytic systems and may lead either to hypercoagulation, which can result in thrombosis, or to hypocoagulation and increased susceptibility to bleeding (also known as hemorrhagic diathesis) (van Herrewegen F et al. 2012a,b; Kumar R & Carcao M 2013). Abnormalities can result from disorders of the platelets (primary hemostasis defect), coagulation factors defects (secondary hemostasis defect), or a combination of both (van Herrewegen F et al. 2012a,b; Kumar R & Carcao M 2013). Coagulation disorders may be inherited or acquired. Further, abnormalities of the coagulation and fibrinolytic systems are coupled to the inflammatory response, which aggravates blood vessel permeability, inflammation, and cell damage in tissues (Sandra Margetic 2012; Kaplan AP & Joseph K 2016).
This Reactome module describes abnormalities of the coagulation cascade (secondary hemostasis) due to defects of coagulation factor proteins such as factor VIII (FVIII), FIX or FXII. The module also describes an abnormal FXII- mediated activation of the pro-inflammatory kallikrein‐kinin system (KKS) that leads to an excessive formation of bradykinin causing increased vascular permeability at the level of the post capillary venule and results in hereditary angioedema (HAE).
R-HSA-5668914 Diseases of metabolism Metabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as the inactivation and elimination of toxic ones generated endogenously or present in the extracellular environment. Mutations that disrupt these processes by inactivating a required enzyme or regulatory protein, or more rarely by changing its specificity can lead to severe diseases. Metabolic diseases annotated here involve aspects of carbohydrate, glycosylation, amino acid (phenylketonuria), surfactant and vitamin metabolism, and biological oxidations. One somatic mutation that affects cytosolic isocitrate metabolism, often found in glioblastomas and some lymphoid neoplasms, is also annotated. Also described are mutated forms of adrenocorticotropic hormone (ACTH) that can lead to obesity, resulting in excessive accumulation of body fat.
R-HSA-9759774 Diseases of mitochondrial beta oxidation Of the array of known defects of mitochondrial lipid metabolism, one is annotated in Reactome, methylmalonic acidurioa due to deficiencies of the MMUT (Methylmalonyl-CoA mutase, mitochondrial) enzyme (Worgan et al. 2006)
R-HSA-9675126 Diseases of mitotic cell cycle Diseases of mitotic cell cycle are caused by mutations in cell cycle regulators (Collins and Garrett 2005, Diaz-Moralli et al. 2013), such as retinoblastoma protein RB1 (Classon and Harlow 2002), as well as proteins involved in telomere maintenance, such as ATRX and DAXX (Sarek et al. 2015). These diseases mainly include different types of cancer, hereditary syndromes such as dyskeratosis congenita that may predispose affected patients to cancer, and neurodegenerative diseases (Webber et al. 2005).
R-HSA-9735804 Diseases of nucleotide metabolism Metabolic reactions disrupted by deficiencies of ADA, APRT, HPRT1, and PNP are annotated here.
R-HSA-9645723 Diseases of programmed cell death Programmed cell death is frequently impaired in cancer and is thought to significantly contribute to resistance to chemotherapy. Mutations and perturbations in expression of different proteins involved in programmed cell death, such as TP53 (p53), BH3-only family proteins, caspases and their regulators enable malignant cells to evade apoptosis (Ghavami et al. 2009, Chao et al. 2011, Wong 2011, Fernald and Kurokawa 2013, Ichim and Tait 2016).
R-HSA-9759785 Diseases of propionyl-CoA catabolism Propionyl-CoA catabolism is the aspect of mitochondrial beta-oxidation affected by the one disease of this process annotated in Reactome.
R-HSA-5663202 Diseases of signal transduction by growth factor receptors and second messengers Signaling processes are central to human physiology (e.g., Pires-da Silva & Sommer 2003), and their disruption by either germ-line and somatic mutation can lead to serious disease. Here, the molecular consequences of mutations affecting visual signal transduction and signaling by diverse growth factors are annotated.
R-HSA-9675143 Diseases of the neuronal system Diseases of the neuronal system can affect sensory cells and transmission of signals between sensory cells and sensory neurons (Martemyanov and Sampath 2017), transmission of signals across electrical and chemical synapses in the nervous system (Picconi et al. 2012, Yin et al. 2012, Kida and Kato 2015), and transmission of signals between motor neurons and muscle cells (Sine 2012, Engel et al. 2015).
We have so far annotated diseases of visual phototransduction due to retinal degeneration caused by defects in the genes involved in the retinoid cycle (Travis et al. 2007, Palczewski 2010, Fletcher et al. 2011, den Hollander et al. 2008).
R-HSA-114516 Disinhibition of SNARE formation The SNARE (SNAp REceptor) family of proteins are critical components of the machinery required for membrane fusion (Söllner et al. 1993, Wu et al. 2017). SNAREs can be grouped into three broad subfamilies: synaptosomal-associated proteins (SNAPs), vesicle-associated membrane proteins (VAMPs) and syntaxins. SNAPs contain two SNARE motifs and lack transmembrane domains, instead they are anchored to the membrane by thioester-linked acyl groups (Hong 2005). VAMPS or R-SNAREs have two subfamilies: short VAMPs or brevins and long VAMPs or longins. Syntaxins are evolutionarily less-well conserved, but except STX11 are transmembrane proteins (Hong 2005). Several SNARE proteins including Syntaxin-2 (STX2), STX4, STX11 and Vesicle-associated membrane protein 8 (VAMP8) are thought to be involved in platelet granule secretion (Golebiewska et al. 2013).
R-HSA-9675151 Disorders of Developmental Biology Developmental disorders affect formation of body organs and organ systems. The causes of defects in human development are diverse and incompletely understood, and include environmental insults such as nutrient deficiency, exposure to toxins and infections (Gilbert 2000, National Research Council (US) Committee on Developmental Toxicology 2000, Taylor and Rogers 2005, Zilbauer et al. 2016, Izvolskaia et al. 2018), as well as genetic causes such as aneuploidy and other chromosomal abnormalities, and germline mutations in genes that regulate normal development. It is estimated that about 40% of human developmental disabilities can be attributed to genetic aberrations (Sun et al. 2015), of which at least 25% are due to mutations affecting single genes (Chong et al. 2015), and this latter group of Mendelian developmental disorders is the focus of curation in Reactome.
Disorders of nervous system development affect the function of the central nervous system (CNS) and impair motor skills, cognition, communication and/or behavior (reviewed by Ismail and Shapiro 2019). So far,we have annotated the role of loss-of-function mutations in methyl-CpG-binding protein 2 (MECP2), an epigenetic regulator of transcription, in Rett syndrome, a pervasive developmental disorder (Pickett and London 2005, Ferreri 2014).
Disorders of myogenesis are rare hereditary muscle diseases that in the case of congenital myopathies are defined by architectural abnormalities in the muscle fibres (Pelin and Wallgren-Pettersson 2019, Phadke 2019, Radke et al. 2019, Claeys 2020) and in the case of muscular dystrophies by increased muscle breakdown that progresses with age (Pasrija and Tadi 2020). Mutations in cadherin family genes are present in some types of muscular dystrophy (Puppo et al. 2015).
Disorders of pancreas development result in pancreatic agenesis, where a critical mass of pancreatic tissue is congenitally absent. For example, the PDX1 gene is a master regulator of beta cell differentiation and homozygous deletions or inactivating mutations in PDX1 gene cause whole pancreas agenesis. PDX1 gene haploinsufficiency impairs glucose tolerance and leads to development of diabetes mellitus (Hui and Perfetti 2002, Babu et al. 2007, Chen et al. 2008).
Left-right asymmetry disorders are caused by mutations in genes that regulate the characteristic asymmetry of internal organs in vertebrates. Normally, cardiac apex, stomach and spleen are positioned towards the left side, while the liver and gallbladder are on the right. Loss-of-function mutations in the CFC1 gene, whose protein product functions as a co-factor in Nodal signaling, result in heterotaxic phenotype in affected patients, manifested by randomized organ positioning (Bamford et al. 2000).
Congenital lipodystrophies are characterized by a lack of adipose tissue, which predisposes affected patient to development of insulin resistance and related metabolic disorders. The severity of metabolic complications is correlates with the extent of adipose tissue loss. Loss-of-function mutations in the PPARG gene, encoding a key transcriptional regulator of adipocyte development and function, are a well-established cause of familial partial lipodystrophy type 3 (FPLD3) (Broekema et al. 2019).
Congenital stem cell disorders are caused by mutations in genes that regulate the balance between stem cells maintenance and commitment to differentiated lineages. Loss-of-function mutations in the SOX2 gene, which encodes a transcription factor involved in the maintenance of totipotency during embryonic preimplantation period, pluripotency of embryonic stem cells, and multipotency of neural stem cells, are the cause of anophthalmia (the absence of an eye) and microphthalmia (the presence of a small eye within the orbit (Verma and Fitzpatrick 2007, Sarlak and Vincent 2016).
HOX-related structural birth defects are caused by loss-of-function mutations in HOX family genes.HOX transcription factors play a fundamental role in body patterning during embryonic development, and HOX mutation are an underlying cause of many congenital limb malformations (Goodman 2002).
Congenital keratinization disorders are caused by dominant negative mutation in keratin genes and depending on where the affected keratin gene is expressed, they affect epithelial tissues such as skin, cornea, hair and/or nails (McLean and Moore 2011).
Disorders of immune system development are caused by mutations in genes that regulate differentiation of blood cell lineages involved in immune defense, leading to immune system defects. For example, mutations in the gene encoding CSF3R, a receptor for the granulocyte-colony stimulating factor, result in congenital neutropenia, characterized by a maturation arrest of granulopoiesis at the level of promyelocytes. Patients with severe congenital neutropenia are prone to recurrent, often life-threatening infections from an early age and may be predisposed to myelodysplastic syndromes or acute myeloid leukemia (Germeshausen et al. 2008; Skokowa et al. 2017).
R-HSA-9697154 Disorders of Nervous System Development Neurodevelopmental disorders are chronic disorders that affect the function of the central nervous system (CNS) and impair motor skills, cognition, communication and/or behavior. While these disorders frequently stem from mutations in genes that directly control CNS development, they can also be a consequence of environmental insults such as hypoxic/ischemic injury, trauma, exposure to toxins, infections and nutritional deficiencies, or be indirectly caused by mutations in metabolic genes (reviewed by Ismail and Shapiro 2019). Disorders of nervous system development have been traditionally classified based on phenotypic traits (clinical presentation). Molecular genetics studies have revealed, however, that indistinguishable clinical presentations may result from pathogenic variants in different genes whose protein products function in connected biological pathways. On the other hand, distinct clinical presentations may be caused by pathogenic mutations in a single gene that functions in multiple biological pathways (Desikan and Bakrovich 2018). In the future, phenotype-based classification of neurodevelopmental disorders may be replaced by a more informative pathway-based nomenclature (Desikan and Bakrovich 2018). Biological pathways frequently impaired in neurodevelopmental disorders are signal transduction pathways such as the mTOR pathway in tuberous sclerosis complex (TSC) (Wong 2019) and the RAS/RAF/MAPK pathway in RASopathies (Kang and Lee 2019), neurotransmission pathways as in some autism spectrum disorders (ASD) (Burnashev and Szepetowski 2015, Hu et al. 2016), and pathways that regulate gene expression as in Mendelian disorders of epigenetic machinery (MDEM) (Fahrner and Bjornsson 2019).
So far,we have annotated the role of loss-of-function mutations in methyl-CpG-binding protein 2 (MECP2), an epigenetic regulator of transcription, in Rett syndrome, a pervasive developmental disorder that belongs to the MDEM category (Pickett and London 2005, Ferreri 2014).
R-HSA-5619115 Disorders of transmembrane transporters Proteins with transporting functions can be roughly classified into 3 categories: ATP hydrolysis-coupled pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the movement of substrates across the membrane against their electrochemical gradient. Channels in their open state can transfer substrates (ions or water) down their electrochemical gradient at an extremely high efficiency (up to 108 s-1). Transporters facilitate the movement of a specific substrate either against or with their concentration gradient at a lower speed (about 102 -104 s-1); as generally believed, conformational change of the transporter protein is involved in the transfer process. Diseases caused by defects in these transporter proteins are detailed in this section. Disorders associated with ABC transporters and SLC transporters are annotated here (Dean 2005).
R-HSA-110357 Displacement of DNA glycosylase by APEX1 Following cleavage of the damaged base, DNA glycosylase is displaced by APEX1, an AP endonuclease (Parikh et al. 1998).
R-HSA-75205 Dissolution of Fibrin Clot The crosslinked fibrin multimers in a clot are broken down to soluble polypeptides by plasmin, a serine protease. Plasmin can be generated from its inactive precursor plasminogen and recruited to the site of a fibrin clot in two ways, by interaction with tissue plasminogen activator at the surface of a fibrin clot, and by interaction with urokinase plasminogen activator at a cell surface. The first mechanism appears to be the major one responsible for the dissolution of clots within blood vessels. The second, although capable of mediating clot dissolution, may normally play a major role in tissue remodeling, cell migration, and inflammation (Chapman 1997; Lijnen 2001).
Clot dissolution is regulated in two ways. First, efficient plasmin activation and fibrinolysis occur only in complexes formed at the clot surface or on a cell membrane - proteins free in the blood are inefficient catalysts and are rapidly inactivated. Second, both plasminogen activators and plasmin itself are inactivated by specific serpins, proteins that bind to serine proteases to form stable, enzymatically inactive complexes (Kohler and Grant 2000).
These events are outlined in the drawing: black arrows connect the substrates (inputs) and products (outputs) of individual reactions, and blue lines connect output activated enzymes to the other reactions that they catalyze.
R-HSA-212676 Dopamine Neurotransmitter Release Cycle Dopamine neurotransmitter cycle occurs in dopaminergic neurons. Dopamine is synthesized and loaded into the clathrin sculpted monoamine transport vesicles. The vesicles are docked, primed and fused with the plasmamembrane in the synapse to release dopamine into the synaptic cleft.
R-HSA-379401 Dopamine clearance from the synaptic cleft The human gene SLC6A3 encodes the sodium-dependent dopamine transporter, DAT which mediates the re-uptake of dopamine from the synaptic cleft (Vandenbergh DJ et al, 2000). Dopamine can then be degraded by either COMT or monoamine oxidase.
R-HSA-390651 Dopamine receptors Dopamine receptors play vital roles in processes such as the control of learning, motivation, fine motor control and modulation of neuroendocrine signaling (Giralt JA and Greengard P, 2004). Abnormalities in dopamine receptor signaling may lead to neuropsychiatric disorders such as Parkinson's disease and schizophrenia. Dopamine receptors are prominent in the CNS and the neurotransmitter dopamine is the primary endogenous ligand for these receptors. In humans, there are five distinct types of dopamine receptor, D1-D5. They are subdivided into two families; D1-like family (D1 and D5) which couple with the G protein alpha-s and are excitatory and D2-like family (D2,D3 and D4) which couple with the G protein alpha-i and are inhibitory (Kebabian JW and Calne DB, 1979).
R-HSA-8863795 Downregulation of ERBB2 signaling Signaling by ERBB2 can be downregulated by ubiquitination and subsequent proteasome-dependent degradation of ERBB2 or activated ERBB2 heterodimers. In addition, protein tyrosine phosphatases that dephosphorylate tyrosine residues in the C-terminus of ERBB2 prevent the recruitment of adapter proteins involved in signal transduction, thus attenuating ERBB2 signaling.
STUB1 (CHIP) and CUL5 are E3 ubiquitin ligases that can target non-activated ERBB2 for proteasome-dependent degradation (Xu et al. 2002, Ehrlich et al. 2009). RNF41 (NRDP1) is an E3 ubiquitin ligase that targets ERBB3 and activated heterodimers of ERBB2 and ERBB3 for proteasome-dependent degradation by ubiquitinating ERBB3 (Cao et al. 2007).
Two protein tyrosine phosphatases of the PEST family, PTPN12 and PTPN18, dephosphorylate tyrosine residues in the C-terminus of ERBB2, thus preventing signal transduction to RAS and PI3K effectors (Sun et al. 2011, Wang et al. 2014).
R-HSA-1358803 Downregulation of ERBB2:ERBB3 signaling Level of plasma membrane ERBB3 is regulated by E3 ubiquitin ligase RNF41 (also known as NRDP1), which binds and ubiquitinates both inactive and activated ERBB3, targeting it for degradation (Cao et al. 2007). RNF41 is subject to self-ubiquitination which keeps its levels low when ERBB3 is not stimulated, and preserves ERBB3 expression on the cell surface (Qiu et al. 2002). Self-ubiquitination of RNF41 is reversible, through the action of ubiquitin protease USP8, an enzyme stabilized by AKT-mediated phosphorylation. Therefore, activation of AKT by ERBB2:ERBB3 signaling leads to phosphorylation of USP8 (Cao et al. 2007), which increases level of RNF41 through deubiquitination, and results in degradation of activated ERBB3 (Cao et al. 2007) - a negative feedback loop of ERBB3 signaling. Downregulation of EGFR and ERBB4 signaling is explained in pathways Signaling by EGFR and Signaling by ERBB4.
R-HSA-1253288 Downregulation of ERBB4 signaling WW-domain binding motifs in the C-tail of ERBB4 play an important role in the downregulation of ERBB4 receptor signaling, enabling the interaction of intact ERBB4, ERBB4 m80 and ERBB4 s80 with NEDD4 family of E3 ubiquitin ligases WWP1 and ITCH. The interaction of WWP1 and ITCH with intact ERBB4 is independent of receptor activation and autophosphorylation. Binding of WWP1 and ITCH ubiquitin ligases leads to ubiquitination of ERBB4 and its cleavage products, and subsequent degradation through both proteasomal and lysosomal routes (Omerovic et al. 2007, Feng et al. 2009). In addition, the s80 cleavage product of ERBB4 JM-A CYT-1 isoform is the target of NEDD4 ubiquitin ligase. NEDD4 binds ERBB4 JM-A CYT-1 s80 (ERBB4jmAcyt1s80) through its PIK3R1 interaction site and mediates ERBB4jmAcyt1s80 ubiquitination, thereby decreasing the amount of ERBB4jmAcyt1s80 that reaches the nucleus (Zeng et al. 2009).
R-HSA-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity Transcriptional activity of SMAD2/3:SMAD4 heterotrimer can be inhibited by formation of a complex with SKI or SKIL (SNO), where SKI or SKIL recruit NCOR and possibly other transcriptional repressors to SMAD-binding promoter elements (Sun et al. 1999, Luo et al. 1999, Strochein et al. 1999). Higher levels of phosphorylated SMAD2 and SMAD3, however, may target SKI and SKIL for degradation (Strochein et al. 1999, Sun et al. 1999 PNAS, Bonni et al. 2001) through recruitment of SMURF2 (Bonni et al. 2001) or RNF111 i.e. Arkadia (Levy et al. 2007) ubiquitin ligases to SKI/SKIL by SMAD2/3. Therefore,the ratio of SMAD2/3 and SKI/SKIL determines the outcome: inhibition of SMAD2/3:SMAD4-mediated transcription or degradation of SKI/SKIL. SKI and SKIL are overexpressed in various cancer types and their oncogenic effect is connected with their ability to inhibit signaling by TGF-beta receptor complex.
SMAD4 can be monoubiquitinated by a nuclear ubiquitin ligase TRIM33 (Ecto, Ectodermin, Tif1-gamma). Monoubiquitination of SMAD4 disrupts SMAD2/3:SMAD4 heterotrimers and leads to SMAD4 translocation to the cytosol. In the cytosol, SMAD4 can be deubiquitinated by USP9X (FAM), reversing TRIM33-mediated negative regulation (Dupont et al. 2009).
Phosphorylation of the linker region of SMAD2 and SMAD3 by CDK8 or CDK9 primes SMAD2/3:SMAD4 complex for ubiquitination by NEDD4L and SMURF ubiquitin ligases. NEDD4L ubiquitinates SMAD2/3 and targets SMAD2/3:SMAD4 heterotrimer for degradation (Gao et al. 2009). SMURF2 monoubiquitinates SMAD2/3, leading to disruption of SMAD2/3:SMAD4 complexes (Tang et al. 2011).
Transcriptional repressors TGIF1 and TGIF2 bind SMAD2/3:SMAD4 complexes and inhibit SMAD-mediated transcription by recruitment of histone deacetylase HDAC1 to SMAD-binding promoter elements (Wotton et al. 1999, Melhuish et al. 2001).
PARP1 can attach poly ADP-ribosyl chains to SMAD3 and SMAD4 within SMAD2/3:SMAD4 heterotrimers. PARylated SMAD2/3:SMAD4 complexes are unable to bind SMAD-binding DNA elements (SBEs) (Lonn et al. 2010).
Phosphorylated SMAD2 and SMAD3 can be dephosphorylated by PPM1A protein phosphatase, leading to dissociation of SMAD2/3 complexes and translocation of unphosphorylated SMAD2/3 to the cytosol (Lin et al. 2006).
R-HSA-2173788 Downregulation of TGF-beta receptor signaling TGF-beta receptor signaling is downregulated by proteasome and lysosome-mediated degradation of ubiquitinated TGFBR1, SMAD2 and SMAD3, as well as by dephosphorylation of TGFBR1, SMAD2 and SMAD3.
In the nucleus, SMAD2/3:SMAD4 complex stimulates transcription of SMAD7, an inhibitory SMAD (I-SMAD). SMAD7 binds phosphorylated TGFBR1 and competes with the binding of SMAD2 and SMAD3 (Hayashi et al. 1997, Nakao et al. 1997). Binding of SMAD7 to TGBR1 can be stabilized by STRAP, a protein that simultaneously binds SMAD7 and TGFBR1 (Datta et al. 2000). BAMBI simultaneously binds SMAD7 and activated TGFBR1, leading to downregulation of TGF-beta receptor complex signaling (Onichtchouk et al. 1999, Yan et al. 2009).
In addition to competing with SMAD2/3 binding to TGFBR1, SMAD7 recruits protein phosphatase PP1 to phosphorylated TGFBR1, by binding to the PP1 regulatory subunit PPP1R15A (GADD34). PP1 dephosphorylates TGFBR1, preventing the activation of SMAD2/3 and propagation of TGF-beta signal (Shi et al. 2004).
SMAD7 associates with several ubiquitin ligases, SMURF1 (Ebisawa et al. 2001, Suzuki et al. 2002, Tajima et al. 2003, Chong et al. 2010), SMURF2 (Kavsak et al. 2000, Ogunjimi et al. 2005), and NEDD4L (Kuratomi et al. 2005), and recruits them to phosphorylated TGFBR1 within TGFBR complex. SMURF1, SMURF2 and NEDD4L ubiquitinate TGFBR1 (and SMAD7), targeting TGFBR complex for proteasome and lysosome-dependent degradation (Ebisawa et al. 2001, Kavsak et al. 2000, Kuratomi et al. 2005). The ubiquitination of TGFBR1 can be reversed by deubiquitinating enzymes, UCHL5 (UCH37) and USP15, which may be recruited to ubiquitinated TGFBR1 by SMAD7 (Wicks et al. 2005, Eichhorn et al. 2012).
Basal levels of SMAD2 and SMAD3 are maintained by SMURF2 and STUB1 ubiquitin ligases. SMURF2 is able to bind and ubiquitinate SMAD2, leading to SMAD2 degradation (Zhang et al. 2001), but this has been questioned by a recent study of Smurf2 knockout mice (Tang et al. 2011). STUB1 (CHIP) binds and ubiquitinates SMAD3, leading to SMAD3 degradation (Li et al. 2004, Xin et al. 2005). PMEPA1 can bind and sequester unphosphorylated SMAD2 and SMAD3, preventing their activation in response to TGF-beta signaling. In addition, PMEPA1 can bind and sequester phosphorylated SMAD2 and SMAD3, preventing formation of SMAD2/3:SMAD4 heterotrimer complexes (Watanabe et al. 2010). A protein phosphatase MTMR4, residing in the membrane of early endosomes, can dephosphorylate activated SMAD2 and SMAD3, preventing formation of SMAD2/3:SMAD4 complexes (Yu et al. 2010).
R-HSA-202424 Downstream TCR signaling Changes in gene expression are required for the T cell to gain full proliferative competence and to produce effector cytokines. Three transcription factors in particular have been found to play a key role in TCR-stimulated changes in gene expression, namely NFkappaB, NFAT and AP-1. A key step in NFkappaB activation is the stimulation and translocation of PRKCQ. The critical element that effects PRKCQ activation is PI3K. PI3K translocates to the plasma membrane by interacting with phospho-tyrosines on CD28 via its two SH2 domains located in p85 subunit (step 24). The p110 subunit of PI3K phosphorylates the inositol ring of PIP2 to generate PIP3 (steps 25). The reverse dephosphorylation process from PIP3 to PIP2 is catalysed by PTEN (step 27). PIP3 may also be dephosphorylated by the phosphatase SHIP to generate PI-3,4-P2 (step 26). PIP3 and PI-3,4-P2 acts as binding sites to the PH domain of PDK1 (step 28) and AKT (step 29). PKB is activated in response to PI3K stimulation by PDK1 (step 30). PDK1 has an essential role in regulating the activation of PRKCQ and recruitment of CBM complex to the immune synapse. PRKCQ is a member of novel class (DAG dependent, Ca++ independent) of PKC and the only member known to translocate to this synapse. Prior to TCR stimulation PRKCQ exists in an inactive closed conformation. TCR signals stimulate PRKCQ (step 31) and release DAG molecules. Subsequently, DAG binds to PRKCQ via the C1 domain and undergoes phosphorylation on tyrosine 90 by LCK to attain an open conformation (step 32). PRKCQ is further phosphorylated by PDK1 on threonine 538 (step 33). This step is critical for PKC activity. CARMA1 translocates to the plasma membrane following the interaction of its SH3 domain with the 'PxxP' motif on PDK1 (step 34). CARMA1 is phosphorylated by PKC-theta on residue S552 (step 35), leading to the oligomerization of CARMA1. This complex acts as a scaffold, recruiting BCL10 to the synapse by interacting with their CARD domains (step 36). BCL10 undergoes phosphorylation mediated by the enzyme RIP2 (step 37). Activated BCL10 then mediates the ubiquitination of IKBKG by recruiting MALT1 and TRAF6. MALT1 binds to BCL10 with its Ig-like domains and undergoes oligomerization (step 38). TRAF6 binds to the oligomerized MALT1 and also undergoes oligomerization (step 39). Oligomerized TRAF6 acts as a ubiquitin-protein ligase, catalyzing auto-K63-linked polyubiquitination (step 40). This K-63 ubiquitinated TRAF6 activates MAP3K7 kinase bound to TAB2 (step 41) and also ubiquitinates IKBKG in the IKK complex (step 44). MAP3K7 undergoes autophosphorylation on residues T184 and T187 and gets activated (step 42). Activated MAP3K7 kinase phosphorylates IKBKB on residues S177 and S181 in the activation loop and activates the IKK kinase activity (step 43). IKBKB phosphorylates the NFKBIA bound to the NFkappaB heterodimer, on residues S19 and S23 (step 45) and directs NFKBIA to 26S proteasome degradation (step 47). The NFkappaB heterodimer with a free NTS sequence finally migrates to the nucleus to regulate gene transcription (step 46).
R-HSA-186763 Downstream signal transduction The role of autophosphorylation sites on PDGF receptors are to provide docking sites for downstream signal transduction molecules which contain SH2 domains. The SH2 domain is a conserved motif of around 100 amino acids that can bind a phosphorylated tyrosine residue. These downstream molecules are activated upon binding to, or phosphorylated by, the receptor kinases intrinsic to PDGF receptors.
Some of the dowstream molecules are themselves enzymes, such as phosphatidylinositol 3'-kinase (PI3K), phospholipase C (PLC-gamma), the Src family of tyrosine kinases, the tyrosine phosphatase SHP2, and a GTPase activating protein (GAP) for Ras. Others such as Grb2 are adaptor molecules which link the receptor with downstream catalytic molecules.
R-HSA-1168372 Downstream signaling events of B Cell Receptor (BCR) Second messengers (calcium, diacylglycerol, inositol 1,4,5-trisphosphate, and phosphatidyinositol 3,4,5-trisphosphate) trigger signaling pathways: NF-kappaB is activated via protein kinase C beta, RAS via RasGRP proteins, NF-AT via calcineurin, and AKT via PDK1 (reviewed in Shinohara and Kurosaki 2009, Stone 2006).
R-HSA-5654687 Downstream signaling of activated FGFR1 Signaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that become tyrosine phosphorylated in response to FGF-stimulation and form a complex with additional complement of signaling proteins.
The activation loop in the catalytic domain of FGFR maintains the PTK domain in an inactive or low activity state. The activation-loop of FGFR1, for instance, contains two tyrosine residues that must be autophosphorylated for maintaining the catalytic domain in an active state. In the autoinhibited configuration, a kinase invariant proline residue at the C-terminal end of the activation loop interferes with substrate binding while allowing access to ATP in the nucleotide binding site.
In addition to the catalytic PTK core, the cytoplasmic domain of FGFR contains several regulatory sequences. The juxtamembrane domain of FGFRs is considerably longer than that of other receptor tyrosine kinases. This region contains a highly conserved sequence that serves as a binding site for the phosphotyrosine binding (PTB) domain of FRS2. A variety of signaling proteins are phosphorylated in response to FGF stimulation, including Shc, phospholipase-C gamma and FRS2 leading to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape.
R-HSA-5654696 Downstream signaling of activated FGFR2 Signaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that become tyrosine phosphorylated in response to FGF-stimulation and form a complex with additional complement of signaling proteins.
The activation loop in the catalytic domain of FGFR maintains the PTK domain in an inactive or low activity state. The activation-loop of FGFR1, for instance, contains two tyrosine residues that must be autophosphorylated for maintaining the catalytic domain in an active state. In the autoinhibited configuration, a kinase invariant proline residue at the C-terminal end of the activation loop interferes with substrate binding while allowing access to ATP in the nucleotide binding site.
In addition to the catalytic PTK core, the cytoplasmic domain of FGFR contains several regulatory sequences. The juxtamembrane domain of FGFRs is considerably longer than that of other receptor tyrosine kinases. This region contains a highly conserved sequence that serves as a binding site for the phosphotyrosine binding (PTB) domain of FRS2. A variety of signaling proteins are phosphorylated in response to FGF stimulation, including Shc, phospholipase-C gamma and FRS2 leading to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape.
R-HSA-5654708 Downstream signaling of activated FGFR3 Signaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that become tyrosine phosphorylated in response to FGF-stimulation and form a complex with additional complement of signaling proteins.
The activation loop in the catalytic domain of FGFR maintains the PTK domain in an inactive or low activity state. The activation-loop of FGFR1, for instance, contains two tyrosine residues that must be autophosphorylated for maintaining the catalytic domain in an active state. In the autoinhibited configuration, a kinase invariant proline residue at the C-terminal end of the activation loop interferes with substrate binding while allowing access to ATP in the nucleotide binding site.
In addition to the catalytic PTK core, the cytoplasmic domain of FGFR contains several regulatory sequences. The juxtamembrane domain of FGFRs is considerably longer than that of other receptor tyrosine kinases. This region contains a highly conserved sequence that serves as a binding site for the phosphotyrosine binding (PTB) domain of FRS2. A variety of signaling proteins are phosphorylated in response to FGF stimulation, including Shc, phospholipase-C gamma and FRS2 leading to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape.
R-HSA-5654716 Downstream signaling of activated FGFR4 Signaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that become tyrosine phosphorylated in response to FGF-stimulation and form a complex with additional complement of signaling proteins.
The activation loop in the catalytic domain of FGFR maintains the PTK domain in an inactive or low activity state. The activation-loop of FGFR1, for instance, contains two tyrosine residues that must be autophosphorylated for maintaining the catalytic domain in an active state. In the autoinhibited configuration, a kinase invariant proline residue at the C-terminal end of the activation loop interferes with substrate binding while allowing access to ATP in the nucleotide binding site.
In addition to the catalytic PTK core, the cytoplasmic domain of FGFR contains several regulatory sequences. The juxtamembrane domain of FGFRs is considerably longer than that of other receptor tyrosine kinases. This region contains a highly conserved sequence that serves as a binding site for the phosphotyrosine binding (PTB) domain of FRS2. A variety of signaling proteins are phosphorylated in response to FGF stimulation, including Shc, phospholipase-C gamma and FRS2 leading to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape.
R-HSA-9748784 Drug ADME Pharmacokinetics (PK) is a branch of pharmacology dedicated to determining the chemical fate of substances in living organisms, from administration to elimination from the body. PK can be described as how an organism affects a drug, whereas pharmacodynamics (PD) is the study of how a drug affects the organism. Both PK and PD are described for each drug annotated in the Drug Absorption, Distribution, Metabolism and Excretion (ADME) pathways. For example, although paracetamol ADME (PK) is described in this section, the pharmacological inhibition (PD) of its targets (PTGS1 and PTGS2) is described in the relevant pathway where these enzymes perform their physiological duties. A connection is made between the two pathways to link PK and PD annotations.
The disposition of a pharmaceutical compound within an organism can be described by four main stages; absorption, distribution, metabolism, and excretion, abbreviated to ADME (Pallasch 1988, Ruiz-Garcia et al. 2008, Currie 2018). Sometimes, separate steps can be tacked on to ADME depending on what is being described. For example, where a drug is released from a pharmaceutical formulation, liberation (L) is added to ADME (LADME) or where the toxicity of a compound is described, T is added (ADMET).
ADME of various drugs is annotated in this section.
R-HSA-9665230 Drug resistance in ERBB2 KD mutants ERBB2 kinase domain (KD) mutants vary in their resistance to various tyrosine kinase inhibitors and therapeutic antibody trastuzumab (herceptin). The following ERBB2 KD mutants are resistant to the therapeutic antibody trastuzumab (herceptin):
ERBB2 L755P (Nagano et al. 2018);
ERBB2 L755S (Nagano et al. 2018);
ERBB2 I767M (Bose et al. 2013);
ERBB2 D769Y (Nagano et al. 2018);
ERBB2 V777L (Nagano et al. 2018);
ERBB2 G778_P780dup (Bose et al. 2013, Nagano et al. 2018);
ERBB2 T798M (Rexer et al. 2013);
ERBB2 V842I (Nagano et al. 2018);
ERBB2 T862A (Nagano et al. 2018);
ERBB2 L869R (Hanker et al. 2017);
For ERBB2 R896C, both resistance (Bose et al. 2013) and sensitivity (Nagano et al. 2018) to trastuzumab have been reported.
R-HSA-9665737 Drug resistance in ERBB2 TMD/JMD mutants With respect to pertuzumab, a therapeutic antibody that block ligand-driven heterodimerization of ERBB2, ERBB2 R678Q is sensitive to pertuzumab, while ERBB2 V659E, ERBB2 G660D, ERBB2 G660R and probably ERBB2 Q709L are resistant (Pahuja et al. 2018).
R-HSA-9700649 Drug resistance of ALK mutants Aberrant ALK activity arises through fusions, point mutations, overexpression or amplifications and has been shown to be an oncogenic driver in a number of cancers including anaplastic large cell lymphoma (ALCL), non-small cell lung cancer (NSCLC), inflammatory myofibroblastic tumors (IMTs) neuroblastomas and more (reviewed in Della Corte et al, 2018; Lin et al, 2017). As a result, ALK is a promising therapeutic target for inhibition with tyrosine kinase inhibitors. Crizotinib, ceritinib, brigatinib, alectinib and lorlatinib are all approved for the treatment of ALK-driven cancers, however resistance commonly develops either as a result of accumulating secondary mutations, or through activation of bypass pathways that remove the dependence on ALK signaling (reviewed in Della Corte et al, 2017; Roskoski, 2013; Lin et al, 2017).
R-HSA-9702506 Drug resistance of FLT3 mutants FLT3 is mutated in ~30% of acute myeloid leukemias (AML), with internal tandem duplications (ITDs) representing the majority of these mutations and activating point mutants occurring at lower frequency. FLT3 mutations also occur at lower rates in other cancers (reviewed in Kazi and Roonstrand, 2018; Daver et al, 2019; Larroas-Garcia and Baer, 2017). Mutation of FLT3 has been identified as a driver in progression of AML and in consequence is a promising therapeutic target. A number of first and second generation inhibitors have been demonstrated to have activity against FLT3, but accumulation of secondary mutations leads to the development of resistance. These secondary mutations further shift the equilibrium of the receptor toward the activated state, making even the second-generation type II TKIs less effective. In consequence, considerable effort is devoted to discovery of type II and, in particular, type I TKIs that are active against highly activated FLT3 alleles (reviewed in Daver et al, 2019; Staudt et al, 2018; Lim et al, 2017; Klug et al, 2018).
R-HSA-9669937 Drug resistance of KIT mutants Activating mutations in the juxtamembrane domain of KIT are common in some cancers, including gastrointestinal stromal tumors, melanoma and acute myeloid leukemia (reviewed in Roskoski, 2018). These mutations are sensitive to inhibition with imatinib, which in 2001 was the first tyrosine kinase inhibitor approved for treatment of cancer (Demetri et al, 2002; Corless et al, 2011; reviewed in Zitvogel, 2016). Although highly successful in prolonging survival, imatinib-resistance develops in most patients due to appearance of secondary mutations, often in the ATP-binding pocket or in the activation loop of the kinase domain (Gajiwala et al, 2008; Serrano et al, 2019; reviewed in Roskoski, 2018; Napolitano and Vincenzi, 2019)
R-HSA-9674415 Drug resistance of PDGFR mutants PDGFRA is mutated in ~10% of gastrointestinal stromal tumors in a mutually exclusive manner with KIT mtutations. In contrast to KIT, PDGFRA GIST mutations occur more frequently in the activation domain, rather than the juxtamembrane domain. In addition to GIST, PDGFRA is subject to missense or small in-frame deletion mutations in haematological cancers and melanoma. In contrast, missense mutations in PDGFRB are rare (Heinrich et al, 2003; Corless et al, 2005; reviewed in Corless et al, 2011). Both PDGFRA and PDGFRB are also subject to oncogenic translocation events leading to the expression of fusion proteins (Cools et al, 2003; Simon et al, 2008; Salemi et al, 2009; Ohashi et al, 2010; reviewed in Appiah-Kubi et al, 2017).
Imatinib is a type II TKIs that is approved as first-line treatment of KIT- and PDGFR-driven tumors; however secondary mutations frequently contribute to the development of imatinib resistance. These secondary mutations further shift the equilibrium of the receptor toward the activated state, making imatinib and even approved second-line type II TKIs less effective. In consequence, considerable effort is devoted to discovery of type II and, in particular, type I TKIs that are active against highly activated PDGFR alleles (Smith et al, 2019; Lierman et al, 2019; reviewed in Roskoski, 2018; Klug et al, 2018).
R-HSA-9750126 Drug-induced formation of DNA interstrand crosslinks This pathway describes how drugs commonly used in the treatment of cancer, psoriasis and severe atopic dermatitis produce DNA interstrand crosslinks that are repaired through the Fanconi anemia pathway. For review, please refer to Deans and West 2011, Fu et al. 2012, and Rycenga and Long 2018.
R-HSA-9754119 Drug-mediated inhibition of CDK4/CDK6 activity Cyclin dependent kinases CDK4 and CDK6 regulate crucial steps in the G1 phase of the cell cycle that commit cells to transition to the S phase and ultimately divide. Many growth signaling pathways, frequently perturbed in cancer, converge on CDK4/CDK6 activation, thus driving cellular proliferation. This makes CDK4 and CDK6 promising targets for anti-cancer therapy. So far, three CDK4/6 inhibitors, palbociclib, ribociclib and abemaciclib, have been approved for clinical use and many others are at different stages of clinical testing. CDK4/6 inhibitors mainly have a cytostatic effect on tumor cells, but can also influence immune response to tumor by targeting immune system cells in the tumor microenvironment. While intact RB1, the main target of CDK4/6 during cell cycle progression, is in general considered to be a prerequisite for the success of CDK4/6-targeted anti-cancer therapy, the status of other, less explored CDK4/6 targets can also affect the treatment outcome. For review, please refer to Asghar et al. 2015, Klein et al. 2018, Álvarez-Fernández and Malumbres 2020, Petroni et al. 2020).
R-HSA-9652282 Drug-mediated inhibition of ERBB2 signaling Signaling by ERBB2 can be pharmacologically inhibited with tyrosine kinase inhibitors (TKIs) (Nelson and Fry 2001, Xia et al. 2002, Wood et al. 2004, Rabindran et al. 2004, Gandreau et al. 2007, Jani et al. 2007, Li et al. 2008, Hichkinson et al. 2010, Traxler et al. 2014, Hanker et al. 2017), and therapeutic antibodies, such as trastuzumab (Hudziak et al. 1989, Carter et al. 1992, Pickl and Ries 2009, Maadi et al. 2018) and pertuzumab (Franklin et al. 2004).
R-HSA-9734091 Drug-mediated inhibition of MET activation MET receptor tyrosine kinase (RTK) is a proto-oncogene that is frequently aberrantly activated in cancer through gene amplification and/or activating mutations that result in hypersensitivity to HGF stimulation or HGF-independent activation. Oncogenic MET activation can occur as a primary mechanism of malignant transformation or be selected secondarily, as a mechanism of resistance to therapeutics that target related RTKs, such as EGFR. MET targeted anti-cancer therapeutics, either recombinant monoclonal antibodies (MAbs) or small tyrosine kinase inhibitors (TKIs), have shown promise as a first-line agents for the treatment of solid tumors with primary MET activation or as second-line agents for the treatment of solid tumors with acquired MET-mediated resistance to other RTK-targeted therapies (reviewed in Comoglio et al. 2018).
R-HSA-5696400 Dual Incision in GG-NER Double incision at the damaged DNA strand excises the oligonucleotide that contains the lesion from the open bubble. The excised oligonucleotide is ~27-30 bases long. Incision 5' to the damage site, by ERCC1:ERCC4 endonuclease, precedes the incision 3' to the damage site by ERCC5 endonuclease (Staresincic et al. 2009).
R-HSA-6782135 Dual incision in TC-NER In transcription-coupled nucleotide excision repair (TC-NER), similar to global genome nucleotide excision repair (GG-NER), the oligonucleotide that contains the lesion is excised from the open bubble structure via dual incision of the affected DNA strand. 5' incision by the ERCC1:ERCC4 (ERCC1:XPF) endonuclease precedes 3' incision by ERCC5 (XPG) endonuclease. In order for the TC-NER pre-incision complex to assemble and the endonucleases to incise the damaged DNA strand, the RNA polymerase II (RNA Pol II) complex has to backtrack - reverse translocate from the damage site. Although the mechanistic details of this process are largely unknown in mammals, it may involve ERCC6/ERCC8-mediated chromatin remodelling/ubiquitination events, the DNA helicase activity of the TFIIH complex and TCEA1 (TFIIS)-stimulated cleavage of the 3' protruding end of nascent mRNA by RNA Pol II (Donahue et al. 1994, Lee et al. 2002, Sarker et al. 2005, Vermeulen and Fousteri 2013, Hanawalt and Spivak 2008, Staresincic et al. 2009, Epshtein et al. 2014).
R-HSA-113510 E2F mediated regulation of DNA replication Progression through G1 and G1 to S-phase transition that initiates DNA synthesis involve many complexes that are regulated by RB1:E2F pathway. RB1:E2F pathway plays a key role in gene expression regulation in proliferating and differentiated cells. As a repressor, E2F remains bound to RB1; it can activate the expression of S-phase genes involved in DNA replication after the phosphorylation of RB1.
E2F proteins regulate expression of genes involved in various processes thereby forming interlinks between cell cycle, DNA synthesis, DNA damage recognition etc.
In this module, activation of replication related genes by E2F1 and two ways by which E2F1 regulates DNA replication initiation are annotated.
R-HSA-113507 E2F-enabled inhibition of pre-replication complex formation Under specific conditions, Cyclin B, a mitotic cyclin, can inhibit the functions of pre-replicative complex. E2F1 activates Cdc25A protein which regulates Cyclin B in a positive manner. Cyclin B/Cdk1 function is restored which leads to the disruption of pre-replicative complex. This phenomenon has been demonstrated by Bosco et al (2001) in Drosophila.
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins E3 ubiquitin ligases catalyze the transfer of an ubiquitin from an E2-ubiquitin conjugate to a target protein. Generally, ubiquitin is transferred via formation of an amide bond to a particular lysine residue of the target protein, but ubiquitylation of cysteine, serine and threonine residues in a few targeted proteins has also been demonstrated (reviewed in McDowell and Philpott 2013, Berndsen and Wolberger 2014). Based on protein homologies, families of E3 ubiquitin ligases have been identified that include RING-type ligases (reviewed in Deshaies et al. 2009, Metzger et al. 2012, Metzger et al. 2014), HECT-type ligases (reviewed in Rotin et al. 2009, Metzger et al. 2012), and RBR-type ligases (reviewed in Dove et al. 2016). A subset of the RING-type ligases participate in CULLIN-RING ligase complexes (CRLs which include SCF complexes, reviewed in Lee and Zhou 2007, Genschik et al. 2013, Skaar et al. 2013, Lee et al. 2014).
Some E3-E2 combinations catalyze mono-ubiquitination of the target protein (reviewed in Nakagawa and Nakayama 2015). Other E3-E2 combinations catalyze conjugation of further ubiquitin monomers to the initial ubiquitin, forming polyubiquitin chains. (It may also be possible for some E3-E2 combinations to preassemble polyubiquitin and transfer it as a unit to the target protein.) Ubiquitin contains several lysine (K) residues and a free alpha amino group to which further ubiquitin can be conjugated. Thus different types of polyubiquitin are possible: K11 linked polyubiquitin is observed in endoplasmic reticulum-associated degradation (ERAD), K29 linked polyubiquitin is observed in lysosomal degradation, K48 linked polyubiquitin directs target proteins to the proteasome for degradation, whereas K63 linked polyubiquitin generally acts as a scaffold to recruit other proteins in several cellular processes, notably DNA repair (reviewed in Komander et al. 2009).
R-HSA-3000178 ECM proteoglycans Proteoglycans are major components of the extracellular matrix. In cartilage the matrix constitutes more than 90% of tissue dry weight. Proteoglycans are proteins substituted with glycosaminoglycans (GAGs), linear polysaccharides consisting of a repeating disaccharide, generally of an acetylated amino sugar alternating
with a uronic acid. Most proteoglycans are located in the extracellular
space. Proteoglycans are highly diverse, both in terms of the core proteins and the subtypes of GAG chains, namely chondroitin sulfate (CS), keratan sulfate (KS), dermatan sulfate (DS) and heparan sulfate (HS). Hyaluronan is a non-sulfated GAG whose molecular weight runs into millions of Dalton; in articular cartilage, a single hyaluronan molecule can hold upto 100 aggrecan molecules and these aggregates are stabilized by a link protein.
R-HSA-2179392 EGFR Transactivation by Gastrin Gastrin, through the action of diacylglycerol produced from downstream G alpha (q) events, transactivates EGFR via a PKC-mediated pathway by activation of MMP3 (Matrix Metalloproteinase 3) which allows formation of mature HBEGF (heparin-binding epidermal growth factor) by cleaving pro-HBEGF. Mature HBEGF is then free to bind the EGFR, resulting in EGFR activation (Dufresne et al. 2006, Liebmann 2011).
R-HSA-182971 EGFR downregulation Regulation of receptor tyrosine kinase (RTK) activity is implicated in the control of almost all cellular functions. One of the best understood RTKs is epidermal growth factor receptor (EGFR). Growth factors can bind to EGFR and activate it to initiate signalling cascades within the cell. EGFRs can also be recruited to clathrin-coated pits which can be internalised into endocytic vesicles. From here, EGFRs can either be recycled back to the plasma membrane or directed to lysosomes for destruction.This provides a mechanism by which EGFR signalling is negatively regulated and controls the strength and duration of EGFR-induced signals. It also prevents EGFR hyperactivation as commonly seen in tumorigenesis.
The proto-oncogene Cbl can negatively regulate EGFR signalling. The Cbl family of RING-type ubiquitin ligases are able to poly-ubiquitinate EGFR, an essential step in EGFR degradation. All Cbl proteins have a unique domain that recognises phosphorylated tyrosine residues on activated EGFRs. They also direct the ubiquitination and degradation of activated EGFRs by recruiting ubiquitin-conjugation enzymes. Cbl proteins function by specifically targeting activated EGFRs and mediating their down-regulation, thus providing a means by which signaling processes can be negatively regulated.
Cbl also promotes receptor internalization via it's interaction with an adaptor protein, CIN85 (Cbl-interacting protein of 85kDa). CIN85 binds to Cbl via it's SH3 domain and is enhanced by the EGFR-induced tyrosine phosphorylation of Cbl. The proline-rich region of CIN85 interacts with endophilins which are regulatory components of clathrin-coated vesicles (CCVs). Endophilins bind to membranes and induce membrane curvature, in conjunction with other proteins involved in CCV formation. The rapid recruitment of endophilin to the activated receptor complex by CIN85 is the mechanism which controls receptor internalization.
R-HSA-212718 EGFR interacts with phospholipase C-gamma Activated epidermal growth factor receptors (EGFR) can stimulate phosphatidylinositol (PI) turnover. Activated EGFR can activate phospholipase C-gamma1 (PLC-gamma1, i.e. PLCG1) which hydrolyses phosphatidylinositol 4,5-bisphosphate (PIP2) to inositol 1,4,5-triphosphate (IP3) and diacylglycerol (DAG). IP3 is instrumental in the release of calcium from intracellular stores and DAG is involved in protein kinase C activation.
R-HSA-9619665 EGR2 and SOX10-mediated initiation of Schwann cell myelination Schwann cells are glial cells of the peripheral nervous system that ensheath the peripheral nerves within a compacted lipid-rich myelin structure that is required for optimal transduction of nerve signals in motor and sensory nerves. Schwann cells develop from the neural crest in a differentiation process driven by factors derived from the Schwann cell itself, from the adjacent neuron or from the extracellular matrix (reviewed in Jessen and Mirsky, 2005). Upon peripheral nerve injury, mature Schwann cells can form repair cells that allow peripheral nerve regeneration through myelin phagocytosis and remyelination of the peripheral nerve. This process in some ways recapitulates the maturation of immature Schwann cells during development (reviewed in Jessen and Mirsky, 2016). Mature, fully myelinated Schwann cells exhibit longitudinal and radial polarization. The axon-distal abaxonal membrane interacts with elements of the basal lamina through integrins and lamins and in this way resembles the basolateral domain of polarized epithelial cells. In contrast, the axon-proximal adaxonal membrane resembles the apical domain of an epithelial cell, and is enriched with adhesion molecules and receptors that mediate interaction with ligands from the axon (reviewed in Salzer, 2015).
Schwann cells express a number of Schwann-cell specific proteins, including components of the myelin sheath such as myelin basic protein (MBP) and myelin protein zero (MPZ). In addition, Schwann cells have high lipid content relative to other membranes, and are enriched in galactosphingolipids, cholesterol and saturated long chain fatty acids (reviewed in Garbay et al, 2000). This protein and lipid profile is driven by a Schwann cell myelination transcriptional program controlled by master regulators SOX10, POU3F1 and EGR2, among others (reviewed in Svaren and Meijer, 2008; Stolt and Wegner, 2016).
R-HSA-9648025 EML4 and NUDC in mitotic spindle formation EML4 and NUDC proteins are required for mitotic spindle formation, attachment of spindle microtubule ends to kinetochores, and alignment of mitotic chromosome at the metaphase plate. EML4 is a WD40 family protein that binds to interphase microtubules and stabilizes them (Houtman et al. 2007, Adib et al. 2019). At mitotic entry, EML4 undergoes phosphorylation (Pollmann et al. 2006, Adib et al. 2019) by serine/threonine kinases NEK6 and NEK7, leading to its dissociation from microtubules, which is necessary for the assembly of a dynamic mitotic spindle (Adib et al. 2019). EML4, through its WD40 repeats, interacts with NUDC and recruits it to the kinetochores of the mitotic spindle (Chen et al. 2015). It is possible that other mitotic kinases, besides NEK6 and NEK7, also phosphorylate EML4. Phosphorylation of different residues of EML4 could reduce or increase affinity of EML4 for specific subpopulations of microtubules in mitosis.
A recurrent genomic rearrangement, reported in about 5% cases of non-small cell lung cancer (NSCLC) fuses the N-terminal portion of EML4 with the C-terminal portion of ALK (anaplastic lymphoma kinase), resulting in a constitutively active ALK (Soda et al. 2007, Richards et al. 2015).
R-HSA-2682334 EPH-Ephrin signaling During the development process cell migration and adhesion are the main forces involved in morphing the cells into critical anatomical structures. The ability of a cell to migrate to its correct destination depends heavily on signaling at the cell membrane. Erythropoietin producing hepatocellular carcinoma (EPH) receptors and their ligands, the ephrins (EPH receptors interacting proteins, EFNs), orchestrates the precise control necessary to guide a cell to its destination. They are expressed in all tissues of a developing embryo and are involved in multiple developmental processes such as axon guidance, cardiovascular and skeletal development and tissue patterning. In addition, EPH receptors and EFNs are expressed in developing and mature synapses in the nervous system, where they may have a role in regulating synaptic plasticity and long-term potentiation. Activation of EPHB receptors in neurons induces the rapid formation and enlargement of dendritic spines, as well as rapid synapse maturation (Dalva et al. 2007). On the other hand, EPHA4 activation leads to dendritic spine elimination (Murai et al. 2003, Fu et al. 2007).
EPH receptors are the largest known family of receptor tyrosine kinases (RTKs), with fourteen total receptors divided into either A- or B-subclasses: EPHA (1-8 and 10) and EPHB (1-4 and 6). EPH receptors can have overlapping functions, and loss of one receptor can be partially compensated for by another EPH receptor that has similar expression pattern and ligand-binding specificities. EPH receptors have an N-terminal extracellular domain through which they bind to ephrin ligands, a short transmembrane domain, and an intracellular cytoplasmic signaling structure containing a canonical tyrosine kinase catalytic domain as well as other protein interaction sites. Ephrins are also sub-divided into an A-subclass (A1-A5), which are tethered to the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor, and a B-subclass (B1-B3), members of which have a transmembrane domain and a short, highly conserved cytoplasmic tail lacking endogenous catalytic activity. The interaction between EPH receptors and its ligands requires cell-cell interaction since both molecules are membrane-bound. Close contact between EPH receptors and EFNs is required for signaling to occur. EPH/EFN-initiated signaling occurs bi-directionally into either EPH- or EFN-expressing cells or axons. Signaling into the EPH receptor-expressing cell is referred as the forward signal and signaling into the EFN-expressing cell, the reverse signal. (Dalva et al. 2000, Grunwald et al. 2004, Davy & Robbins 2000, Cowan et al. 2004)
R-HSA-3928665 EPH-ephrin mediated repulsion of cells Despite high-affinity multimeric interaction between EPHs and ephrins (EFNs), the cellular response to EPH-EFN engagement is usually repulsion between the two cells and signal termination. These repulsive responses induce an EPH receptor-expressing cell to retract from an ephrin-expressing cell after establishing initial contact. The repulsive responses mediated by EPH receptors in the growth cone at the leading edge of extending axons and in axonal collateral branches contribute to the formation of selective neuronal connections. It is unclear how high affinity trans-cellular interactions between EPHs and ephrins are broken to convert adhesion into repulsion. Two possible mechanisms have been proposed for the repulsion of EPH-EFN bearing cells: the first one involves regulated cleavage of ephrin ligands or EPH receptors by transmembrane proteases following cell-cell contact, while the second one is rapid endocytosis of whole EPH:EFN complexes during the retraction of the interacting cells or neuronal growth cones (Egea & Klein 2007, Janes et al. 2005). RAC also plays an essential role during growth cone collapse by promoting actin polymerization that drives membrane internalization by endocytosis (Marston et al. 2003).
R-HSA-3928663 EPHA-mediated growth cone collapse EPH/Ephrin signaling is coupled to Rho family GTPases such as Rac, Rho and Cdc42 that connect bidirectional receptor-ligand interactions to changes in the actin cytoskeleton (Noren & Pasquale 2004, Groeger & Nobes 2007). RHOA regulates actin dynamics and is involved in EPHA-induced growth cone collapse. This is mediated by ephexins. Ephexin, a guanine nucleotide exchange factor for Rho GTPases, interacts with the EPHA kinase domain and its subsequent activation differentially affects Rho GTPases, such that RHOA is activated, whereas Cdc42 and Rac1 are inhibited. Activation of RHOA, and inhibition of Cdc42 and Rac, shifts actin cytoskeleton to increased contraction and reduced expansion leading to growth-cone collapse (Shamah et al. 2001, Sahin et al. 2005). The activation of EPH receptors in growing neurons typically, but not always, leads to a growth cone collapse response and retraction from an ephrin-expressing substrate (Poliakov et al. 2004, Pasquale 2005). EPHA-mediated repulsive responses prevent axons from growing into regions of excessive ephrin-A concentration, such as the posterior end of the superior colliculus (Pasquale 2005).
R-HSA-3928662 EPHB-mediated forward signaling Multiple EPHB receptors contribute directly to dendritic spine development and morphogenesis. These are more broadly involved in post-synaptic development through activation of focal adhesion kinase (FAK) and Rho family GTPases and their GEFs. Dendritic spine morphogenesis is a vital part of the process of synapse formation and maturation during CNS development. Dendritic spine morphogenesis is characterized by filopodia shortening followed by the formation of mature mushroom-shaped spines (Moeller et al. 2006). EPHBs control neuronal morphology and motility by modulation of the actin cytoskeleton. EPHBs control dendritic filopodia motility, enabling synapse formation. EPHBs exert these effects through interacting with the guanine exchange factors (GEFs) such as intersectin and kalirin. The intersectin-CDC42-WASP-actin and kalirin-RAC-PAK-actin pathways have been proposed to regulate the EPHB receptor mediated morphogenesis and maturation of dendritic spines in cultured hippocampal and cortical neurons (Irie & Yamaguchi 2002, Penzes et al. 2003). EPHBs are also involved in the regulation of dendritic spine morphology through FAK which activates the RHOA-ROCK-LIMK-1 pathway to suppress cofilin activity and inhibit cofilin-mediated dendritic spine remodeling (Shi et al. 2009).
R-HSA-901032 ER Quality Control Compartment (ERQC) Proteins that are released from the CNX or CRT complex with folding defects accumulate in a compartment of the ER called ERQC (Kamhi-Nesher et al. 2001). Here, the enzymes UGGG1 or UGGG2 are able to recognize glycoproteins with minor folding process and re-add the glucose on the alpha,1,3 branch; this is a signal for the transport of these glycoproteins back to the ER, where they can interact again with CNX or CRT in order to achieve a correct folding. At the same time that the glycoprotein is in the ERQC, the enzyme ER mannosidase I progressively removes the mannoses at positions 1A, 2A, B, C on N-glycans; when the mannose on 1A is trimmed, UDP-Glc:glycoprotein glucosyltransferases 1 and 2 (UGGT1 and 2) are no longer able to re-add the glucose, and therefore the protein is destined for ERAD. Glycoproteins subject to endoplasmic reticulum-associated degradation (ERAD) undergo reglucosylation, deglucosylation, and mannose trimming to yield Man6GlcNAc2 and Man5GlcNAc2. These structures lack the mannose residue that is the acceptor of glucose transferred by UGGT1 and 2. For years it has been thought that the removal of the mannose in position B of the N-glycan was the signal to direct proteins to degradation. However, this mechanism has been described better by Avezov et al (Avezov et al. 2008) and it has been demonstrated that even glycoproteins with Man8 or Man7 glycans can be re-glucosylated and interact again with CNX or CRT (for a review on this topic, see Lederkremer 2009 and Maattanen P et al, 2010).
R-HSA-199977 ER to Golgi Anterograde Transport Secretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus for further processing. About 25% of the proteome may be exported from the ER in human cells. This cargo is recognized and concentrated into COPII vesicles, which range in size from 60-90 nm, and move cargo from the ER to the ERGIC. Soluble cargo in the ER lumen is concentrated into COPII vesicles through interaction with a receptor with the receptor subsequently recycled to the ER in COPI vesicles through retrograde traffic. The ERGIC (ER-to-Golgi intermediate compartment, also known as vesicular-tubular clusters, VTCs) is a stable, biochemically distinct compartment located adjacent to ER exit sites. Retrograde traffic makes use of microtubule-directed COPI-coated vesicles, carrying ER proteins and membrane back to the ER.
R-HSA-1236974 ER-Phagosome pathway The other TAP-dependent cross-presentation mechanism in phagocytes is the endoplasmic reticulum (ER)-phagosome model. Desjardins proposed that ER is recruited to the cell surface, where it fuses with the plasma membrane, underneath phagocytic cups, to supply membrane for the formation of nascent phagosomes (Gagnon et al. 2002). Three independent studies simultaneously showed that ER contributes to the vast majority of phagosome membrane (Guermonprez et al. 2003, Houde et al. 2003, Ackerman et al. 2003). The composition of early phagosome membrane contains ER-resident proteins, the components required for cross-presentation. This model is similar to the phagosome-to-cytosol model in that Ag is translocated to cytosol for proteasomal degradation, but differs in that antigenic peptides are translocated back into the phagosome (instead of ER) for peptide:MHC-I complexes. ER fusion with phagosome introduces molecules that are involved in Ag transport to cytosol (Sec61) and proteasome-generated peptides back into the phagosome (TAP) for loading onto MHC-I.
Although the ER-phagosome pathway is controversial, the concept remains attractive as it explains how peptide-receptive MHC-I molecules could intersect with a relatively high concentration of exogenous antigens, presumably a crucial prerequisite for efficient cross-presentation (Basha et al. 2008).
R-HSA-8847993 ERBB2 Activates PTK6 Signaling PTK6 (BRK) is activated downstream of ERBB2 (HER) (Xiang et al. 2008, Peng et al. 2015) and other receptor tyrosine kinases, such as EGFR (Kamalati et al. 1996) and MET (Castro and Lange 2010). However, it is not clear if MET and EGFR activate PTK6 directly or act through ERBB2, since it is known that ERBB2 forms heterodimers with EGFR (Spivak-Kroizman et al. 1992), and MET can heterodimerize with both EGFR and ERBB2 (Tanizaki et al. 2011).
R-HSA-6785631 ERBB2 Regulates Cell Motility Activated ERBB2 heterodimers regulate cell motility through association with MEMO1. MEMO1 retains activated RHOA GTPase and its associated protein DIAPH1 at the plasma membrane, thus linking ERBB2 activation with the microtubule and actin dynamics downstream of the RHOA:GTP:DIAPH1 complex (Marone et al. 2004, Qiu et al. 2008, Zaoui et al. 2008, Zaoui et al. 2010).
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression About half of the rRNA genes in the genome are actively expressed, being transcribed by RNA polymerase I (reviewed in Nemeth and Langst 2008, Bartova et al. 2010, Goodfellow and Zomerdijk 2012, Grummt and Langst 2013). As inferred from mouse, those genes that are expressed are activated by ERCC6 (also known as Cockayne Syndrome protein, CSB) which interacts with TTF-I bound to the T0 terminator region (also know as the Sal Box) of rRNA genes (Yuan et al. 2007, reviewed in Birch and Zomerdijk 2008, Grummt and Langst 2013). ERCC6 recruits the histone methyltransferase EHMT2 (also known as G9a) which dimethylates histone H3 at lysine-9 in the coding region of rRNA genes. The dimethylated lysine is bound by CBX3 (also known as Heterochromatic Protein-1gamma, HP1gamma) and increases expression of the rRNA gene. Continuing dimethylation depends on continuing transcription. Mutations in CSB result in dysregulation of RNA polymerase I transcription, which plays a role in the symptoms of Cockayne Syndrome (reviewed in Hannan et al. 2013).
R-HSA-198753 ERK/MAPK targets ERK/MAPK kinases have a number of targets within the nucleus, usually transcription factors or other kinases. The best known targets, ELK1, ETS1, ATF2, MITF, MAPKAPK2, MSK1, RSK1/2/3 and MEF2 are annotated here.
R-HSA-202670 ERKs are inactivated MAP Kinases are inactivated by a family of protein named MAP Kinase Phosphatases (MKPs). They act through dephosphorylation of threonine and/or tyrosine residues within the signature sequence -pTXpY- located in the activation loop of MAP kinases (pT=phosphothreonine and pY=phosphotyrosine). MKPs are divided into three major categories depending on their preference for dephosphorylating; tyrosine, serine/threonine and both the tyrosine and threonine (dual specificity phoshatases or DUSPs). The tyrosine-specific MKPs include PTP-SL, STEP and HePTP, serine/threonine-specific MKPs are PP2A and PP2C, and many DUSPs acting on MAPKs are known. Activated MAP kinases trigger activation of transcription of MKP genes. Therefore, MKPs provide a negative feedback regulatory mechanism on MAPK signaling, by inactivating MAPKs via dephosphorylation, in the cytoplasm and the nucleus. Some MKPs are more specific for ERKs, others for JNK or p38MAPK.
R-HSA-8939211 ESR-mediated signaling Estrogens are a class of hormones that play a role in physiological processes such as development, reproduction, metabolism of liver, fat and bone, and neuronal and cardiovascular function (reviewed in Arnal et al, 2017; Haldosen et al, 2014). Estrogens bind estrogen receptors, members of the nuclear receptor superfamily. Ligand-bound estrogen receptors act as nuclear transcription factors to regulate expression of genes that control cellular proliferation and differentiation, among other processes, but also play a non-genomic role in rapid signaling from the plasma membrane (reviewed in Hah et al, 2014;Schwartz et al, 2016).
R-HSA-162594 Early Phase of HIV Life Cycle In the early phase of HIV lifecycle, an active virion binds and enters a target cell mainly by specific interactions of the viral envelope proteins with host cell surface receptors. The virion core is uncoated to expose a viral nucleoprotein complex containing RNA and viral proteins. HIV RNA genome is reverse transcribed by the viral Reverse Transcriptase to form a cDNA copy, that gets inserted into host cell DNA. The viral Integrase enzyme is vital to carry out the integration of the viral cDNA into the host genome. The host DNA repair enzymes probably repair the breaks in DNA at the sites of integration.
R-HSA-9772572 Early SARS-CoV-2 Infection Events The initial steps of SARS-CoV-2 infection involve the specific binding of the coronavirus spike (S) protein to the cellular entry receptor, angiotensin-converting enzyme 2 (ACE2). The expression and tissue distribution of entry receptors consequently influence viral tropism and pathogenicity. Besides receptor binding, the proteolytic cleavage of coronavirus S proteins by host cell-derived proteases is essential to permit fusion. SARS-CoV has been shown to use the cell-surface serine protease TMPRSS2 for priming and entry, although the endosomal cysteine proteases cathepsin B (CatB) and CatL can also assist in this process. During the intracellular life cycle SARS-CoV-2 express and replicate their genomic RNA to produce full-length copies that are incorporated into newly produced viral particles. Coronaviruses possess remarkably large RNA genomes flanked by 5' and 3' untranslated regions that contain cis-acting secondary RNA structures essential for RNA synthesis. At the 5' end, the genomic RNA features two large open reading frames (ORFs; ORF1a and ORF1b) that occupy two-thirds of the capped and polyadenylated genome. Coronavirus S proteins are homotrimeric class I fusion glycoproteins that are divided into two functionally distinct parts (S1 and S2). The surface-exposed S1 contains the receptor-binding domain (RBD) that specifically engages the host cell receptor, thereby determining virus cell tropism and pathogenicity. Besides receptor binding, the proteolytic cleavage of coronavirus S proteins by host cell-derived proteases is essential to permit fusion. SARS-CoV has been shown to use the cell-surface serine protease TMPRSS2 for priming and entry, although the endosomal cysteine proteases cathepsin B (CatB) and CatL can also assist in this process The release of the coronavirus genome into the host cell cytoplasm upon entry marks the onset of a complex programme of viral gene expression, which is highly regulated in space and time. The translation of ORF1a and ORF1b from the genomic RNA produces two polyproteins, pp1a and pp1ab, respectively. ORF1a and ORF1b encode 15-16 non-structural proteins (nsp), of which 15 compose the viral replication and transcription complex (RTC) that includes, amongst others, RNA-processing and RNA-modifying enzymes and an RNA proofreading function necessary for maintaining the integrity of the >30kb coronavirus genome. The establishment of the viral RTC is crucial for virus replication The release of the coronavirus genome into the host cell cytoplasm upon entry marks the onset of a complex programme of viral gene expression, here divided into early and late.
R-HSA-114508 Effects of PIP2 hydrolysis Hydrolysis of phosphatidyl inositol-bisphosphate (PIP2) by phospholipase C (PLC) produces diacylglycerol (DAG) and inositol triphosphate (IP3). Both are potent second messengers. IP3 diffuses into the cytosol, but as DAG is a hydrophobic lipid it remains within the plasma membrane. IP3 stimulates the release of calcium ions from the smooth endoplasmic reticulum, while DAG activates the conventional and unconventional protein kinase C (PKC) isoforms, facilitating the translocation of PKC from the cytosol to the plasma membrane. The effects of DAG are mimicked by tumor-promoting phorbol esters. DAG is also a precursor for the biosynthesis of prostaglandins, the endocannabinoid 2-arachidonoylglycerol and an activator of a subfamily of TRP-C (Transient Receptor Potential Canonical) cation channels 3, 6, and 7.
R-HSA-391903 Eicosanoid ligand-binding receptors Eicosanoids, derived from polyunsaturated 20-carbon fatty acids, are paracrine and autocrine regulators of inflammation, smooth muscle contraction, and blood coagulation. The actions of eicosanoids are mediated by eicosanoid receptors, most of which are GPCRs. There are four types of eicosanoid GPCRs in humans; leukotriene, lipoxin (Brink C et al, 2003), prostanoid (Coleman RA et al, 1994) and oxoeicosanoid (Brink C et al, 2004) receptors.
R-HSA-211979 Eicosanoids Arachidonic acid is metabolized via three major enzymatic pathways: cyclooxygenase, lipoxygenase, and cytochrome P450. The cytochrome P450 pathway metabolites are oxygenated metabolites of arachidonic acid.
R-HSA-1566948 Elastic fibre formation Elastic fibres (EF) are a major structural constituent of dynamic connective tissues such as large arteries and lung parenchyma, where they provide essential properties of elastic recoil and resilience. EF are composed of a central cross-linked core of elastin, surrounded by a mesh of microfibrils, which are composed largely of fibrillin. In addition to elastin and fibrillin-1, over 30 ancillary proteins are involved in mediating important roles in elastic fibre assembly as well as interactions with the surrounding environment. These include fibulins, elastin microfibril interface located proteins (EMILINs), microfibril-associated glycoproteins (MAGPs) and Latent TGF-beta binding proteins (LTBPs). Fibulin-5 for example, is expressed by vascular smooth muscle cells and plays an essential role in the formation of elastic fibres through mediating interactions between elastin and fibrillin (Yanigasawa et al. 2002, Freeman et al. 2005). In addition, it plays a role in cell adhesion through integrin receptors and has been shown to influence smooth muscle cell proliferation (Yanigasawa et al. 2002, Nakamura et al. 2002). EMILINs are a family of homologous glycoproteins originally identified in extracts of aortas. Found at the elastin-fibrillin interface, early studies showed that antibodies to EMILIN can affect the process of elastic fibre formation (Bressan et al. 1993). EMILIN1 has been shown to bind elastin and fibulin-5 and appears to coordinate their common interaction (Zanetti et al. 2004). MAGPs are found to co-localize with microfibrils. MAGP-1, for example, binds strongly to an N-terminal sequence of fibrillin-1. Other proteins found associated with microfibrils include vitronectin (Dahlback et al. 1990).
Fibrillin is most familiar as a component of elastic fibres but microfibrils with no elastin are found in the ciliary zonules of the eye and invertebrate circulatory systems. The addition of elastin to microfibrils is a vertebrate adaptation to high pulsatile pressures in their closed circulatory systems (Faury et al. 2003). Elastin appears to have emerged after the divergence of jawless vertebrates from other vertebrates (Sage 1982).
Fibrillin-1 is the major structural component of microfibrils. Fibrillin-2 is expressed earlier in development than fibrillin-1 and may be important for elastic fiber formation (Zhang et al. 1994). Fibrillin-3 arose as a duplication of fibrillin-2 that did not occur in the rodent lineage. It was first isolated from human brain (Corson et al. 2004).
Fibrillin assembly is not as well defined as elastin assembly. The primary structure of fibrillin is dominated by calcium binding epidermal growth factor like repeats (Kielty et al. 2002). Fibrillin may form dimers or trimers before secretion. However, multimerisation predominantly occurs outside the cell. Formation of fibrils appears to require cell surface structures suggesting an involvement of cell surface receptors. Fibrillin is assembled pericellularly (i.e. on or close to the cell surface) into microfibrillar arrays that undergo time dependent maturation into microfibrils with beaded-string appearance. Transglutaminase forms gamma glutamyl epsilon lysine isopeptide bonds within or between peptide chains. Additionally, intermolecular disulfide bond formation between fibrillins is an important contributor to fibril maturation (Reinhardt et al. 2000).
Models of fibrillin-1 microfibril structure suggest that the N-terminal half of fibrillin-1 is asymmetrically exposed in outer filaments, while the C-terminal half is buried in the interior (Kuo et al. 2007). Fibrillinopathies include Marfan syndrome, familial ectopia lentis, familial thoracic aneurysm, all due to mutations in the fibrillin-1 gene FBN1, and congenital contractural arachnodactyly which is caused by mutation of FBN2 (Maslen & Glanville 1993, Davis & Summers 2012).
In vivo assembly of fibrillin requires the presence of extracellular fibronectin fibres (Sabatier et al. 2009). Fibrillins have Arg-Gly-Asp (RGD) sequences that interact with integrins (Pfaff et al. 1996, Sakamoto et al. 1996, Bax et al., 2003, Jovanovic et al. 2008) and heparin-binding domains that interact with a cell-surface heparan sulfate proteoglycan (Tiedemann et al. 2001) possibly a syndecan (Ritty et al. 2003). Fibrillins also have a major role in binding and sequestering growth factors such as TGF beta into the ECM (Neptune et al. 2003). Proteoglycans such as versican (Isogai et al. 2002), biglycan, and decorin (Reinboth et al. 2002) can interact with the microfibrils. They confer specific properties including hydration, impact absorption, molecular sieving, regulation of cellular activities, mediation of growth factor association, and release and transport within the extracellular matrix (Buczek-Thomas et al. 2002). In addition, glycosaminoglycans have been shown to interact with tropoelastin through its lysine side chains (Wu et al. 1999), regulating tropoelastin assembly (Tu & Weiss 2008).
Elastin is synthesized as a 70kDa monomer called tropoelastin, a highly hydrophobic protein composed largely of two types of domains that alternate along the polypeptide chain. Hydrophobic domains are rich in glycine, proline, alanine, leucine and valine. These amino acids occur in characteristic short (3-9 amino acids) tandem repeats, with a flexible and highly dynamic structure (Floquet et al. 2004). Unlike collagen, glycine in elastin is not rigorously positioned every 3 residues. However, glycine is distributed frequently throughout all hydrophobic domains of elastin, and displays a strong preference for inter-glycine spacing of 0-3 residues (Rauscher et al. 2006).
Elastic fibre formation involves the deposition of tropoelastin onto a template of fibrillin rich microfibrils. Recent results suggest that the first step of elastic fiber formation is the organization of small globules of elastin on the cell surface followed by globule aggregation into microfibres (Kozel et al. 2006). An important contribution to the initial stages assembly is thought to be made by the intrinsic ability of the protein to direct its own polymeric organization in a process termed 'coacervation' (Bressan et al. 1986). This self-assembly process appears to be determined by interactions between hydrophobic domains (Bressan et al. 1986, Vrhovski et al. 1997, Bellingham et al. 2003, Cirulis & Keeley 2010) which result in alignment of the cross-linking domains, allowing the stabilization of elastin through the formation of cross-links generated through the oxidative deamination of lysine residues, catalyzed by members of the lysyl oxidase (LOX) family (Reiser et al. 1992, Mithieux & Weiss 2005). The first step in the cross-linking reaction is the oxidative formation of the delta aldehyde, known as alpha aminoadipic semialdehyde or allysine (Partridge 1963). Subsequent reactions that are probably spontaneous lead to the formation of cross-links through dehydrolysinonorleucine and allysine aldol, a trifunctional cross-link dehydromerodesmosine and two tetrafunctional cross-links desmosine and isodesmosine (Lucero & Kagan 2006), which are unique to elastin. These cross-links confer mechanical integrity and high durability. In addition to their role in self-assembly, hydrophobic domains provide elastin with its elastomeric properties, with initial studies suggesting that the elastomeric propereties of elastin are driven through changes in entropic interactions with surrounding water molecules (Hoeve & Flory 1974).
A very specific set of proteases, broadly grouped under the name elastases, is responsible for elastin remodelling (Antonicelli et al. 2007). The matrix metalloproteinases (MMPs) are particularly important in elastin breakdown, with MMP2, 3, 9 and 12 explicitly shown to degrade elastin (Ra & Parks 2007). Nonetheless, elastin typically displays a low turnover rate under normal conditions over a lifetime (Davis 1993).
R-HSA-112303 Electric Transmission Across Gap Junctions Electrical synapses are found in all nervous systems, including the human brain. The membranes of the two communicating neurons come extremely close at the synapse and are actually linked together by an intercellular specialization called a gap junction. Gap junctions contain precisely aligned, paired channels in the membrane of the pre- and postsynaptic neurons, such that each channel pair forms a pore. Electrical synapses thus work by allowing ionic current to flow passively through the gap junction pores from one neuron to another. Because passive current flow across the gap junction is virtually instantaneous, communication can occur without the delay that is characteristic of chemical synapses.
R-HSA-2395516 Electron transport from NADPH to Ferredoxin NADPH, ferredoxin reductase (FDXR, Adrenodoxin reductase), and ferredoxins (FDX1, FDX1L) comprise a short electron transport chain that provides electrons for biosynthesis of iron-sulfur clusters and steroid hormones (Sheftel et al. 2010, Shi et al. 2012, reviewed in Grinberg et al. 2000, Lambeth et al. 1982).
R-HSA-139853 Elevation of cytosolic Ca2+ levels Activation of non- excitable cells involves the agonist-induced elevation of cytosolic Ca2+, an essential process for platelet activation. It occurs through Ca2+ release from intracellular stores and Ca2+ entry through the plasma membrane. Ca2+ store release involves phospholipase C (PLC)-mediated production of inositol-1,4,5-trisphosphate (IP3), which in turn stimulates IP3 receptor channels to release Ca2+ from intracellular stores. This is followed by Ca2+ entry into the cell through plasma membrane calcium channels, a process referred to as store-operated calcium entry (SOCE). Stromal interaction molecule 1 (STIM1), a Ca2+ sensor molecule in intracellular stores, and the four transmembrane channel protein Orai1 are the key players in platelet SOCE. Other major Ca2+ entry mechanisms are mediated by the direct receptor-operated calcium (ROC) channel, P2X1 and transient receptor potential channels (TRPCs).
R-HSA-211976 Endogenous sterols A number of CYPs take part in cholesterol biosynthesis and elimination, thus playing an important role in maintaining cholesterol homeostasis. Under normal physiological conditions, cholesterol intake (diet or synthesized de novo from acetyl CoA) equals cholesterol elimination (degraded to bile salts, secreted in bile and used in steroid hormone synthesis). These processes are under tight regulatory control and any disruption leads to increased cholesterol levels resulting in cardiovacular disease. The CYPs involved in cholesterol homeostasis could serve as potential targets for cholesterol-lowering drugs (Lewis 2004, Guengerich 2006, Pikuleva 2006).
R-HSA-917729 Endosomal Sorting Complex Required For Transport (ESCRT) Many plasma membrane proteins are in a constant flux throughout the internal trafficking pathways of the cell. Some receptors are continuously internalized into recycling endosomes and returned to the cell surface. Others are sorted into intralumenal vesicles of morphologically distinctive endosomes that are known as multivesicular bodies (MVBs). These MVBs fuse with lysosomes, resulting in degradation of their cargo by lysosomal acidic hydrolases.
Endosomes can be operationally defined as being either early or late, referring to the relative time it takes for endocytosed material to reach either stage. Ultrastructural studies indicate that early endosomes are predominantly tubulovesicular structures, which constitute a major sorting platform in the cell, whereas late endosomes show the characteristics of typical MVBs and are capable of fusing with lysosomes.
A well characterized signal for shunting membrane proteins into the degradative MVB pathway is the ubiquitylation of these cargoes. At the center of a vast protein:protein and protein:lipid interaction network that underpins ubiquitin mediated sorting to the lysosome are the endosomal sorting complexes required for transport (ESCRTs), which are conserved throughout all major eukaryotic taxa.
R-HSA-1236977 Endosomal/Vacuolar pathway Some antigens are cross-presented through a vacuolar mechanism that involves generation of antigenic peptides and their loading on to MHC-I molecules within the endosomal compartment in a proteasome and TAP-independent manner. Antigens within the endosome are processed by cathepsin S and other proteases into antigenic peptides. Loading of these peptides onto MHC-I molecules occurs directly within early and late endosomal compartments. Why certain antigens are cross-presented exclusively by the cytosolic pathway while others use the vacuolar pathway is unknown. It may be because some epitopes cannot be generated by endosomal proteolysis, or are completely destroyed. Alternatively, the physical form of the antigen may influence its accessibility to the endosomal or vacuolar pathways (Shen et al. 2004).
R-HSA-380972 Energy dependent regulation of mTOR by LKB1-AMPK Upon formation of a trimeric LKB1:STRAD:MO25 complex, LKB1 phosphorylates and activates AMPK. This phosphorylation is immediately removed in basal conditions by PP2C, but if the cellular AMP:ATP ratio rises, this activation is maintained, as AMP binding by AMPK inhibits the dephosphorylation. AMPK then activates the TSC complex by phosphorylating TSC2. Active TSC activates the intrinsic GTPase activity of Rheb, resulting in GDP-loaded Rheb and inhibition of mTOR pathway.
R-HSA-9845620 Enhanced binding of GP1BA variant to VWF multimer:collagen The Reactome event describes gain-of-function variants of glycoprotein Ib α (GPIbα, encoded by GP1BA) that cause macrothrombocytopenia and mucocutaneous bleeding in patients with platelet-type von Willebrand disease (PT-VWD) due to enhanced affinity for von Willebrand factor (VWF).
R-HSA-9845619 Enhanced cleavage of VWF variant by ADAMTS13 Under normal physiological conditions, a disintegrin and metalloproteinase with thrombospondin type 1 repeats 13 (ADAMTS13) downregulates von Willebrand factor (VWF) procoagulant activity by cleaving the peptide bond between Tyr1605 and Met1606 of VWF in a shear-dependent manner. This Reactome event describes von Willebrand disease (VWD)-associated missense mutations VWF Y1584C (Bowen DJ et al., 2005; Keeney S et al., 2007; Pruss CM et al., 2012), I1568N, G1579R, G1631D, and C1099P (Jacobi PM et al., 2012), which showed enhanced susceptibility to ADAMTS13-mediated proteolysis.
R-HSA-168275 Entry of Influenza Virion into Host Cell via Endocytosis Virus particles bound to the cell surface can be internalized by four mechanisms. Most internalization appears to be mediated by clathrin-coated pits, but internalization via caveolae, macropinocytosis, and by non-clathrin, non-caveolae pathways has also been described for influenza viruses.
R-HSA-379398 Enzymatic degradation of Dopamine by monoamine oxidase Alternately dopamine is metabolized to homovanillic acid in a two-step reaction in which dopamine is first oxidized to 3,4-dihydroxypheylacetic acid (DOPAC) and then converted to homovanillic acid by catecholamine o-methyltransferase.
R-HSA-379397 Enzymatic degradation of dopamine by COMT Dopamine once taken up by the dopamine transporter from the extracellular space into the cytosol is metabolized in a two step reaction to homovanillic acid.The first reaction is catalyzed by catecholamine o-methyl transferase and the subsequent reaction is catalyzed by monoamine oxidase A.
R-HSA-3928664 Ephrin signaling The interaction between ephrin (EFN) ligands and EPH receptors results not only in forward signaling through the EPH receptor, but also in 'reverse' signaling through the EFN ligand itself. Reverse signaling through EFNB is required for correct spine morphogenesis and proper path-finding of corpus callosum and dorsal retinal axons. The molecular mechanism by which EFNBs transduce a reverse signal involves phosphorylation of multiple, conserved tyrosines on the intracellular domain of B-type ephrins, facilitating binding of the SH2/SH3 domain adaptor protein GRB4 and subsequent cytoskeletal remodeling (Bruckner et al. 1997, Cowan & Henkemeyer 2001, Lu et al. 2001). The other mechanism of reverse signaling involves the C-terminus PSD-95/Dlg/ZO-1 (PDZ)-binding motif of EFNBs which recruits various PDZ domain containing proteins. Phosphorylation and PDZ-dependent reverse signaling by ephrin-B1 have each been proposed to play important roles in multiple contexts in development and disease (Bush & Soriano 2009).
R-HSA-9917777 Epigenetic regulation by WDR5-containing histone modifying complexes
WDR5 is a component of six histone methyltransferases and three histone acetyltransferases involved in epigenetic regulation of gene expression (reviewed in Guarnaccia and Tansey 2018).
The WDR5 histone methyltransferase complexes (KMT2 complexes) include the Mixed Lineage Leukemia (MLL) 1-4, SET1A, and SET1B. All KMT2 complexes consist of a histone methyltransferase (KMT2A, KMT2B, KMT2C, KMT2D, SETD1A, or SETD1B, respectively) and the WRAD subcomplex composed of WDR5, RBBP5, ASH2L, and DPY30. The WRAD complex regulates the enzymatic activity of histone methyltransferases and enables their recruitment to chromatin. Additional transcription cofactors associate with each KMT2 histone methyltransferase complex, enabling their functional diversification. All KMT2 complexes methylate lysine K5 of histone H3 (K4 in mature histone H3 peptides, as the initiator methionine is removed), which is associated with transcriptional activation. Different KMT2 complexes preferentially monomethylate, dimethylate, or trimethylate H3K4, depending on the presence of accessory subunits, transcriptional co-factors, and posttranslational modifications. The KMT2A and KMT2B complexes preferentially methylate H3K4 at a limited number of target gene promoters, while KMT2C and KMT2D complexes preferentially methylate H3K4 at a limited number of target gene enhancers. SETD1A and SETD1B complexes are responsible for the bulk of cellular H3K4 methylation and show less target specificity. For a detailed overview, please refer to Cho et al. 2007, Song and Kingston 2008, Patel et al. 2009, Wang et al. 2009, Takahashi et al. 2011, Couture and Skiniotis 2013, van Nuland et al. 2013, Rao and Dou 2015, Klonou et al. 2021.
WDR5 is also a component of three histone acetyltransferase complexes, GCN5-ATAC, PCAF-ATAC, and MOF/KAT8-NSL. The role of WDR5 in epigenetic regulation of gene expression through histone acetylation is under investigation (reviewed in Guarnaccia and Tansey 2018).
The KMT2C (MLL3) complex, together with the related KMT2D (MLL4) complex, is most similar to Drosophila Trr (Trithorax-related) and mediates hitone H3 lysine-4 (H3K4 - lysine 5 in nascent histone H3) monomethylation, with the establishment of the H3K4me1 epigenetic marks, at transcription enhancers throughout the human genome, with estimates ranging from approximately 12,000 to over 20,000 sites, depending on the cell type and developmental stage. While H3K4 monomethylation by MLL3 and MLL4 complexes may not be essential for expression of developmental genes, it is likely important for fine tuning of transcription levels and timing, both during normal development and in cancer. For review, please refer to Hu et al. 2013, Piunti and Shilatifard 2016, Fagan and Dingwall 2019, and Klonou et al. 2021.
Based on mouse studies, MLL3 and MLL4 complexes play an important role in adipogenesis and myogenesis. During adipogenesis, the KMT2D (MLL4) complex preferentially localizes to active enhancers, marked by the presence of mono- or dimethylated histone H3 lysine-4 (H3K4me1/2, residue K4 corresponds to residue K5 in nascent histone H3), acetylated H3 lysine-27 (H3K27ac), and the presence of RNA Pol II. KMT2D localizes to these active enhancers together with the adipogenic transcription factors CEBPB, CEBPA, and PPARG, and is especially enriched at high confidence enhancers that are both CEBP and PPARG positive (Lee et al. 2013).
R-HSA-9851695 Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes During adipogenesis, the KMT2D (MLL4) complex preferentially localizes to active enhancers, marked by the presence of mono- or dimethylated histone H3 lysine-4 (H3K4me1/2, residue K4 corresponds to residue K5 in nascent histone H3), acetylated H3 lysine-27 (H3K27ac), and the presence of RNA Pol II. KMT2D localizes to these active enhancers together with the adipogenic transcription factors CEBPB, CEBPA, and PPARG, and is especially enriched at high confidence enhancers that are both CEBP and PPARG positive (Lee et al. 2013). Single Kmt2c (Mll3) knockout in mouse brown preadipocytes led to a modest decrease of H3K4me1, while double Kmt2c;Kmt2d (Mll4) knockout led to a global decrease of H3K4me1/2 (Lee et al. 2013). Most MLL4-binding sites are marked by both H3K4me1 and H3K4me2 during adipogenesis (Lee et al. 2013). Double knockout of Kmt2c and Kmt2d in differentiating mouse adipocytes prevented increase in H3K4me1/2, H3K27ac, Mediator complex and RNA Pol II on adipogenic enhancers, specifically on Cebpa and Pparg gene loci (Lee et al. 2013). KMT2D-dependent deposition of H3K4me1/2 marks was also detected on some adipogenic promoters, but was less pronounced than on adipogenic enhancers (Lee et al. 2013). Deletion of Kmt2d significantly decreased expression of genes associated with Kmt2d+ adipogenic enhancers (Lee et al. 2013). The expression of KMT2C, the catalytic subunit of the MLL3 complex, is upregulated during brown adipocyte differentiation (Son et al. 2016).Cytosolic enzymes capable of oxidizing acetaldehyde to acetate have also been identified and characterized in vitro (Inoue et al. 1979) so a purely cytosolic pathway for ethanol oxidation to acetate and conversion to acetyl-CoA can be annotated. The role of this pathway in vivo is unclear, though limited attempts to correlate deficiencies in the cytosolic enzyme with alcohol intolerance have yielded suggestive data (Yoshida et al. 1989). Additional peroxisomal and microsomal pathways for the oxidation of ethanol to acetaldehyde have been described; their physiological significance is unclear and they are not annotated here.
R-HSA-156842 Eukaryotic Translation Elongation The translation elongation cycle adds one amino acid at a time to a growing polypeptide according to the sequence of codons found in the mRNA. The next available codon on the mRNA is exposed in the aminoacyl-tRNA (aa-tRNA) binding site (A site) on the 30S subunit.
A: Ternary complexes of aa -tRNA:eEF1A:GTP enter the ribosome and enable the anticodon of the tRNA to make a codon/anticodon interaction with the A-site codon of the mRNA. B: Upon cognate recognition, the eEF1A:GTP is brought into the GTPase activating center of the ribosome, GTP is hydrolyzed and eEF1A:GDP leaves the ribosome. C: The peptidyl transferase center of ribosome catalyses the formation of a peptide bond between the incoming amino acid and the peptide found in the peptidyl-tRNA binding site (P site). D: In the pre-translocation state of the ribosome, the eEF2:GTP enters the ribosome, physically translocating the peptidyl-tRNA out of the A site to P site and leaves the ribosome eEF2:GDP. This action of eEF2:GTP accounts for the precise movement of the mRNA by 3 nucleotides.Consequently, deacylated tRNA is shifted to the E site. A ribosome associated ATPase activity is proposed to stimulate the release of deacylated tRNA from the E site subsequent to translocation (Elskaya et al., 1991). In this post-translocation state, the ribosome is now ready to receive a new ternary complex.
This process is illustrated below with: an amino acyl-tRNA with an amino acid, a peptidyl-tRNA with a growing peptide, a deacylated tRNA with an -OH, and a ribosome with A,P and E sites to accommodate these three forms of tRNA.
R-HSA-72613 Eukaryotic Translation Initiation Initiation of translation in the majority of eukaryotic cellular mRNAs depends on the 5'-cap (m7GpppN) and involves ribosomal scanning of the 5' untranslated region (5'-UTR) for an initiating AUG start codon. Therefore, this mechanism is often called cap-dependent translation initiation. Proximity to the cap, as well as the nucleotides surrounding an AUG codon, influence the efficiency of the start site recognition during the scanning process. However, if the recognition site is poor enough, scanning ribosomal subunits will ignore and skip potential starting AUGs, a phenomenon called leaky scanning. Leaky scanning allows a single mRNA to encode several proteins that differ in their amino-termini. Merrick (2010) provides an overview of this process and hghlights several features of it that remain incompletely understood.
Several eukaryotic cell and viral mRNAs initiate translation by an alternative mechanism that involves internal initiation rather than ribosomal scanning. These mRNAs contain complex nucleotide sequences, called internal ribosomal entry sites, where ribosomes bind in a cap-independent manner and start translation at the closest downstream AUG codon.
Initiation on several viral and cellular mRNAs is cap-independent and is mediated by binding of the ribosome to internal ribosome entry site (IRES) elements. These elements are often found in characteristically long structured regions on the 5'-UTR of an mRNA that may or may not have regulatory upstream open reading frames (uORFs). Both of these features on the 5'-end of the mRNA hinder ribosomal scanning, and thus promote a cap-independent translation initiation mechanism. IRESs act as specific translational enhancers that allow translation initiation to occur in response to specific stimuli and under the control of different trans-acting factors, as for example when cap-dependent protein synthesis is shut off during viral infection. Such regulatory elements have been identified in the mRNAs of growth factors, protooncogenes, angiogenesis factors, and apoptosis regulators, which are translated under a variety of stress conditions, including hypoxia, serum deprivation, irradiation and apoptosis. Thus, cap-independent translational control might have evolved to regulate cellular responses in acute but transient stress conditions that would otherwise lead to cell death, while the same mechanism is of major importance for viral mRNAs to bypass the shutting-off of host protein synthesis after infection. Encephalomyocarditis virus (EMCV) and hepatitis C virus exemplify two distinct mechanisms of IRES-mediated initiation. In contrast to cap-dependent initiation, the eIF4A and eIF4G subunits of eIF4F bind immediately upstream of the EMCV initiation codon and promote binding of a 43S complex. Accordingly, EMCV initiation does not involve scanning and does not require eIF1, eIF1A, and the eIF4E subunit of eIF4F. Nonetheless, initiation on some EMCV-like IRESs requires additional non-canonical initiation factors, which alter IRES conformation and promote binding of eIF4A/eIF4G. Initiation on the hepatitis C virus IRES is simpler: a 43S complex containing only eIF2 and eIF3 binds directly to the initiation codon as a result of specific interaction of the IRES and the 40S subunit.
R-HSA-72764 Eukaryotic Translation Termination The arrival of any of the three stop codons (UAA, UAG and UGA) into the ribosomal A-site triggers the binding of a release factor (RF) to the ribosome and subsequent polypeptide chain release. In eukaryotes, the RF is composed of two proteins, eRF1 and eRF3. eRF1 is responsible for the hydrolysis of the peptidyl-tRNA, while eRF3 provides a GTP-dependent function. The ribosome releases the mRNA and dissociates into its two complex subunits, which can reassemble on another molecule to begin a new round of protein synthesis. It should be noted that at present, there is no factor identified in eukaryotes that would be the functional equivalent of the bacterial ribosome release (or recycling) factor, RRF, that catalyzes dissociation of the ribosome from the mRNA following release of the polypeptide
R-HSA-9833109 Evasion by RSV of host interferon responses Infection with human respiratory syncytial virus (hRSV) is typically associated with low to undetectable levels of type I interferons (IFNs). Several hRSV proteins interact with host innate immune system factors that support the type I interferon response. Nonstructural proteins NS1 and NS2 localize to mitochondria and nucleus where they bind MAVS, DDX58, TRIM25, IRF3, and CREBBP, affecting DDX58/IFIH1-mediated interferon induction (reviewed by Thornhill & Verhoeven, 2020). Additionally, hRSV nucleoprotein interacts with MDA5 downregulating the interferon response and with PKR (EIF2AK2) blocking the innate immune system signal for shutting down protein translation. Further interactions of the M, SH, and G proteins are reviewed by van Royen et al, 2022.
R-HSA-9630791 Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 Missense mutations and small indels in the CDKN2A gene, which result in amino acid changes in p16INK4A that impair its ability to bind to CDK4, interfere with p16INK4A-mediated induction of cellular senescence in response to oncogenic signaling (Jones et al. 2007).
Loss-of-function mutations in p16INK4A can also contribute to cancer by interfering with p16INK4A-mediated inhibition of NFKB signaling (Becker et al. 2005).
R-HSA-9630794 Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 Missense and nonsense mutations in the CDKN2A gene that result in amino acid substitutions in p16INK4A or p16INK4A truncations, impairing its ability to bind to CDK4 and CDK6, interfere with p16INK4A-mediated induction of cellular senescence in response to oncogenic signaling (Haferkamp et al. 2008).
Loss-of-function mutations in p16INK4A can also contribute to cancer by interfering with p16INK4A-mediated inhibition of NFKB signaling (Becker et al. 2005).
R-HSA-9646303 Evasion of Oncogene Induced Senescence Due to p14ARF Defects In cell culture, p14ARF (CDKN2A transcript 4, CDKN2A-4, ARF), one of the two main protein products of the CDKN2A gene, contributes to oncogene induced senescence by stabilizing TP53 (p53). The function of p14ARF in p53 stabilization through sequestration of MDM2, a p53 ubiquitin ligase, depends on the nuclear localization of p14ARF and its ability to interact with MDM2. The nuclear localization signal and the MDM2 interaction domain map to the first 15 amino acids of the N-terminus of p14ARF. This region is encoded by the p14ARF-specific exon 1beta of CDKN2A. An independent MDM2-binding domain localized to the C-terminus of p14ARF (Lohrum et al. 2000). Insertion of 16 nucleotides in exon 1beta results in a frameshift truncation of p14ARF, responsible for a familial melanoma syndrome in which the p16INK4A product of the CDKN2A gene is unaffected. This mutation is rare and has so far been reported in one family only. The mutant protein, p14ARF V22Pfs*46 has the nucleotide localization signal and the N-terminal MDM2 interaction region preserved, but is unable to translocate from the cytosol to the nucleus, possibly due to aberrant conformation (Rizos, Puig et al. 2001), and also lacks the C-terminal MDM2 interaction region. Relocation of wild type p14ARF to the cytosol has been observed in melanoma (Rizos, Darmanian et al. 2001) and aggressive thyroid papillary carcinoma (Ferru et al. 2006). Genomic deletion of exon 1beta, with exons 1alpha, 2 and 3 intact, has been reported in about 30% of melanoma cases with genomic deletions involving the CDKN2A locus (Freedberg et al. 2008). Several different familial melanoma germline mutations map to the exon 1beta splice donor site (Harland et al. 2005).
The ability of p14ARF to localize to the nucleolus also plays a role in p14ARF-mediated stabilization of p53. Mutations in exon 2 of the CDKN2A gene can lead to missense mutations in p14ARF that affect its nucleolar localization and p53 stabilization, but the exact mechanism has not been fully elucidated (Zhang and Xiong 1999, reviewed by Fontana et al. 2019).
R-HSA-9630750 Evasion of Oncogene Induced Senescence Due to p16INK4A Defects The CDKN2A gene consists of four exons, exon 1beta, exon 1alpha, exon 2 and exon 3, going from the proximal to the distal gene end. There are two promoters in the CDKN2A gene locus. The promoter located between exons 1beta and 1alpha regulates transcription of the p16INK4A mRNA, which consists of exon 1alpha, exon 2 and exon 3 (only partially translated), and encodes a cyclin-dependent kinase inhibitor p16INK4A (also known as CDKN2A isoform 1, p16, INK4A, CDKN2A, CDK4I or MTS-1). The promoter located upstream of exon 1beta regulates transcription of the p14-ARF mRNA, which consists of exon 1beta, exon 2 (partially translated) and exon 3 (untranslated). The p14ARF mRNA is translated in a different reading frame from the p16INK4A mRNA and produces the tumor suppressor ARF (also known as p14ARF or CDKN2A isoform 4), an inhibitor of MDM2 E3 ubiquitin ligase-mediated degradation of TP53 (p53).
Wild type p16INK4A is able to form a complex with either CDK4 or CDK6 and prevent formation of catalytically active CDK complexes consisting of CDK4 or CDK6 and D-type cyclins (CCND). Thus, p16INK4A prevents hyperphosphorylation of RB-family proteins, required for initiation of DNA replication in RB1-competent cells. Expression of p16INK4A increases in response to strong oncogenic signaling, leading to accelerated cellular senescence (programmed cell cycle arrest). Expression of p16INK4A also increases after excessive proliferation, including that following oncogene activation by mutation in vivo. Loss-of-function of p16INK4A frequently occurs in cancer, usually through loss of p16INK4A protein expression due to promoter hypermethylation or CDKN2A gene deletion (Merlo et al. 1995, Herman et al. 1995, Gonzalez-Zulueta et al. 1995, Wong et al. 1997, Witkiewicz et al. 2011, Shima et al. 2011, Tamayo-Orrego et al. 2016). Missense, nonsense and frameshift mutations in the CDKN2A locus can also impair p16INK4A function through expression of non-functional substitution mutants or truncated proteins (Kamb et al. 1994, Bartsch et al. 1995, Castellano et al. 1997). Germline intronic CDKN2A mutations that create aberrant splicing sites and result in expression of non-functional splicing variants of p16INK4A have been reported in familial melanoma (Harland et al. 2001, Harland et al. 2005). A CDKN2A gene mutation in the region encoding the 5'UTR of p16INK4A, reported in familial melanoma, creates a novel translation start codon and diminishes translation from the wild type start codon (Liu et al. 1999). However, mutations in the non-coding regions of the CDKN2A gene are rare (Pollock et al. 2001).
Based on cell culture studies, p16INK4A defects enable precancerous and cancerous cells to delay or evade senescence under oncogenic signaling stress (Ruas et al. 1999, Haferkamp et al. 2008, Rayess et al. 2012, Jeanblanc et al. 2012, LaPak and Burd 2014, Sharpless and Sherr 2015). Establishment of an in vivo role of oncogene induced senescence, and thus an in vivo role of p16INK4A in this context, have been difficult owing to lack of specific biomarkers and interconnectedness of various senescence triggers (Baek and Ryeom 2017, reviewed in Sharpless and Sherr 2015).
Genomic deletions in the CDKN2A locus affect p14ARF, unless they are limited to exon 1alpha. The p14ARF promoter can also be hypermethylated in cancer, leading to loss of p14ARF expression. Some missense mutations occurring in exon 2 of the CDKN2A gene affect the p14ARF protein sequence. However, p14ARF mutants usually appear to be less functionally compromised than their p16INK4A counterparts. Most functional tests on p14ARF mutants examine the effect of mutations on MDM2 binding and TP53-mediated transcription of CDKN1A (p21), as well as sub-nuclear localization of p14ARF (Zhang and Xiong 1999, Schmitt et al. 1999, Eischen et al. 1999, Pinyol et al. 2000, Bostrom et al. 2001, Laud et al. 2006). Still, there are poorly explored functions of p14ARF that may be significantly affected in mutant p14ARF proteins detected in cancer (Itahana and Zhang 2008, Dominguez-Brauer et al. 2010).
R-HSA-9632697 Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 Missense mutations and small indels in the CDKN2A gene, which result in amino acid changes in p16INK4A that impair its ability to bind to CDK4, interfere with p16INK4A-mediated, oxidative stress-induced, cellular senescence (Chen 2000, Vurusaner et al. 2012).
Loss-of-function mutations in p16INK4A can also contribute to cancer by interfering with p16INK4A-mediated inhibition of NFKB signaling (Becker et al. 2005).
R-HSA-9632700 Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 Missense and nonsense mutations in the CDKN2A gene that result in amino acid substitutions in p16INK4A or p16INK4A truncations, respectively, impairing its ability to bind to CDK4 and CDK6, interfere with p16INK4A-mediated induction of cellular senescence in response to oxidative stress (Chen 2000, Vurusaner et al. 2012).
Loss-of-function mutations in p16INK4A can also contribute to cancer by interfering with p16INK4A-mediated inhibition of NFKB signaling (Becker et al. 2005).
R-HSA-9646304 Evasion of Oxidative Stress Induced Senescence Due to p14ARF Defects One of the two main protein products of the CDKN2A gene, p14ARF (CDKN2A transcript 4, CDKN2A-4, ARF), contributes to oxidative stress induced cellular senescence by stabilizing TP53 (p53). The function of p14ARF in p53 stabilization through sequestration of MDM2, a p53 ubiquitin ligase, depends on the nuclear localization of p14ARF and its ability to interact with MDM2. The nuclear localization signal and the MDM2 interaction domain map to the first 15 amino acids of the N-terminus of p14ARF. This region is encoded by the p14ARF-specific exon 1beta of CDKN2A. An independent MDM2-binding domain is localized at the C-terminus of p14ARF (Lohrum et al. 2000). Insertion of 16 nucleotides in exon 1beta results in a frameshift truncation of p14ARF, responsible for a familial melanoma syndrome in which the p16INK4A product of the CDKN2A gene is unaffected. This mutation is rare and has so far been reported in one family only. The mutant protein, p14ARF V22Pfs*46 has the nucleotide localization signal and the N-terminal MDM2 interaction region preserved, but is unable to translocate from the cytosol to the nucleus, possibly due to aberrant conformation (Rizos, Puig et al. 2001), and also lacks the C-terminal MDM2 interaction region. Relocation of wild type p14ARF to the cytosol has been observed in melanoma (Rizos, Darmanian et al. 2001) and aggressive thyroid papillary carcinoma (Ferru et al. 2006). Genomic deletion of exon 1beta, with exons 1alpha, 2 and 3 intact, has been reported in about 30% of melanoma cases with genomic deletions involving the CDKN2A locus (Freedberg et al. 2008). Several different familial melanoma germline mutations map to the exon 1beta splice donor site (Harland et al. 2005).
The ability of p14ARF to localize to the nucleolus also plays a role in p14ARF-mediated stabilization of p53. Mutations in exon 2 of the CDKN2A gene can lead to missense mutations in p14ARF that affect its nucleolar localization and p53 stabilization, but the exact mechanism has not been fully elucidated (Zhang and Xiong 1999, reviewed by Fontana et al. 2019).
R-HSA-9632693 Evasion of Oxidative Stress Induced Senescence Due to p16INK4A Defects The CDKN2A gene consists of four exons, exon 1beta, exon 1alpha, exon 2 and exon 3, going from the proximal to the distal gene end. There are two promoters in the CDKN2A gene locus. The promoter located between exons 1beta and 1alpha regulates transcription of the p16INK4A mRNA, which consists of exon 1alpha, exon 2 and exon 3 (only partially translated), and encodes a cyclin-dependent kinase inhibitor p16INK4A (also known as CDKN2A isoform 1, p16, INK4A, CDKN2A, CDK4I or MTS-1). The promoter located upstream of exon 1beta regulates transcription of the p14ARF mRNA, which consists of exon 1beta, exon 2 (partially translated) and exon 3 (untranslated). The p14ARF mRNA is translated in a different reading frame from the p16INK4A mRNA and produces the tumor suppressor ARF (also known as p14ARF or CDKN2A isoform 4), an inhibitor of MDM2 E3 ubiquitin ligase-mediated degradation of TP53 (p53).
Wild type p16INK4A is able to form a complex with either CDK4 or CDK6 and prevent formation of catalytically active CDK complexes consisting of CDK4 or CDK6 and D-type cyclins (CCND). Thus, p16INK4A prevents hyperphosphorylation of RB-family proteins, required for initiation of DNA replication in RB1-competent cells. Expression of p16INK4A increases in response to oxidative stress, leading to cellular senescence (programmed cell cycle arrest) under conditions of prolonged oxidative stress. Loss-of-function of p16INK4A frequently occurs in cancer, usually through loss of p16INK4A protein expression due to promoter hypermethylation or CDKN2A gene deletion (Merlo et al. 1995, Herman et al. 1995, Gonzalez-Zulueta et al. 1995, Wong et al. 1997, Witkiewicz et al. 2011, Shima et al. 2011, Tamayo-Orrego et al. 2016). Missense, nonsense and frameshift mutations in the CDKN2A locus can also impair p16INK4A function through expression of non-functional substitution mutants or truncated proteins (Kamb et al. 1994, Bartsch et al. 1995, Castellano et al. 1997). Germline intronic CDKN2A mutations that create aberrant splicing sites and result in expression of non-functional splicing variants of p16INK4A have been reported in familial melanoma (Harland et al. 2001, Harland et al. 2005). A CDKN2A gene mutation in the region encoding the 5'UTR of p16INK4A, reported in familial melanoma, creates a novel translation start codon and diminishes translation from the wild type start codon (Liu et al. 1999). However, mutations in the non coding regions of the CDKN2A gene are rare (Pollock et al. 2001).
p16INK4A defects enable cancerous cells to evade cell cycle arrest and senescence under prolonged oxidative stress (Tanaka et al. 1999, Chen 2000, Chen et al. 2004, Vurusaner et al. 2012, Rayess et al. 2012, LaPak and Burd 2014, Sharpless and Sherr 2015, Zhang et al. 2017). A cell cycle-independent role of p16INK4A in regulation of intracellular oxidative stress has been reported (Jenkins et al. 2011, Vurusaner et al. 2012, Jenkins et al. 2013).
Genomic deletions in the CDKN2A locus affect p14ARF, unless they are limited to exon 1alpha. The p14ARF promoter can also be hypermethylated in cancer, leading to loss of p14ARF expression. Some missense mutations occurring in exon 2 of the CDKN2A gene affect the p14ARF protein sequence. However, p14ARF mutants usually appear to be less functionally compromised than their p16INK4A counterparts. Most functional tests on p14ARF mutants examine the effect of mutations on MDM2 binding and TP53-mediated transcription of CDKN1A (p21), as well as sub-nuclear localization of p14ARF (Zhang and Xiong 1999, Schmitt et al. 1999, Eischen et al. 1999, Pinyol et al. 2000, Bostrom et al. 2001, Laud et al. 2006). Still, there are poorly explored functions of p14ARF that may be significantly affected in mutant p14ARF proteins detected in cancer (Itahana and Zhang 2008, Dominguez-Brauer et al. 2010).
R-HSA-8941413 Events associated with phagocytolytic activity of PMN cells When neutrophils engulf bacteria they enclose them in small vacuoles (phagosomes) into which superoxide is released by activated NADPH oxidase (NOX2) on the internalized neutrophil membrane. The directional nature of NOX2 activity creates a charge imbalance that must be counteracted to prevent depolarization of the membrane and the shutdown of activity (Winterbourn CC et al. 2016). Also, protons are produced in the cytosol and consumed in the external compartment (for example, the phagosome) through the dismutation of superoxide. Both situations are largely overcome by a balancing flow of protons transported by voltage-gated proton channels, primarily VSOP/HV1, which are activated in parallel with the oxidase (Demaurex N & El Chemaly A 2010; El Chemaly A et al. 2010; Petheo GL et al. 2010; Kovacs I et al. 2014; Henderson LM et al. 1987, 1988). The pH of the phagosome is regulated by these activities. In contrast to the phagosomes of macrophages, in which pH drops following particle ingestion, neutrophil phagosomes remain alkaline during the period that the oxidase is active. Until recently, their pH has been accepted to lie between 7.5 and 8. However, in a 2015 study using a probe that is more sensitive at higher pH, an average pH closer to 9 was measured in individual phagosomes (Levine AP et al. 2015).
The superoxide dismutates to hydrogen peroxide, which is used by myeloperoxidase (MPO) to generate other oxidants, including the highly microbicidal species such as hypochlorous acid (Winterbourn CC et al. 2013, 2016).
R-HSA-168274 Export of Viral Ribonucleoproteins from Nucleus Influenza genomic RNA (vRNA), synthesized in the nucleus of the infected host cell, is packaged into ribonucleoprotein (RNP) complexes containing viral polymerase proteins and NP (nucleocapsid). NP trimers bind the sugar phosphate backbone of the vRNA. As influenza viral RNP complexes are too large for passive diffusion out of the nucleus, utilization of the cellular nuclear export machinery is achieved by viral adaptor proteins. Matrix protein (M1) is critical for export of the complex from the nucleus, mediating the interaction of the RNP complex with the viral NEP/NS2 protein, which in turn interacts with host cell CRM1/exportin-1 nuclear export protein (Martin, 1991; O'Neill, 1998; Neumann et al., 2000; Elton, 2001; Cros, 2003; Ye, 2006; reviewed in Boulo, 2006).
R-HSA-9036866 Expression and Processing of Neurotrophins Neurotrophins function as ligands for receptor tyrosine kinases of the NTRK (TRK) family, as well as the death receptor NGFR (p75NTR). While all four neurotrophins, NGF, BDNF, NTF3 (NT-3) and NTF4 (NT-4, NT-5, NTF5) can bind to and activate NGFR, they show different specificity for NTRKs. NGF exclusively activates NTRK1 (TRKA). BDNF and NTF4 are high affinity ligands for NTRK2 (TRKB). NTF3 is a high affinity ligand for NTRK3 (TRKC) and a low affinity ligand for NTRK2. Neurotrophins play pivotal roles in survival, differentiation, and plasticity of neurons in the peripheral and central nervous system. They are produced, and secreted in minute amounts, by a variety of tissues. For review, please refer to Lessmann et al. 2003, Chao 2003, and Park and Poo 2013.
Human NGF, also knowns as the nerve growth factor, is encoded by a gene on chromosome 1, which produces a single transcript. Nascent NGF protein, pre-pro-NGF, is 241 amino acids long. As pre-pro-NGF enters the endoplasmic reticulum (ER), the signal peptide, consisting of eighteen amino acids at the N-terminus, is cleaved, producing pro-NGF. Two molecules of pro-NGF form homodimers in the ER. After transport of pro-NGF homodimers to the Golgi, 103 amino acids at the N-terminus of pro-NGF are cleaved, producing mature NGF homodimers. Both pro-NGF homodimers and mature NGF homodimers are secreted to the extracellular space. Mature NGF homodimers activate NTRK1 signaling, while NGFR signaling can be activated by both mature and pro-NGF homodimers. Secreted pro-NGF homodimers may be cleaved by extracellular matrix proteases to produce mature NGF homodimers. For review, please refer to Poo 2001, Lu et al. 2005, Skaper et al. 2012, Bradshaw et al. 2015.
Human BDNF, also known as brain-derived neurotrophic factor, is encoded by a gene on chromosome 11, which, through the use of 9 alternative promoters and alternative splicing, produces 17 protein-coding transcripts. Most BDNF transcripts result in the same pre-pro-BDNF protein of 247 amino acids, but alternative promoters and different 5' and 3’UTRs allow to fine-tune regulation of BDNF expression at different developmental stages and at different levels of neuronal activity. Similar to NGF, pre-pro-BDNF is processed by proteolytic cleavage in the ER to produce pro-BDNF homodimers. It is unclear whether proteolytic processing of pro-BDNF, to produce mature BDNF homodimers, occurs in the Golgi or in the secretory granules. Extracellular matrix proteases can also cleave secreted pro-BDNF to produce mature BDNF homodimers. Secreted mature BDNF homodimers can activate NTRK2 signaling, while secreted pro-BDNF homodimers can activate NGFR signaling. For review, please refer to Poo 2001, Lu et al. 2005, Skaper et al. 2012, Park and Poo 2013.
Human NTF4, also known as neurotrophin-4, is transcribed from a gene on chromosome 19. A single experimentally confirmed transcript produces a pre-pro-NTF4 protein of 210 amino acids. After proteolytic processing in the ER and Golgi, mature NTF4 homodimers are secreted and can activate NTRK2 signaling (Hibbert et al. 2003). For review, please refer to Poo 2001, Skaper et al. 2012.
Human NTF3, also known as neurotrophin-3, is transcribed from a gene on chromosome 12. Two NTF3 transcripts have been experimentally confirmed, but only the longer NTF3 splice variant of 270 amino acids has been studied. After proteolytic processing in the ER and Golgi, mature NTF3 homodimers are secreted and can activate NTRK3 signaling (Seidah et al. 1996, Farhadi et al. 2000). For review, please refer to Poo 2001, Skaper et al. 2012.
R-HSA-9752946 Expression and translocation of olfactory receptors Olfactory receptors (ORs) are 7-pass transmembrane G protein-coupled receptors (GPCRs) located on dendritic cilia of olfactory sensory neurons (OSNs) of the olfactory epithelium (reviewed in Persuy et al. 2015). ORs are also located on cells of some other tissues (reviewed in Oh 2015). ORs bind ligands, called odorants, and activate downstream signaling through a heterotrimeric G-protein leading to opening of olfactory cyclic nucleotide-gated channels (CNG channels) and depolarization of the OSN. The human genome contains about 857 OR genes of which about 394 appear to be capable of encoding a functional OR. The remaining putative OR genes appear to be pseudogenes functionally inactivated by mutations.
Each OR binds a particular odorant or family of odorants. In order to provide odor discrimination, each OSN expresses only one OR gene and connects to specific olfactory bulb glomeruli according to the specific OR expressed (reviewed in Monahan and Lomvardas 2015, McClintock et al. 2020, Sakano et al. 2020). The choice of which OR gene to express is made by an epigenetic mechanism (reviewed in Bashkirova and Lomvardas 2019). Initially during OSN development, OR genes are heterochromatic. A few OR genes become weakly expressed and one then becomes dominant while all other OR genes remain silenced by heterochromatin. During activation of an OR gene, LHX2, LDB1, and EBF1 bind several (~60) intergenic enhancers located between OR genes on 18 chromosomes. The LHX2:LDB1:EBF1:enhancer complexes assemble into an interchromosomal super-enhancer that associates with the expressed OR gene and drives transcription.
Accumulation of OR protein in the endoplasmic reticulum membrane activates the unfolded protein response (UPR) that activates translation of ADCY3, which downregulates the histone methyltransferase KDM1A (LSD1) thereby preventing activation of any other OR genes (Lyons et al. 2013, Dalton et al. 2013).
Most OR proteins are inefficiently translocated from the endoplasmic reticulum membrane to the plasma membrane when they are expressed in heterologous cells. OSNs contain specific proteins that act as chaperones to increase subcellular translocation of at least some ORs (reviewed in Mainland and Matsunami 2012). The short isoform of RTP1 (RTP1S) and RTP2 bind the OR in the endoplasmic reticulum, are translocated with the OR to the plasma membrane, and remain at the plasma membrane. REEP1 more weakly increases translocation of ORs by an uncharacterized mechanism.
R-HSA-9911233 Expression of NOTCH2NL genes
The NOTCH2NL gene family includes four genes, NOTCH2NLA, NOTCH2NLB, NOTCH2NLC, and NOTCH2NLR, which originated from the partial duplication of the first four exons and introns of the NOTCH2 gene. Three of the duplicated genes, NOTCH2NLA, NOTCH2NLB, and NOTCH2NLC, reside at the chromosomal band 1q21.1, while NOTCH2NLR resides at 1p12, in the vicinity of NOTCH2. NOTCH2NLA was originally cloned as a gene highly expressed in white blood cells (Duan et al. 2004). Several studies suggest that ,NOTCH2NL genes may have played a role in the evolutionary expansion of the human brain (Florio et al. 2018, Fiddes et al. 2018, Suzuki et al. 2018, Lodewijk et al. 2020). NOTCH2NL genes are present only in the Hominidae family and, while they are functional in humans, they exist as pseudogenes in chimpanzees and gorillas. In addition, these genes are highly expressed during brain development (Florio et al. 2018) and have the ability to delay differentiation of neuronal progenitors (Fiddes et al. 2018, Suzuki et al. 2018). The study of sequence polymorphism and copy number variation in NOTCH2NL genes in modern humans (Fiddes et al. 2018, Lodewijk et al. 2020), and comparative analysis of NOTCH2NL gene sequences between modern humans, Denisovans and Neanderthals (Lodewijk et al. 2020), is suggestive of an ongoing adaptive evolution of modern human NOTCH2NL genes trending toward lower levels of NOTCH2NL proteins. Downstream of each of the NOTCH2NL genes is an NBPF gene in the same orientation as its NOTCH2NL partner and co-expressed with it (NBPF10 downstream of NOTCH2NLA, NBPF14 downstream of NOTCH2NLB, NBPF19 downstream of NOTCH2NLC, and NBPF26 downstream of NOTCH2NLR), and these NOTCH2NL-NBPF pairs likely function in a coordinated, complementary fashion to promote neurogenesis and human brain expansion (Fiddes et al. 2019).
The neurodevelopmental disorder known as 1q21.1 distal deletion/duplication syndrome involves copy number gain or loss of the 1q21.1 chromosomal region that includes NOTCH2NLA and NOTCH2NLB genes. Copy number loss is associated with microcephaly, while copy number gain is associated with macrocephaly (Fiddes et al. 2018), and both gain and loss are accompanied with severe neurological disorders (Fiddes et al. 2018, Lodewijk et al. 2020). Breakpoints within NOTCH2NL gene loci are also associated with neurological disorders (Lodewijk et al. 2020).
Expansion of the GGC repeat in the 5’UTR of the NOTCH2NLC gene was identified as an important contributor to neuronal intranuclear inclusion disease (NIID) and may play a role in other neurodegenerative disorders such as Parkinson’s disease, Alzheimer’s disease, frontotemporal dementia (FTD), and amyotrophic lateral sclerosis (ALS), to name a few. The underlying pathogenic mechanism has not been elucidated. For review of NOTCH2NLC-related trinucleotide expansion disorders, please refer to Cao et al. 2021 and Huang et al. 2021.
R-HSA-180786 Extension of Telomeres Telomerase acts as reverse transcriptase in the elongation of telomeres (Smogorzewska and de Lange 2004).
R-HSA-9009391 Extra-nuclear estrogen signaling In addition to its well-characterized role in estrogen-dependent transcription, estrogen (beta-estradiol, also known as E2) also plays a rapid, non-genomic role through interaction with receptors localized at the plasma membrane by virtue of dynamic palmitoylation. Estrogen receptor palmitoylation is a prerequisite for the E2-dependent activation of extra-nuclear signaling both in vitro and in animal models (Acconcia et al, 2004; Acconcia et al, 2005; Marino et al, 2006; Marino and Ascenzi, 2006). Non-genomic signaling through the estrogen receptor ESR1 also depends on receptor arginine methylation by PMRT1 (Pedram et al, 2007; Pedram et al, 2012; Le Romancer et al, 2008; reviewed in Arnal, 2017; Le Romancer et al, 2011 ).
E2-evoked extra-nuclear signaling is independent of the transcriptional activity of estrogen receptors and occurs within seconds to minutes following E2 administration to target cells. Extra-nuclear signaling consists of the activation of a plethora of signaling pathways including the RAF/MAP kinase cascade and the PI3K/AKT signaling cascade and governs processes such as apoptosis, cellular proliferation and metastasis (reviewed in Hammes et al, 2007; Handa et al, 2012; Lange et al, 2007; Losel et al, 2003; Arnal et al, 2017; Le Romancer et al, 2011). ESR-mediated signaling also cross-talks with receptor tyrosine kinase, NF- kappa beta and GPCR signaling pathways by modulating the post-translational modification of enzymes and other proteins and regulating second messengers (reviewed in Arnal et al, 2017; Schwartz et al, 2016; Boonyaratanakornkit, 2011; Biswas et al, 2005). In the nervous system, E2 affects neural functions such as cognition, behaviour, stress responses and reproduction in part by inducing such rapid extra-nuclear responses (Farach-Carson and Davis, 2003; Losel et al, 2003), while in endothelial cells, non-genomic ESR-dependent signaling also regulates vasodilation through the eNOS pathway (reviewed in Levin, 2011).
Extra-nuclear signaling additionally cross-talks with nuclear estrogen receptor signaling and is required to control ER protein stability (La Rosa et al, 2012)
Recent data have demonstrated that the membrane ESR1 can interact with various endocytic proteins to traffic and signal within the cytoplasm. This receptor intracellular trafficking appears to be dependent on the phyical interaction of ESR1 with specific trans-membrane receptors such as IGR-1R and beta 1-integrin (Sampayo et al, 2018)
R-HSA-1474244 Extracellular matrix organization The extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded in a viscoelastic gel of anionic proteoglycan polymers. It performs many functions in addition to its structural role; as a major component of the cellular microenvironment it influences cell behaviours such as proliferation, adhesion and migration, and regulates cell differentiation and death (Hynes 2009).
ECM composition is highly heterogeneous and dynamic, being constantly remodeled (Frantz et al. 2010) and modulated, largely by matrix metalloproteinases (MMPs) and growth factors that bind to the ECM influencing the synthesis, crosslinking and degradation of ECM components (Hynes 2009). ECM remodeling is involved in the regulation of cell differentiation processes such as the establishment and maintenance of stem cell niches, branching morphogenesis, angiogenesis, bone remodeling, and wound repair. Redundant mechanisms modulate the expression and function of ECM modifying enzymes. Abnormal ECM dynamics can lead to deregulated cell proliferation and invasion, failure of cell death, and loss of cell differentiation, resulting in congenital defects and pathological processes including tissue fibrosis and cancer.
Collagen is the most abundant fibrous protein within the ECM constituting up to 30% of total protein in multicellular animals. Collagen provides tensile strength. It associates with elastic fibres, composed of elastin and fibrillin microfibrils, which give tissues the ability to recover after stretching. Other ECM proteins such as fibronectin, laminins, and matricellular proteins participate as connectors or linking proteins (Daley et al. 2008).
Chondroitin sulfate, dermatan sulfate and keratan sulfate proteoglycans are structural components associated with collagen fibrils (Scott & Haigh 1985; Scott & Orford 1981), serving to tether the fibril to the surrounding matrix. Decorin belongs to the small leucine-rich repeat proteoglycan family (SLRPs) which also includes biglycan, fibromodulin, lumican and asporin. All appear to be involved in collagen fibril formation and matrix assembly (Ameye & Young 2002).
ECM proteins such as osteonectin (SPARC), osteopontin and thrombospondins -1 and -2, collectively referred to as matricellular proteins (reviewed in Mosher & Adams 2012) appear to modulate cell-matrix interactions. In general they induce de-adhesion, characterized by disruption of focal adhesions and a reorganization of actin stress fibers (Bornstein 2009). Thrombospondin (TS)-1 and -2 bind MMP2. The resulting complex is endocytosed by the low-density lipoprotein receptor-related protein (LRP), clearing MMP2 from the ECM (Yang et al. 2001).
Osteopontin (SPP1, bone sialoprotein-1) interacts with collagen and fibronectin (Mukherjee et al. 1995). It also contains several cell adhesive domains that interact with integrins and CD44.
Aggrecan is the predominant ECM proteoglycan in cartilage (Hardingham & Fosang 1992). Its relatives include versican, neurocan and brevican (Iozzo 1998). In articular cartilage the major non-fibrous macromolecules are aggrecan, hyaluronan and hyaluronan and proteoglycan link protein 1 (HAPLN1). The high negative charge density of these molecules leads to the binding of large amounts of water (Bruckner 2006). Hyaluronan is bound by several large proteoglycans proteoglycans belonging to the hyalectan family that form high-molecular weight aggregates (Roughley 2006), accounting for the turgid nature of cartilage.
The most significant enzymes in ECM remodeling are the Matrix Metalloproteinase (MMP) and A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) families (Cawston & Young 2010). Other notable ECM degrading enzymes include plasmin and cathepsin G. Many ECM proteinases are initially present as precursors, activated by proteolytic processing. MMP precursors include an amino prodomain which masks the catalytic Zn-binding motif (Page-McCawet al. 2007). This can be removed by other proteinases, often other MMPs. ECM proteinases can be inactivated by degradation, or blocked by inhibitors. Some of these inhibitors, including alpha2-macroglobulin, alpha1-proteinase inhibitor, and alpha1-chymotrypsin can inhibit a large variety of proteinases (Woessner & Nagase 2000). The tissue inhibitors of metalloproteinases (TIMPs) are potent MMP inhibitors (Brew & Nagase 2010).
R-HSA-140834 Extrinsic Pathway of Fibrin Clot Formation Factor VII, the protease that initiates the normal blood clotting cascade, circulates in the blood in both its proenzyme (factor VII) and its activated (factor VIIa) forms. No clotting occurs, however, because neither form of the protein has any catalytic activity when free in solution. Blood clotting is normally initiated when tissue factor (TF), an intrinsic plasma membrane protein, is exposed to the blood by injury to the wall of a blood vessel. TF is then able to bind factor VIIa from plasma, and possibly also factor VII, to form complexes capable of catalyzing the conversion of factor X, from plasma, into its activated form, factor Xa. Factor Xa catalyzes the conversion of additional factor VII molecules to their activated form, increasing the amount of tissue factor:factor VIIa complex available at the site of injury, accelerating the generation of factor Xa, and allowing the activation of factor IXa as well. This process is self-limiting because as levels of factor Xa increase, tissue factor:factor VIIa complexes become trapped in the form of catalytically inactive heterotetramers with factor Xa and the protein TFPI (tissue pathway factor inhibitor). At this point the intinsic pathway, as an independent source of activated factor X, is thought to become critical for the continuation of clot formation (Broze 1995; Mann et al. 2003).
The nature of the initial tissue factor:factor VII complexes formed is controversial. One model, building on the observation that the complex of factor VII and TF has low but measurable proteolytic activity on factor X, suggests that this complex begins the activation of factor X, and that as factor VIIa accumulates, tissue factor:factor VIIa complexes also form, accelerating the process (Nemerson 1988). A second model, building on the observation that normal plasma contains low levels of activated factor VII constitutively, suggests that complexes with factor VIIa form immediately at the onset of clotting (Rapaport and Rao 1995). The two models are not mutually exclusive, and in any event, the central roles of tissue factor and factor VIIa in generating an initial supply of factors IXa and Xa, and the self-limiting nature of the process due to the action of TFPI, are all well-established.
R-HSA-9837092 FASTK family proteins regulate processing and stability of mitochondrial RNAs Fas-activated serine/threonine kinase (FASTK) and its homologs FASTKD1-5 each contain three conserved domains (FAST_1, FAST_2, and RAP) that bind RNA (Castello et al. 2012, Baltz et al. 2012). FASTKD1-5 and the short isoform of FASTK localize to mitochondria where they participate in regulating the processing and stability of RNA (Simarro et al. 2010, reviewed in Jourdain et al. 2017).
FASTK interacts with the 3' end of the MT-ND6 mRNA and protects the mRNA from degradation by the degradosome, SUPV3L1:PNPT1 (Jourdain et al. 2015). The MT-ND6 mRNA is unusual in being processed from the large L-strand precursor without flanking tRNA genes and thus without canonical processing by RNAse P and RNase Z. FASTK may, therefore, participate in an uncharacterized non-canonical mechanism of RNA processing or protect 3' ends produced by such a mechanism.
FASTKD1 acts to reduce the abundance of the MT-ND3 mRNA by an uncharacterized mechanism (Boehm et al. 2017).
FASTKD2 binds the 16S rRNA and the MT-ND6 mRNA and participates in their processing and expression (Antonicka and Shoubridge 2015, Popow et al. 2015). FASTKD2 interacts with several mitochondrial proteins including MTERFD1, TRUB2, WBSCR16, and NGRN (Antonicka et al. 2017).
FASTKD3 increases levels of five mitochondrial mRNAs (MT-ND2, MT-ND3, MT-CYB, MT-CO2, and the MT-ATP8/6 bicistronic mRNA) and increases translation of MT-CO1 mRNA through uncharacterized mechanisms (Boehm et al. 2016, Ohkubo et al. 2021).
TBRG4 (FASTKD4) binds most RNAs transcribed from the H-strand and enhances the expression levels of MT-ATP8/6, MT-CO1, MT-CO2, MT-CO3, MT-ND3, MT-CYB, and MT-ND5 mRNAs (Wolf and Mootha 2014, Boehm et al. 2017, Ohkubo et al. 2021). TBRG4 stabilizes MT-CO1, MT-ND3, and MT-CO2 mRNAs and assists the processing of MT-ND5 and MT-CYB mRNAs (Boehm et al. 2017, Ohkubo et al. 2021).
FASTKD5 binds 12S rRNA and all mRNAs except MT-ND3 and reduces levels of MT-ATP8/6, MT-CO1, MT-CO3, MT-ND5, and MT-CYB mRNAs (Antonicka and Shoubridge 2015, Ohkubo et al. 2021). .
R-HSA-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis The protein levels of aurora kinase A (AURKA) during mitotic entry and in early mitosis can be reduced by the action of the SCF-FBXL7 E3 ubiquitin ligase complex consisting of SKP1, CUL1, RBX1 and FBXL7 subunits. FBXL7 is the substrate recognition subunit of the SCF-FBXL7 complex that associates with the centrosome-bound AURKA, promoting its ubiquitination and proteasome-mediated degradation. Overexpression of FBXL7 results in G2/M cell cycle arrest and apoptosis (Coon et al. 2011).
FBXL7 protein levels are down-regulated by the action of the SCF-FBXL18 E3 ubiquitin ligase complex, consisting of SKP1, CUL1, RBX1 and the substrate recognition subunit FBXL18. FBXL18 binds to the FQ motif of FBXL7, targeting it for ubiquitination and proteasome-mediated degradation, counteracting its pro-apoptotic activity (Liu et al. 2015). Cell cycle stage-dependency of down-regulation of FBXL7 by FBXL18 is unknown.
R-HSA-2644605 FBXW7 Mutants and NOTCH1 in Cancer FBXW7 (FBW7) is a component of the SCF (SKP1, CUL1, and F-box protein) ubiquitin ligase complex SCF-FBW7 which is involved in the degradation of NOTCH1 (Oberg et al. 2001, Wu et al. 2001, Fryer et al. 2004). Loss of function mutations in FBXW7 are frequently found in T-cell acute lymphoblastic leukemia (Akhoondi et al. 2007, Thompson et al. 2007, O'Neil et al. 2007) and are mutually exclusive with NOTCH1 PEST domain mutations (Thompson et al. 2007, O'Neil et al. 2007).
R-HSA-2871809 FCERI mediated Ca+2 mobilization Increase of intracellular calcium in mast cells is most crucial for mast cell degranulation. Elevation of intracellular calcium is achieved by activation of PLC-gamma. Mast cells express both PLC-gamma1 and PLC-gamma2 isoforms and activation of these enzymes leads to conversion of phosphatidylinositol 4,5-bisphosphate (PIP2) into inositol triphosphate (IP3) and diacylglycerol (DAG). The production of IP3 leads to mobilization of intracellular Ca+2, which later results in a sustained Ca+2 flux response that is maintained by an influx of extracellular Ca+2. In addition to degranulation, an increase in intracellular calcium concentration also activates the Ca2+/calmodulin-dependent serine phosphatase calcineurin. Calcineurin dephosphorylates the nuclear factor for T cell activation (NFAT) which exposes nuclear-localization signal sequence triggering translocation of the dephosphorylated NFAT-CaN complex to the nucleus. Once in the nucleus, NFAT regulates the transcription of several cytokine genes (Kambayashi et al. 2007, Hoth & Penner 1992, Ebinu et al. 2000, Siraganian et al).
R-HSA-2871796 FCERI mediated MAPK activation Formation of the LAT signaling complex leads to activation of MAPK and production of cytokines. The sequence of events that leads from LAT to cytokine production has not been as clearly defined as the sequence that leads to degranulation. However, the pathways that lead to cytokine production require the guanine-nucleotide-exchange factors SOS and VAV that regulate GDP-GTP exchange of RAS. After its activation, RAS positively regulates the RAF-dependent pathway that leads to phosphorylation and, in part, activation of the mitogen-activated protein kinases (MAPKs) extracellular-signal-regulated kinase 1 (ERK1) and ERK2 (Gilfillan & Tkaczyk 2006).
R-HSA-2871837 FCERI mediated NF-kB activation The increase in intracellular Ca+2 in conjunction with DAG also activates PKC and RasGRP, which inturn contributes to cytokine production by mast cells (Kambayashi et al. 2007). Activation of the FCERI engages CARMA1, BCL10 and MALT1 complex to activate NF-kB through PKC-theta (Klemm et al. 2006, Chen et al. 2007). FCERI stimulation leads to phosphorylation, and degradation of IkB which allows the release and nuclear translocation of the NF-kB proteins. Activation of the NF-kB transcription factors then results in the synthesis of several cytokines. NF-kB activation by FCERI is critical for proinflammatory cytokine production during mast cell activation and is crucial for allergic inflammatory diseases (Klemm et al. 2006).
R-HSA-2029481 FCGR activation Cross-linking of FCGRs with IgG coated immune complexes results in tyrosine phosphorylation of the immuno tyrosine activation motif (ITAMs) of the rececptor by membrane-bound tyrosine kinases of the SRC family. The phosphorylated ITAM tyrosines serve as docking sites for Src homology 2 (SH2) domain-containing SYK kinase. Recruitment and activation of SYK is critical for FCGR-mediated signaling in phagocytosis, but the exact role of SYK in this process is unclear. Activated SYK then transmits downstream signals leading to actin polymerization and particle internalization.
R-HSA-9664323 FCGR3A-mediated IL10 synthesis Interleukin 10 (IL-10) is an important immunoregulatory cytokine produced by many cell populations; in macrophages it is induced after the stimulation of TLRs, Fcγ receptors or by the TLR-FcγR crosstalk (Vogelpoel et al. 2014 & Saninet al. 2015). Classically, its function is considered to be the limitation and termination of inflammatory responses and the regulation of differentiation of several immune cells (Asadullah et al. 2003). There is increasing evidence of the role of IL-10 in parasite infection outcomes either as a protective or a pathological mediator (Asadullah et al. 2003). In the context of the parasitic disease cutaneous leishmaniasis, Leishmania amastigotes opsonized by IgG induce IL-10 response through FcγRs, which in turn supresses the killing mechanisms in phagocytic cells. (Chu et al. 2010).
R-HSA-9664422 FCGR3A-mediated phagocytosis The Fc gamma receptors (FCGRs) have been reported to facilitate Leishmania internalization, especially when in its amastigote form (Ueno et al. 2012). Following cell-to-cell propagation within an established infection or reinfection of a previously infected host, the IgG produced by the host covers the surface of Leishmania amastigote parasites, making them more susceptible to phagocytosis through FCGRs (Polando et al. 2013).
Classically, phagocytosis via FCGRs has been associated with the subsequent activation of Rac GTPases and Cdc42 which in turn activate the phagocyte's NADPH oxidase, contributing to the activation of killing mechanisms (Ueno et al. 2012).
R-HSA-190242 FGFR1 ligand binding and activation The vertebrate fibroblast growth factor receptor 1 (FGFR1) is alternatively spliced generating multiple variants that are differentially expressed during embryo development and in the adult body. The restricted expression patterns of FGFR1 isoforms, together with differential expression and binding of specific ligands, leads to activation of common FGFR1 signal transduction pathways, but may result in distinctively different biological responses as a result of differences in cellular context. FGFR1 isoforms are also present in the nucleus in complex with various fibroblast growth factors where they function to regulate transcription of target genes.
FGFR is probably activated by NCAM very differently from the way by which it is activated by FGFs, reflecting the different conditions for NCAM-FGFR and FGF-FGFR interactions. The affinity of FGF for FGFR is approximately 10e6 times higher than that of NCAM for FGFR. Moreover, in the brain NCAM is constantly present on the cell surface at a much higher (micromolar) concentration than FGFs, which only appear transiently in the extracellular environment in the nanomolar range.
R-HSA-1839124 FGFR1 mutant receptor activation The FGFR1 gene has been shown to be subject to activating mutations, chromosomal rearrangements and gene amplification leading to a variety of proliferative and developmental disorders depending on whether these events occur in the germline or arise somatically (reviewed in Webster and Donoghue, 1997; Burke, 1998; Cunningham, 2007; Wesche, 2011; Greulich and Pollock, 2011). Many of the resulting mutant FGFR1 proteins can dimerize and promote signaling in a ligand-independent fashion, although signal transduction may still be amplified in the presence of ligand (reviewed in Turner and Gross, 2010; Greulich and Pollock, 2011; Wesche et al, 2011).
R-HSA-190370 FGFR1b ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR1b. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-190374 FGFR1c and Klotho ligand binding and activation FGF23 is a member of the endocrine subfamily of FGFs. It is produced in bone tissue and regulates kidney functions. Klotho is essential for endogenous FGF23 function as it converts FGFR1c into a specific FGF23 receptor.
R-HSA-190373 FGFR1c ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR1c. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-6803529 FGFR2 alternative splicing Alternative splicing of the FGFR2 nascent mRNA generates an epithelial specific isoform (FGFR2 IIIb) and a mesenchymal specific isoform (FGFR2 IIIc). The inclusion of exon 8 in FGFR2 IIIb or exon 9 in FGFR2 IIIc alters the C-terminal half of the D3 loop of the receptor and is responsible for the different ligand-binding specificities of the two isoforms (reviewed in Eswarakumar et al, 2005). In recent years, a number of cis- and trans-acting elements have been identified that regulate the alternative splicing event. Exon IIIb repression is mediated by the presence of weak splice sites flanking the exon, an exonic silencing sequence (ESS) within the IIIb exon and both intronic silencing sequences (ISS) upstream and downstream (Carstens et al, 2000; Del Gatto and Breathnach, 1995; Del Gatto et al, 1996; Wagner et al 2005; Wagner and Garcia-Blanco, 2001). Binding of hnRNPA1, PTB1, SR family proteins and other factors to these elements represses the IIIb exon and promotes FGFR2 IIIc expression in mesenchymal cells (Del Gatto-Konczak et al, 1999; Carstens et al, 2000; Wagner et al, 2005; Wagner and Garcia-Blanco, 2001; Wagner and Garcia-Blanco, 2002). In epithelial cells, recruitment of epithelial specific factors shifts the splicing events to favour inclusion of exon 8. ESPN1 and ESPN2 are epithelial-specific factors that bind to an ISE/ISS-3 (intronic splicing enhancer/intronic splicing silencer-3) region within intron 8 to promote FGFR2 IIIb-specific splicing (Warzecha et al, 2009). A complex of RBFOX2, hnRNPH1 and hnRNPF also contribute to epithelial-specific splicing by competing for binding to a site that is occupied by the SR proteins ASF/SF2 in mesenchymal cells (Baraniak et al, 2006; Mauger et al, 2008). Other proteins and sequences have also been identified that appear to contribute to the regulated expression of FGFR2b and FGFR2c, but the full details of the alternative splicing event remain to be worked out (Muh et al, 2002; Newman et al, 2006; Del Gatto et al, 2000; Hovhannisyan and Carstens, 2007).
R-HSA-190241 FGFR2 ligand binding and activation Dominant mutations in the fibroblast growth factor receptor 2 (FGFR2) gene have been identified as causes of four phenotypically distinct craniosynostosis syndromes, including Crouzon, Jackson- Weiss, Pfeiffer, and Apert syndromes. FGFR2 binds a number of different FGFs preferentially, as illustrated in this pathway.
FGFR is probably activated by NCAM very differently from the way by which it is activated by FGFs, reflecting the different conditions for NCAM-FGFR and FGF-FGFR interactions. The affinity of FGF for FGFR is approximately 10e6 times higher than that of NCAM for FGFR. Moreover, in the brain NCAM is constantly present on the cell surface at a much higher (micromolar) concentration than FGFs, which only appear transiently in the extracellular environment in the nanomolar range.
R-HSA-1839126 FGFR2 mutant receptor activation Autosomal dominant mutations in FGFR2 are associated with the development of a range of skeletal disorders including Beare-Stevensen cutis gyrata syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome, Crouzon syndrome and Apert Syndrome (reveiwed in Burke, 1998; Webster and Donoghue 1997; Cunningham, 2007). Activating point mutations have also been identified in FGFR2 in ~15% of endometrial cancers, as well as to a lesser extent in ovarian and gastric cancers (Dutt, 2008; Pollock, 2007; Byron, 2010; Jang, 2001). Activating mutations in FGFR2 are thought to contribute to receptor activation through diverse mechanisms, including constitutive ligand-independent dimerization (Robertson, 1998), expanded range and affinity for ligand (Ibrahimi, 2004b; Yu, 2000) and enhanced kinase activity (Byron, 2008; Chen, 2007). FGFR2 amplifications have been identified in 10% of gastric cancers, where they are associated with poor prognosis diffuse cancers (Hattori, 1996; Ueda, 1999; Shin, 2000; Kunii, 2008) , and in ~1% of breast cancers (Turner, 2010; Tannheimer, 2000). FGFR2 amplification often occur in conjunction with deletions of C-terminal exons, resulting in expression of a internalization- and degradation-resistant form of the receptor (Takeda, 2007; Cha, 2008, 2009). Signaling through overexpressed FGFR2 shows evidence of being ligand-independent and sensitive to FGFR inhibitors (Lorenzi, 1997; Takeda, 2007; Cha, 2009). More recently, FGFR2 fusion proteins have been identified in a number of cancers; these are thought to form constitutive ligand-independent dimers based on the dimerization domains of the 3' fusion partners and contribute to cellular proliferation and tumorigenesis in a kinase-inhibitor sensitive manner (Wu, 2013; Arai, 2013; Seo, 2012; reviewed in Parker, 2014).
R-HSA-190377 FGFR2b ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR2b. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-190375 FGFR2c ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR2c. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-190239 FGFR3 ligand binding and activation FGFR3 is a receptor tyrosine kinase of the FGF receptor family, known to have a negative regulatory effect on long bone growth. Somatically, some of the same activating mutations are associated with hypochondroplasia, multiple myeloma, and cervical and vesical carcinoma.
R-HSA-2033514 FGFR3 mutant receptor activation The FGFR3 gene has been shown to be subject to activating mutations and gene amplification leading to a variety of proliferative and developmental disorders depending on whether these events occur in the germline or arise somatically. As is the case for the other receptors, many of the activating mutations that are seen in FGFR3-related cancers mimic the germline FGFR3 mutations that give rise to autosomal skeletal disorders and include both ligand-dependent and independent mechanisms (reviewed in Webster and Donoghue, 1997; Burke et al, 1998; Wesche et al, 2011). In addition to activating mutations, the FGFR3 gene is subject to a translocation event in 15% of multiple myelomas (Avet-Loiseau et al, 1998; Chesi et al, 1997). This chromosomal rearrangement puts the FGFR3 gene under the control of the highly active IGH promoter and promotes overexpression and constitutive activation of FGFR3 (Otsuki et al, 1999). In a small proportion of multiple myelomas, the translocation event is accompanied by activating mutations in the FGFR3 coding sequence (Chesi et al, 1997; Onwuazor et al, 2003; Ronchetti et al, 2001).
Finally, FGFR3 is subject to fusion events in a number of cancers, including lung, bladder and glioblastoma (Singh et al, 2012; Parker et al, 2013; Williams et al, 2013; Wu et al, 2013; Capelletti et al, 2014; Yuan et al, 2014; Wang et al, 2014; Carneiro et al, 2015; reviewed in Parker et al, 2014). These fusions are constitutively active based on dimerization domains provided by the fusion partners and support transformation and proliferation through downstream signaling pathways such as ERK and AKT (Singh et al, 2012; Williams et al, 2013; Parker et al, 2013; reviewed in Parker et al, 2014).
R-HSA-190371 FGFR3b ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR3b. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-190372 FGFR3c ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR3c. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-190322 FGFR4 ligand binding and activation FGFR4 is expressed mainly in mature skeletal muscle, and disruption of FGFR4 signaling interrupts limb muscle formation in vertebrates.
R-HSA-1839128 FGFR4 mutant receptor activation FGFR4 is perhaps the least well studied of the FGF receptors, and unlike the case for the other FGFR genes, mutations in FGFR4 are not known to be associated with any developmental disorders. Recently, however, somatically arising mutations in the FGFR4 coding sequence have begun to be identified in some cancers. (Taylor, 2009; Ruhe, 2007; Roidl, 2010). The resulting mutant versions of FGFR4 promote aberrant signaling through ligand-independent dimerization and enhanced autophosphorylation, among other mechanisms (Roidl, 2009; Taylor, 2009).
R-HSA-5658623 FGFRL1 modulation of FGFR1 signaling FGFRL1 is a fifth member of the FGFR family of receptors. The extracellular region has 40% sequence similarity with FGFR1-4, but FGFRL1 lacks the internal kinase domain of the other FGF receptors and how it acts in FGFR signaling is unclear. Some models suggest FGFRL1 restricts canonical FGFR signaling by sequestering ligand away from kinase-active receptors, while other models suggest that FGFRL1 may promote canonical signaling by nucleating signaling complexes or enhancing ERK1/2 activation (reviewed in Trueb, 2011; Trueb et al, 2013).
R-HSA-9607240 FLT3 Signaling Feline McDonough Sarcoma-like tyrosine kinase (FLT3) (also known as FLK2 (fetal liver tyrosine kinase 2), STK-1 (stem cell tyrosine kinase 1) or CD135) is a member of the class III receptor tyrosine kinase family involved in the differentiation, proliferation and survival of hematopoietic progenitor cells and of dendritic cells. Upon FLT3 ligand (FL) binding, the receptor forms dimers and is phosphorylated. Consequently, adapter and signaling molecules bind with the active receptor and trigger the activation of various pathways downstream including PI3K/Akt and MAPK cascades (Grafone T et al. 2012).
R-HSA-9702509 FLT3 mutants bind TKIs Aberrant signaling by activated forms of FLT3 can be inhibited by tyrosine kinase inhibitors (TKIs). FLT3 receptors are class III receptor tyrosine kinase receptors, also known as dual-switch. Dual-switch receptors are activated through a series of phosphorylation and conformational changes that move the receptor from the inactive form to the fully activated form. Type II TKIs bind to the inactive form of the receptor at a site adjacent to the ATP-binding cleft, while type I TKIs bind to the active form (reviewed in Klug et al, 2018; Daver et al, 2019).
FLT3 internal tandem duplications (ITDs) are found in ~25-30% of acute myeloid leukemias, and are present at lower frequencies in other cancers (reviewed in Kazi and Roostrand, 2019; Patnaik et al, 2018). These ITDs generally occur in a tyrosine-rich region of exon 14, encoding the juxtamembrane domain region of the protein; at a lower frequency, ITDs are found in the first tyrosine kinase domain (TKD1). In addition to ITDs, a number of point mutations in the juxtamembrane domain have also been identified. Juxtamembrane domain mutations affect an autoinhibitory loop, shifting the equilibrium of the receptor towards the activated state; despite this, however, juxtamembrane domain mutants remain predominantly in the inactive state and as such are susceptible to inhibition by type II TKIs (reviewed in Patnaik et al, 2018; Kazi and Roonstrand et al, 2019).
Activation loop mutations more strongly favor the active conformation of the receptor and are susceptible to inhibition by both type II and type I TKIs. The most prevalent FLT3 mutation, D835Y, promotes the active conformation strongly enough to be resistant to type II TKIs (Patnaik et al, 2017; Klug et al, 2018; Daver et al, 2019).
R-HSA-9706377 FLT3 signaling by CBL mutants Missense and splicing mutants have been identified in the E3 ubiquitin ligase CBL in a number of cancers including acute and chronic myeloid leukemias, among others. These cancers show elevated signaling through FLT3 as a result of impaired CBL-mediated downregulation of the receptor (Sargin et al, 2007; Reindl et al, 2009; Caligiuri et al, 2007; Abbas et al, 2008).
R-HSA-9682385 FLT3 signaling in disease FLT3 is a type III receptor tyrosine kinase (RTK). The extracellular domain consists of 5 immunoglobulin (Ig) domains that contribute to dimerization and ligand binding. The intracellular region has a juxtamembrane domain that plays a role in autoinhibiting the receptor in the absence of ligand, and a bi-lobed kinase region with an activation loop and the catalytic cleft (reviewed in Klug et al, 2018). Signaling through FLT3 occurs after ligand-induced dimerization and transautophosphorylation, and promotes signaling through the MAP kinase, PI3K and STAT5 pathways, among others. FLT3 signaling promotes cellular proliferation and differentiation and contributes to haematopoeisis. FLT3 is mutated in up to 30% of acute myeloid leukemias. ~25% of the FLT3 mutations in AML cases occur as internal tandem duplications (ITDs) either in the juxtamembrane domain region encoded by exon 14 or the tyrosine kinase domain (TKD), while ~7-10% of AML cases contain FLT3 missense mutations in the TKD (reviewed in Klug et al, 2018; Daver et al, 2019). These mutations all support ligand-independent activation of the receptor and result in constitutive activation and signaling (Zheng et al, 2004; reviewed in Klug et al, 2018; Kazi and Roonstrand, 2019). In rare cases, the FLT3 locus is also subject to translocations that generate constitutively active fusion proteins (reviewed in Kazi and Roonstrand, 2019). Oncogenic FLT3 activity can be targeted with tyrosine kinase inhibitors, although resistance often arises due to secondary mutations or activation of bypass pathways (reviewed in Staudt et al, 2018; Daver et al, 2019).
R-HSA-9706374 FLT3 signaling through SRC family kinases Several SRC family kinases (SFKs) have been shown to interact with active FLT3 to modulate downstream signaling. These include FYN, HCK, LCK and SYK (Heiss et al, 2006; Mitina et al, 2007; Chougule et al, 2016; Dosil et al, 1993; Marhall et al, 2017; Puissant et al, 2014; reviewed in Kazi and Ronnstrand, 2019a,b). The role of SFKs downstream of FLT3 is complex and not fully elucidated. Some family members appear to contribute positively to signaling, as assessed by elevated STAT5 signaling, while others may contribute to ubiquitin ligation and downregulation of the receptor through interaction with CBL (Chougule et al, 2016; Heiss et al, 2006; Marhall et al, 2017; reviewed in Kazi and Ronnstrand, 2019a,b).
R-HSA-217271 FMO oxidises nucleophiles Flavin-containing monooxygenases (FMOs) are the second family of microsomal oxidative enzymes with broad and overlapping specificity. The major reactions FMOs catalyze are nucleophilic hetero-atom compounds such as nitrogen, sulfur or phosphorus as the hetero-atom to form N-oxides, S-oxides or P-oxides respectively. Despite the functional overlap with cytochrome P450s, the mechanism of action differs. FMOs bind and activate molecular oxygen before the substrate binds to the enzyme (picture). They also require flavin adenosine dinucleotide (FAD) as a cofactor. Unlike cytochrome P450 enzymes, FMOs are heat-labile, a useful way to distinguish which enzyme system is at work for researchers studying metabolism. Also, FMOs are not inducible by substrates, unlike the P450 enzymes.\n(1) NADPH binds to the enzyme and reduces the prosthetic group FAD to FADH2. NADP+ remains bound to the enzyme.\n(2) Incorporation of molecular oxygen to form a hydroperoxide.\n(3) A peroxide oxygen is transferred to the substrate.\n(4) Water is released.\n(5) NADP+ dissociates returning the enzyme to its initial state.\n\nTo date, there are 6 isozymes of FMO (FMO1-6) in humans, the most prominent and active one being FMO3. The FMO6 gene does not encode for a functional enzyme although it has the greatest sequence similarity with FMO3 (71%), whilst the others range from 50-58% sequence similarity with FMO3. FMO1-3 are the ones that exhibit activity towards nucleophiles, the others are insignificant in this respect (Cashman 2003, Krueger & Williams 2005).
R-HSA-9614085 FOXO-mediated transcription The family of FOXO transcription factors includes FOXO1, FOXO3, FOXO4 and FOXO6. FOXO transcription factors integrate pathways that regulate cell survival, growth, differentiation and metabolism in response to environmental changes, such as growth factor deprivation, starvation and oxidative stress (reviewed by Accili and Arden 2004, Calnan and Brunet 2008, Eijkelenboom and Burgering 2013).
R-HSA-9617828 FOXO-mediated transcription of cell cycle genes FOXO transcription factors induce expression of several genes that negatively regulate proliferation of different cell types, such as erythroid progenitors (Bakker et al. 2004, Wang et al. 2015) and neuroepithelial progenitor cells in the telencephalon (Seoane et al. 2004).
Transcription of cyclin-dependent kinase (CDK) inhibitors CDKN1A (p21Cip1) is directly stimulated by FOXO1, FOXO3 and FOXO4 (Seoane et al. 2004, Tinkum et al. 2013). FOXO transcription factors can cooperate with the SMAD2/3:SMAD4 complex to induce CDKN1A transcription in response to TGF-beta signaling (Seoane et al. 2004).
FOXO transcription factors FOXO1, FOXO3 and FOXO4 stimulate transcription of the CDKN1B (p27Kip1) gene, but direct binding of FOXOs to the CDKN1B gene locus has not been demonstrated (Dijkers et al. 2000, Medema et al. 2000, Lees et al. 2008).
FOXO3 and FOXO4, and possibly FOXO1, directly stimulate transcription of the GADD45A gene (Tran et al. 2002, Furukawa Hibi et al. 2002, Hughes et al. 2011, Sengupta et al. 2011, Ju et al. 2014).
Transcription of the retinoblastoma family protein RBL2 (p130), involved in the maintenance of quiescent (G0) state, is directly stimulated by FOXO1, FOXO3 and FOXO4 (Kops et al. 2002, Chen et al. 2006).
Transcription of the anti-proliferative protein CCNG2 is directly stimulated by FOXO1 and FOXO3, and possibly FOXO4 (Martinez Gac et al. 2004, Chen et al. 2006). Transcription of the anti-proliferative protein BTG1 is directly stimulated by FOXO3 (Bakker et al. 2004, Bakker et al. 2007, Wang et al. 2015).
Transcription of CAV1, encoding caveolin-1, involved in negative regulation of growth factor receptor signaling and establishment of quiescent cell phenotype, is directly stimulated by FOXO1 and FOXO3 (van den Heuvel et al. 2005, Roy et al. 2008, Nho et al. 2013, Sisci et al. 2013).
FOXO1 and FOXO3 promote transcription of the KLF4 gene, encoding a transcription factor Krueppel-like factor 4, which inhibits proliferation of mouse B cells (Yusuf et al. 2008).
FOXO1, together with the p-2S-SMAD2/3:SMAD4 complex, stimulates transcription of the MSTN gene, encoding myostatin, a TGF-beta family member that stimulates differentiation of myoblasts (Allen and Unterman 2007).
R-HSA-9614657 FOXO-mediated transcription of cell death genes FOXO transcription factors promote expression of several pro-apoptotic genes, such as FASLG (Brunet et al. 1999, Ciechomska et al. 2003, Chen et al. 2013, Li et al. 2015), PINK1 (Mei et al. 2009, Sengupta et al. 2011), BCL2L11 (BIM) (Gilley et al. 2003, Urbich et al. 2005, Chuang et al. 2007, Hughes et al. 2011, Chen et al. 2013, Wang et al. 2016), BCL6 (Tang et al. 2002, Fernandez de Mattos et al. 2004, Shore et al. 2006) and BBC3 (PUMA) (Dudgeon et al. 2010, Hughes et al. 2011, Liu et al. 2015, Wu et al. 2016, Liu et al. 2017, Fitzwalter et al. 2018). FOXO-mediated induction of cell death genes is important during development, for example during nervous system development, where FOXO promotes neuronal death upon NGF withdrawal (Gilley et al. 2003), and also contributes to the tumor-suppressive role of FOXO factors (Arimoto Ishida et al. 2004). FOXO1 transcriptional activity is implicated in the cell death of enteric nervous system (ENS) precursors. RET signaling, which activates PI3K/AKT signaling, leading to inhibition of FOXO mediated transcription, ensures survival of ENS precursors (Srinivasan et al. 2005).
Transcription of the STK11 (LKB1) gene, encoding Serine/threonine-protein kinase STK11 (also known as Liver kinase B1), which regulates diverse cellular processes, including apoptosis, is directly stimulated by FOXO3 and FOXO4 (Lutzner et al. 2012).
R-HSA-9615017 FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes FOXO6, the least studied member of the FOXO family, directly stimulates transcription of PLXNA4 gene, encoding a co-factor for the semaphorin SEMA3A receptor. FOXO6-mediated regulation of PLXNA4 expression plays an important role in radial glia migration during cortical development (Paap et al. 2016).
FOXO-mediated up-regulation of genes involved in reduction of the oxidative stress burden is not specific to neurons, but plays an important role in neuronal survival and neurodegenerative diseases. FOXO3 and FOXO4, and possibly FOXO1, directly stimulate transcription of the SOD2 gene, encoding mitochondrial manganese-dependent superoxide dismutase, which converts superoxide to the less harmful hydrogen peroxide and oxygen (Kops et al. 2002, Hori et al. 2013, Araujo et al. 2011, Guan et al. 2016). FOXO4 stimulates SOD2 gene transcription in collaboration with ATXN3, a protein involved in spinocerebellar ataxia type 3 (SCA3) (Araujo et al. 2011). FOXO3 and FOXO6, and possibly FOXO1, directly stimulate transcription of the CAT gene, encoding catalase, an enzyme that converts hydrogen peroxide to water and oxygen, thus protecting cells from the oxidative stress (Awad et al. 2014, Kim et al. 2014, Rangarajan et al. 2015, Song et al. 2016, Liao et al. 2016, Guo et al. 2016).
FOXO transcription factors regulate transcription of several genes whose protein products are secreted from hypothalamic neurons to control appetite and food intake: NPY gene, AGRP gene and POMC gene. At low insulin levels, characteristic of starvation, FOXO transcription factors bind to insulin responsive elements (IRES) in the regulatory regions of NPY, AGRP and POMC gene. FOXO1 directly stimulates transcription of the NPY gene, encoding neuropeptide-Y (Kim et al. 2006, Hong et al. 2012), and the AGRP gene, encoding Agouti-related protein (Kitamura et al. 2006, Kim et al. 2006), which both stimulate food intake. At the same time, FOXO1 directly represses transcription of the POMC gene, encoding melanocyte stimulating hormone alpha , which suppresses food intake (Kitamura et al. 2006, Kim et al. 2006). When, upon food intake, blood insulin levels rise, insulin-mediated activation of PI3K/AKT signaling inhibits FOXO transcriptional activity.
In liver cells, FOXO transcription factors regulate transcription of genes involved in gluconeogenesis: G6PC gene, encoding glucose-6-phosphatase and PCK1 gene, encoding phosphoenolpyruvate carboxykinase. Actions of G6PC and PCK1 enable steady glucose blood levels during fasting. FOXO1, FOXO3 and FOXO4 directly stimulate PCK1 gene transcription (Hall et al. 2000, Yang et al. 2002, Puigserver et al. 2003), while all four FOXOs, FOXO1, FOXO3, FOXO4 and FOXO6 directly stimulate G6PC gene transcription (Yang et al. 2002, Puigserver et al. 2003, Onuma et al. 2006, Kim et al. 2011). FOXO-mediated induction of G6PC and PCK1 genes is negatively regulated by insulin-induced PI3K/AKT signaling.
FOXO1, FOXO3 and FOXO4 directly stimulate transcription of the IGFBP1 gene, encoding insulin growth factor binding protein 2 (Tang et al. 1999, Kops et al. 1999, Hall et al. 2000, Yang et al. 2002), which increases sensitivity of cells to insulin.
FOXO1 and FOXO3 directly stimulate transcription of the ABCA6 (ATP-binding cassette sub-family A member 6) gene, encoding a putative transporter protein that is thought to be involved in lipid homeostasis (Gai et al. 2013). The GCK (glucokinase) gene is another gene involved in lipid homeostasis that is regulated by FOXOs. FOXO1, acting with the SIN3A:HDAC complex, directly represses the GCK gene transcription, thus repressing lipogenesis in the absence of insulin (Langlet et al. 2017). The SREBF1 (SREBP1) gene, which encodes a transcriptional activator required for lipid homeostasis, is directly transcriptionally repressed by FOXO1 (Deng et al. 2012). Transcription of the RETN gene, encoding resistin, an adipocyte specific hormone that suppresses insulin-mediated uptake of glucose by adipose cells, is directly stimulated by FOXO1 (Liu et al. 2014).
Transcription of two genes encoding E3 ubiquitin ligases FBXO32 (Atrogin-1) and TRIM63 (MURF1), involved in degradation of muscle proteins and muscle wasting during starvation, is positively regulated by FOXO transcription factors (Sandri et al. 2004, Waddell et al. 2008, Raffaello et al. 2010, Senf et al. 2011, Bollinger et al. 2014, Wang et al. 2017).
R-HSA-5654693 FRS-mediated FGFR1 signaling The FRS family of scaffolding adaptor proteins has two members, FRS2 (also known as FRS2 alpha) and FRS3 (also known as FRS2beta or SNT-2). Activation of FGFR tyrosine kinase allows FRS proteins to become phosphorylated on tyrosine residues and then bind to the adaptor GRB2 and the tyrosine phosphatase PPTN11/SHP2. Subsequently, PPTN11 activates the RAS-MAP kinase pathway and GRB2 activates the RAS-MAP kinase , PI-3-kinase and ubiquitinations/degradation pathways by binding to SOS, GAB1 and CBL, respectively, via the SH3 domains of GRB2. FRS2 acts as a central mediator in FGF signaling mainly because it induces sustained levels of activation of ERK with ubiquitous expression.
R-HSA-5654700 FRS-mediated FGFR2 signaling The FRS family of scaffolding adaptor proteins has two members, FRS2 (also known as FRS2 alpha) and FRS3 (also known as FRS2beta or SNT-2). Activation of FGFR tyrosine kinase allows FRS proteins to become phosphorylated on tyrosine residues and then bind to the adaptor GRB2 and the tyrosine phosphatase PPTN11/SHP2. Subsequently, PPTN11 activates the RAS-MAP kinase pathway and GRB2 acti