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Objective: The aggressive basal-like molecular subtype of pancreatic ductal adenocarcinoma (PDAC) harbours a ΔNp63 (p40) gene expression signature reminiscent of a basal cell type. Distinct from other epithelia with basal tumours, ΔNp63+ basal cells reportedly do not exist in the normal pancreas. Design: We evaluated ΔNp63 expression in human pancreas, chronic pancreatitis (CP) and PDAC. We further studied in depth the non-cancerous tissue and developed a three-dimensional (3D) imaging protocol (FLIP-IT, Fluorescence Light sheet microscopic Imaging of Paraffin-embedded or Intact Tissue) to study formalin-fixed paraffin-embedded samples at single cell resolution. Pertinent mouse models and HPDE cells were analysed. Results: In normal human pancreas, rare ΔNp63+ cells exist in ducts while their prevalence increases in CP and in a subset of PDAC. In non-cancer tissue, ΔNp63+ cells are atypical KRT19+ duct cells that overall lack SOX9 expression while they do express canonical basal markers and pertain to a niche of cells expressing gastrointestinal stem cell markers. 3D views show that the basal cells anchor on the basal membrane of normal medium to large ducts while in CP they exist in multilayer dome-like structures. In mice, ΔNp63 is not found in adult pancreas nor in selected models of CP or PDAC, but it is induced in organoids from larger Sox9low ducts. In HPDE, ΔNp63 supports a basal cell phenotype at the expense of a classical duct cell differentiation programme. Conclusion: In larger human pancreatic ducts, basal cells exist. ΔNp63 suppresses duct cell identity. These cells may play an important role in pancreatic disease, including PDAC ontogeny, but are not present in mouse models., SCOPUS: ar.j, info:eu-repo/semantics/published

SUMMARYObjectiveAn aggressive basal-like molecular subtype of pancreatic ductal adenocarcinoma (PDAC) exists, driven by ΔNp63. In other epithelia, ΔNp63+basal cells have stem cell capacity and can be at the origin of tumors. In the pancreas, basal cells have not been identified.DesignWe assessed basal cell markers in human and mouse pancreas, chronic pancreatitis and PDAC, and developed a 3D imaging protocol (FLIP-IT) to study sizeable samples at single cell resolution. We generated organoid cultures of ducts from Sox9-eGFP reporter mice.ResultsIn normal human pancreas, rare ΔNp63+cells exist in ducts that expand in chronic pancreatitis. ΔNp63+cells express KRT19 and canonical basal markers (KRT5, KRT14 and S100A2) but lack markers of duct cells such as CA19.9 and SOX9. In addition, ΔNp63+cells pertain to a niche of cells expressing gastrointestinal stem cell markers. 3D views of the ductal tree in formalin fixed paraffin embedded samples show that basal cells are localized on the basal membrane of medium to large ducts and expand as multilayer dome-like structures in chronic pancreatitis. In mice, ΔNp63 expression is induced when culturing organoids from Sox9-low ductal cells but could not be found in normal pancreas nor in models of pancreatitis or pancreatic cancer.ConclusionWe discovered a novel ductal cell population in normal human pancreas similar to basal cells in other tissues. Using FLIP-IT, we provide unprecedented 3D visualization of these cells in archival clinical specimens. ΔNp63+cells may play an important role in pancreatic tissue regeneration and cancer.SUMMARY BOXWhat is already known about this subject?ΔNp63 has a central role in determining the basal-like subtype of pancreatic ductal adenocarcinoma (PDAC).Different to other tissues with basal cancers, the normal pancreas reportedly does not contain (ΔNp63-expressing) basal cells.Current protocols face severe limitations for marker-based identification and 3D imaging of individual (rare) cells in archival pancreatic samples.What are the new findings?We report a rare and atypical pancreatic duct cell that expresses ΔNp63, other basal cell markers and g.i. stem cell markers.The number of these basal cells increases in diseases such as chronic pancreatitis and pancreatic cancer.We provide an easy to implement protocol for 3D clearing and high-resolution imaging of sizeable samples of (fresh or FFPE) human pancreas or an entire mouse pancreas.Except after culturing medium to large ducts as organoids, we fail to detect basal cells in mouse experimental pancreatic models.How might it impact on clinical practice in the foreseeable future?Extrapolating from knowledge in other organs, basal cells in the pancreas may have a stem cell/progenitor role, including in diseases such as (basal) pancreatic cancer.Use of the 3D imaging protocol in archival clinical specimens will allow unprecedented insights in pancreatic histopathology.For above mentioned diseases, we caution for findings in experimental mouse models that may not (fully) recapitulate the etiopathogenesis.