Trunk bipotent pancreatic progenitor cells (bi-PPs) give rise to pancreatic ductal cells or they commit to the pancreatic endocrine lineage, producing pancreatic endocrine progenitors (Jennings et al. 2013, Mamidi et al. 2018, Olaniru et al. 2023, Ma et al. 2023, reviewed in Shih et al. 2013, Jennings et al. 2015). The ultimate fate of trunk bipotent pancreatic progenitors depends on their unique history of exposure to the extracellular matrix, with exposure to fibronectin and vitronectin favoring the ductal fate, and exposure to laminin and collagen favoring the endocrine fate (Mamidi et al. 2018).

By single cell RNA sequencing (scRNA-seq) analysis of embryonic human pancreas from post-conception weeks (PCW) 4 to 11, corresponding to gestation weeks GW6 to GW13, duct cells emerge after PCW10 (Ma et al. 2023). NOTCH signaling appears to play an important role in the commitment of trunk cells to the ductal lineage in developing human pancreas (Mamidi et al. 2018), with trunk cells committed to the ductal lineage expressing high levels of HES1 (Mamidi et al. 2018, Ma et al. 2023), HEY1 (Ma et al. 2023), and HES4 (Ma et al. 2023) transcripts. NOTCH signaling in the ductal lineage may be activated through NOTCH1, NOTCH2, and NOTCH3 receptors expressed by trunk and ductal cells and NOTCH ligands DLK1 and JAG1 expressed by fibroblasts and pericytes of the developing pancreas (Ma et al. 2023). ID4, expressed in human trunk cells, may contribute to HES4 upregulation (Ma et al. 2023). Other signaling pathways that likely contribute to differentiation of trunk cells into ductal cells are FGFR2 signaling and NTRK2 signaling (Ma et al. 2023). Trunk and duct cells express high levels of FGFR2, while its ligands FGF7 and FGF9 are expressed by fibroblasts and mesothelial cells (Ma et al. 2023). NTRK2 is also expressed by duct lineage cells, while its ligands NTF4 and BDNF are expressed by mesothelial cells and pericytes, respectively (Ma et al. 2023). As functional evidence linking FGF7, FGF9, BDNF and NTF4 to differentiation of trunk bipotent progenitors into pancreatic ductal cells is lacking, they are not explicitly annotated as regulators.

Pancreatic ductal cells are epithelial cells that line the pancreatic ducts. Pancreatic ducts, together with the pancreatic acini that consist of digestive enzyme-producing acinar cells, constitute the exocrine pancreas (reviewed in Kim and MacDonald 2002, Murtaugh and Melton 2003). Pancreatic ductal cells secrete a bicarbonate fluid that flushes acinar cell-secreted digestive enzymes from the pancreatic ducts into the duodenum, the starting portion of the small intestine (reviewed in Kim and MacDonald 2002, Murtaugh and Melton 2003; Salpeter and Dor 2006). Ducts connected to the acinar lumen have the smallest diameter (intercalated ducts), but their merging produces progressively larger intralobular and interlobular ducts (reviewed in Murtaugh and Melton 2003), finally forming the duct of Wirsung that drains ducts of the ventral pancreas through the major papilla of duodenum, and the duct of Santorini that drains the ducts of the dorsal pancreas through the minor papilla of duodenum (Arvanitakis, "Anatomy of the Pancreas", pp.91-99). Although there are indications that ductal cells lining ducts of different diameter exhibit some distinct features, including the existence in larger ducts of progenitor-like ductal cells positive for PDX1, BPMR1A (ALK3), and some (KRT19, CDH1, SOX9) but not other (CA2) ductal markers (Qadir et al. 2020, Doke et al. 2023, reviewed in Dominguez-Bendala et al. 2019), only a generic pancreatic ductal cell is annotated until more data becomes available. Organoids derived from pancreatic tissue express typical ductal markers, such as SOX9, KRT19, and MUC1, implying that progenitor potential is associated with a ductal phenotype (reviewed in Alvarez Fallas et al. 2021). Several studies suggest that adult pancreatic ductal cells may acquire a progenitor state in response to injury or inflammation (reviewed in Alvarez Fallas et al. 2021), and in mouse this process involves activation of WNT signaling (Huch et al. 2013).

Pancreatic ductal cells show weak expression of PDX1 (Jennings et al. 2013) and PDX1 is therefore not annotated as a marker.

Pancreatic ductal cells do not express GATA4 and NKX6.1 (Jennings et al. 2013).

Annexins are a family of Ca2+-regulated membrane-binding proteins that are involved in cellular stress response (reviewed in Gerke et al. 2024). Several Annexin A family members, ANXA1, ANXA2, and ANXA3, have been identified as protein markers of human pancreatic ductal cells and confirmed as RNA markers of human pancreatic ductal cells by scRNA-seq (please refer to the table above). CFTR may be needed for ANXA1 protein stability (Bensalem et al. 2005). ANXA4 and ANXA9 have only been identified as RNA markers of pancreatic ductal cells by scRNA-seq (please refer to the table above). ANXA4 has also been reported as an RNA marker of acinar cells (Muraro et al. 2016). ANXA2 mRNA was reported to be differentially expressed in human trunk progenitor cells, too (Olaniru et al. 2023), and to be highly expressed in mouse trunk cells that are also MUC1-positive (Yu et al. 2019).

AQP1 (Aquaporin-1), a small plasma membrane channel exclusively permeable to water, mainly localizes to the apical membrane of human pancreatic ductal cells (Venglovecz et al. 2018), but can also localize to basolateral domain of ductal cells (Burghardt et al. 2003). AQP1 expression was reported to decline with distance along the small interlobular ducts and to not be detectable in larger interlobular ducts (Burghardt et al. 2003). AQP1 was also reported to be expressed in centroacinar cells (Burghardt et al. 2003), a poorly characterized cell type that localizes to the acino-ductal boundaries.

CA2 (also known as CAII or Carbonic anhydrase 2 or Carbonic anhydrase C) is a protein marker (Kumpulainen and Jalovaara 1981; Lardon et al. 2008) and RNA marker (Li et al. 2016; Muraro et al. 2016) of pancreatic ductal cells. CA2 catalyzes the reversible hydration of carbon dioxide, generating bicarbonate, which is secreted by pancreatic ductal cells to increase luminal pH and prevent the activation of acinar cell-secreted digestive enzymes before their delivery to the duodenum (reviewed in Dominguez-Bendala et al. 2019).

CD74 (HLA class II histocompatibility antigen gamma chain) protein is involved in antigen presentation, serves as a receptor for macrophage migration inhibitory factor and Helicobacter pylori, and is involved in inflammation and carcinogenesis in the gastrointestinal tract (reviewed in Beswick and Reyes 2009). In normal adult human pancreas, CD74 protein is observed in ductal cells, and it is overexpressed in pancreatic ductal adenocarcinoma (PDAC) (Zhang et al. 2014).

CLDN10 (claudin-10), a component of tight junctions, has been reported as an RNA marker (Muraro et al. 2016; Segerstolpe et al. 2016; Doke et al. 2023) and a protein marker (Danielsson et al. 2014) of human pancreatic ductal cells, possibly restricted to the epithelium of intercalated ducts. An immunohistochemical study of mouse pancreas reports that CLDN10 is mostly expressed on the apical surface of acinar cells (Qu et al. 2015).

CFTR (Cystic fibrosis transmembrane conductance regulator) is a protein that, in the pancreas, is specifically expressed on the apical surface of proximal duct epithelial cells (Marino et al. 1991, Kulaksiz et al. 2001, Shik Mun et al. 2019), where its function in cAMP-regulated chloride and bicarbonate transport plays a key role in normal pancreatic secretory function (reviewed in Kunzelmann et al. 2017). By scRNA-seq and immunohistochemistry, there is a spatial separation between pancreatic ductal cells that express CFTR and those that express MUC1 in both human and mouse pancreas (Baron et al. 2016). MUC1, however, is not consistently used as a marker of ductal cells and is therefore not annotated, similar to other mucin family members.

ERICH5 (C8ORF47) is a poorly characterized protein identified as differentially expressed at the mRNA level in the exocrine pancreas (Danielsson et al. 2014) and pancreatic ductal cells (Muraro et al. 2016), and confirmed as a protein marker of pancreatic ductal cell membranes both in intercalated and interlobular ducts (Danielsson et al. 2014). ERICH5 has been identified as a substrate for protein N-myristoyltransferases NMT1 and NMT2 (Su et al. 2021).

HNF1B transcription factor is expressed in the majority of human pancreatic ductal cells by immunohistochemistry, albeit high levels are detectable only in a small percentage of adult ductal cells (Rezanejad et al. 2018; Martens et al. 2021). By scRNA-seq, HNF1B has been identified as differentially expressed in a single study (Muraro et al. 2016).

Keratins that are well-established protein markers of normal pancreatic ductal epithelium cells include KRT7 (Keratin-7) (Ramaekers et al. 1987; Kasper et al. 1991; Schüssler et al. 1992; Real et al. 1993) and KRT19 (Keratin-19) (Kasper et al. 1991; Schüssler et al. 1992; Real et al. 1993; Yao et al. 2004; Lardon et al. 2008). scRNA-seq studies confirmed KRT7 (Li et al. 2016; Muraro et al. 2016; Doke et al. 2023) and KRT19 (Muraro et al. 2016; Segerstolpe et al. 2016; Lawlor et al. 2017; Doke et al. 2023) as markers of pancreatic ductal cells at the mRNA level. The role of KRT17 (keratin-17), identified as a protein marker (Real et al. 1993; Qadir et al. 2020) and an RNA marker (Muraro et al. 2016) of pancreatic ductal cells, is less established.

PROM1 (also known as Prominin-1 or CD133) is an RNA marker (Lardon et al. 2008; Li et al. 2016, Muraro et al. 2016, Lawlor et al. 2017) and protein marker (Lardon et al. 2008; Immervoll et al. 2008; Karbanová et al. 2008; Shimizu et al. 2009; Immervoll et al. 2011) of human pancreatic ductal cells, predominantly localizing to the apical surface of ductal cells (Immervoll et al. 2008; Immervoll et al. 2011).

SLC4A4 (also known as Electrogenic sodium bicarbonate cotransporter 1 or Sodium bicarbonate cotransporter or NBC1 or NBCE1), an intracellular pH regulator, is a protein marker of pancreatic ductal cells (Abuladze et al. 1998, Satoh et al. 2003) and was also confirmed as an RNA marker (Muraro et al. 2016, Lawlor et al. 2017; Doke et al. 2023). In pancreatic duct cells, SLC4A4 is activated by cystic fibrosis transmembrane conductance regulator (CFTR) and plays an important role in HCO3- secretion (reviewed in Soleimani and Burnham 2001).

SOX9 transcription factor, a marker of pancreatic progenitor cells, continues to be detectable in over half of adult human pancreatic ductal cells by immunohistochemistry, albeit high levels are detectable only in a small percentage of adult ductal cells (Rezanejad et al. 2018; Martens et al. 2021). Only one scRNA-seq study has identified SOX9 as differentially expressed in adult pancreatic ductal cells (Muraro et al. 2016).

TFPI2 (also known as Tissue factor pathway inhibitor 2, or Placental protein 5, or PP5) is a secreted protease inhibitor identified as an RNA marker of pancreatic ductal cells by scRNA-seq (Li et al. 2016; Muraro et al. 2016, Lawlor et al. 2017). TFPI2 protein was found to be expressed in normal pancreatic ductal cells by immunohistochemistry (Wojtukiewicz et al. 2003). By electron microscopy, TFPI2 can be seen on the surface of the endoplasmic reticulum, probably during posttranslational processing in the secretory pathway (Udagawa et al. 2002). In PDAC, the TFPI2 gene is frequently silenced through promoter hypermethylation (Sato et al. 2005).

Potential pancreatic ductal cell markers that have only been identified at the RNA level in at least three scRNA-seq studies, but whose involvement in normal ductal cell biology is unknown or has been contradicted by other studies or are thought to be ubiquitous have been excluded. They may be included in the future if more information becomes available.
Some of these potential scRNA-seq-based markers were previously implicated in the function of other pancreatic cell types rather than ductal.
AKAP7 (also known as AKAP18) is highly expressed in human brain and pancreas (Fraser et al. 1998). AKAP7 serves as a protein kinase A (PKA) anchoring protein and may act to increase cAMP-responsive Ca2+ currents at the plasma membrane (Fraser et al. 1998, Smith et al. 2018). AKAP7 splicing isoforms were shown to have different effects, either stimulatory or inhibitory, on insulin secretion from pancreatic beta cell lines RINm5F (Fraser et al. 1998) and INS-1E (Josefsen et al. 2010), but their role in pancreatic ductal cells has not been investigated.
The AMBP gene produces three protein products: alpha-1-microglobulin (A1M), bikunin, (Inter-alpha-trypsin inhibitor light chain or ITI-LC) and trypstatin, where a single peptide, called alpha-1-microgolobulin-bikunin precursor is cleaved in the Golgi into A1M and bikunin, (reviewed in Bergwik et al. 2021). In mast cells trypstatin is released by an additional cleavage of bikunin (Itoh et al. 1994). AMBP protein products serve as inhibitors of several proteases, including trypsin (Itoh et al. 1994, reviewed in Bergwik et al. 2021). Bikunin is immunohistochemically detected on the surface of human pancreatic acinar cells where it is thought to play a role in preventing autodigestion by exocrine cells (Itoh et al. 1996). No immunostaining for bikunin is observed on the surface of ductal and endocrine cells (Itoh et al. 1996) and secretion of bikunin by pancreatic ductal cells has not been reported.
DEFB1 (also known as human beta defensin-1 or hBD1) is, by RNA in situ hybridization, expressed in human adult acinar and not ductal cells (Schnapp et al. 1998).
Plasma protease inhibitors SERPINA1, SERPINA5, and SERPING1 are known to be mainly produced by hepatocytes, and while small amounts can be produced by epithelial cells, their production has not been attributed to pancreas (reviewed in Janciauskiene et al. 2024). SLPI (also known as secretory leucocyte protease inhibitor) was reported to be expressed in human pancreatic beta cells (Nyström et al. 1999).
Other potential scRNA-seq-based markers of pancreatic ductal cells have previously been associated with pancreatic cancer or with pancreatitis.
ALDH1A3 (Aldehyde dehydrogenase family 1 member A3), which catalyzes NAD-dependent oxidation of aldehyde substrates (Moretti et al. 2016), has been identified as a beta cell de-differentiation marker in human pancreatic cancer (Tsuchiya et al. 2022), and in mice during diet-induced obesity and dysglycemia (Tersey et al. 2018), and is highly expressed in pancreatic cancer cell lines and tumor tissue (Jia et al. 2013).
BICC1 (Protein bicaudal C homolog 1), is an RNA-binding protein that regulates cytosolic mRNAs and is implicated in stemness and chemotherapy resistance in pancreatic ductal adenocarcinoma (PDAC) (Sun et al. 2024). CD9 (tetraspanin) protein, involved in integrin signaling, cell adhesion and migration (reviewed in Powner et al. 2011) was reported to be a marker of pancreatic ductal adenocarcinoma (PDAC) stem cells, but its expression in normal pancreatic cell types has not been characterized.
CD9 expression is also characteristic of immature human endocrine progenitors (Morisseau et al. 2023), and CD9 was also reported as a marker of a subpopulation of human pancreatic beta cells (Dorrell et al. 2016).
CEACAM7 (Carcinoembryonic antigen-related cell adhesion molecule 7) protein is expressed at a low level in a very small number of cells in the normal pancreas (Raj et al. 2021, Dhasmana et al. 2024), on the apical surface of isolated ductal epithelial cells (Schölzel et al. 2000), and is overexpressed in PDAC (Raj et al. 2021, Dhasmana et al. 2024).
CCN2 (CTGF), by RNA in situ hybridization, is not expressed in normal ductal and acinar pancreatic cells of the adult human pancreas, only in remaining ductal and acinar cells during acute necrotizing pancreatitis (di Mola et al. 2002).
CCN1 (CY61), was identified as a protein involved in disruption of normal pancreatic islet architecture and progression of pancreatic neuroendocrine tumors (Huang et al. 2016).
COL18A1, Collagen alpha-1(XVIII) chain, whose cleavage product is Endostatin, is a part of the extracellular matrix and thought to be stroma-derived (Franklin et al. 2015). COL18A1 serves as a marker of pancreatic ductal adenocarcinoma (PDAC) progression, and is involved in angiogenesis (Franklin et al. 2015).
CTSH (cathepsin H), by immunohistochemistry, is highly expressed in ductal and other pancreatic cell types, including endocrine cells (Im et al. 1989).
CXCL1 and CXCL6 are inflammation-related cytokines that are highly expressed in pancreatic ductal adenocarcinoma and at a low level in normal pancreatic ducts (Saxena et al. 2022).
DAB2 is barely or not detectable in normal ductal and acinar cells, and is overexpressed in primary PDAC (Huang et al. 2001).
EDN1 (also known as endothelin-1 or ET-1) is a part of the inflammatory infiltrate in chronic pancreatitis and in a rat model of chronic pancreatitis, but is not expressed in ductal cells of non-inflamed pancreas (Kakugawa et al. 1996).
FLNA (also known as filamin-A) is only expressed in chronic pancreatitis according to proteomic analysis of formalin-fixed paraffin-embedded human pancreatic tissue (Paulo et al. 2012).
ITGB1 (also known as Integrin beta-1) is overexpressed in human pancreatic cancer, with low levels in normal tissue (by Liu et al. 2020), and unknown relevance to normal ductal cells.
LGALS4 (also known as Galectin-4 or Gal-4) mRNA is expressed at a higher level in PDAC compared to normal pancreatic ducts and LGLAS4 protein is undetectable in normal ducts compared to PDAC (Lidström et al. 2023).
MMP7 (also known as Matrilysin or Matrix metalloproteinase-7) mRNA is detectable in ~ 30% of normal pancreas specimens and ~90% of pancreatic cancers by Northern blotting (Bramhall et al. 1997), but the protein is never detected in normal pancreas by immunohistochemistry (Crawford et al. 2002).
NEURL3 is a marker of pancreatitis or pancreatic injury (Dunbar et al. 2024).
ONECUT2 was reported to not be expressed in normal acinar and ductal cells but only in neoplastic and metaplastic cells (Schlesinger et al. 2020).
S100A14 and S100A16 are overexpressed in pancreatic cancer compared to normal pancreas at both mRNA and protein levels (Li et al. 2021), but specific expression in ductal cells was not examined.
SPP1 (also known as osteopontin) protein is not detectable in normal human ductal cells, but is expressed in chronic pancreatitis (Nakamura et al. 2002, Takada et al. 2009), and might be a marker of murine ductal cells (Kilic et al. 2006).
UGT2A3 (also known as UDP-glycosyltransferase 2A3) mRNA is highly expressed in PDAC (Hu et al. 2021), but its relevance to normal pancreas is unknown.
TSPAN8 (also known as Tetraspanin-8) expression in normal pancreas is not excluded, but it is primarily expressed on the surface of PDAC cells (Schäfer et al. 2021).
VTCN1 (also known as B7H4 or V-set domain-containing T-cell activation inhibitor 1) shows low level protein expression in normal pancreas and high in PDAC (Awadallah et al. 2008). In normal human pancreas, VTCN1 protein level is higher in beta-cells than in exocrine pancreas (Cheung et al. 2014)), but no specific data on protein expression in pancreatic ductal cells is available.
WFDC2 (also known as WAP four-disulfide core domain protein 2, or WAP5 or HE4) is frequently overexpressed in PDAC (O’Neal et al. 2013), but data on specific expression in normal pancreatic ductal cells is lacking).
Some of the scRNA-seq-based putative markers have been excluded based on their more generic function in ubiquitous cellular processes.
CAV2 (Caveolin-2) is one of the markers of caveolae, flask-shaped or spherical invaginations of the plasma membrane, considered to be a subtype of lipid rafts (reviewed in Stan 2005).
CCND1 and GMNN were excluded as generic cell cycle genes.
CLDN1 (claudin-1), a major component of tight junctions, is widely expressed but, by immunohistochemical staining, more highly in human acinar than ductal cells (Tsukahara et al. 2005).
CDH1 (E-cadherin) is a component of adherens junctions in various epithelial cells, while EPCAM is likely associated with tight junctions in epithelial cells. By immunohistochemical analysis of adult human pancreas, EPCAM is expressed throughout the pancreas and not colocalized to a specific cell population, while CDH1 expression is the most prominent in the islets of Langerhans (Seeberger et al. 2009).
Finally, some potential scRNA-seq-identified markers of pancreatic ductal cells have been excluded because their relevance for pancreas in general is unknown. This is the case for DCDC2, GYPC (also known as Glycophorin C), IFITM2 (also known as Interferon-induced transmembrane protein 2), LITAF (also known as Lipopolysaccharide-induced tumor necrosis factor-alpha factor), NUAK2, PDLIM3, PLPP2 (also known as Phospholipid phosphatase 2 or PPAP2C), RHPN2 (also known as Rhophilin-2) TNFAIP2 (also known as Tumor necrosis factor alpha-induced protein 2), and TPM1 (also known as Tropomyosin alpha-1 chain), and several genes whose transcripts have been previously detected in the pancreas by Northern blotting, such as GSTM4 (also known as Glutathione S-transferase Mu 4) (Comstock et al. 1993), HSD17B2 (also known as 17-beta-hydroxysteroid dehydrogenase type 2) (Casey et al. 1994), LIPH (also known as Lipase member H) (Jin et al. 2002), and OCC1 (Overexpressed in colon carcinoma 1 protein, also known as C12ORF75) (Pibouin et al. 2002).