Discovery and 3D imaging of a novel ΔNp63-expressing basal cell type in human pancreatic ducts with implications in disease

Objective An 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. Design We 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. Results In 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. Conclusion We 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 BOX What is already known about this subject? What are the new findings? How might it impact on clinical practice in the foreseeable future? ### Competing Interest Statement The authors have declared no competing interest.