Discovery and 3D imaging of a novel Delta Np63-expressing basal cell type in human pancreatic ducts with implications in disease

Objective The aggressive basal-like molecular subtype of pancreatic ductal adenocarcinoma (PDAC) harbours a Delta Np63 (p40) gene expression signature reminiscent of a basal cell type. Distinct from other epithelia with basal tumours, Delta Np63(+) basal cells reportedly do not exist in the normal pancreas. Design We evaluated Delta Np63 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 Delta Np63(+) cells exist in ducts while their prevalence increases in CP and in a subset of PDAC. In non-cancer tissue, Delta Np63(+) 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, Delta Np63 is not found in adult pancreas nor in selected models of CP or PDAC, but it is induced in organoids from larger Sox9(low) ducts. In HPDE, Delta Np63 supports a basal cell phenotype at the expense of a classical duct cell differentiation programme. Conclusion In larger human pancreatic ducts, basal cells exist. Delta Np63 suppresses duct cell identity. These cells may play an important role in pancreatic disease, including PDAC ontogeny, but are not present in mouse models.