Regulatory network analysis of Dclk1 gene expression reveals a tuft cell-ILC2 axis that inhibits pancreatic tumor progression [RNA-seq]

Dclk1 expression defines a rare population of cells in normal pancreas whose frequency is increased at early stages pancreatic tumors. The identity and the precise roles of Dclk1 expressing cells in pancreas are matter of debate, although the concept of their involvement in a number of key functions, including regeneration and neoplasia, has emerged. We employed a novel Dclk1 reporter mouse model and single cell RNAseq analysis to define Dclk1 expressing cells in normal pancreas and pancreatic neoplasia. In normal pancreas, Dclk1 epithelial expression identifies subsets of ductal, islet and acinar cells. In pancreatic neoplasia, Dclk1 expression identifies five epithelial cell populations, among which acinar-to-ductal metaplasia (ADM)-like cells and tuft-like cells represent the main ones. These cells play opposing roles in pancreatic neoplasia, with Dclk1+ ADM-like cells sustaining tumor growth and Dclk1+ tuft-like cells restraining tumor progression. The differentiation of Kras mutant acinar cells into Dclk1+ tuft-like cells requires the activation of SPIB and is further supported by a cellular loop involving cancer group 2 innate lymphoid cells (ILC2) and activated fibroblasts (CAFs) that provide IL13 and IL33, respectively. In turn, Dclk1+ tuft-like cells release angiotensinogen that play protective roles against pancreatic neoplasia. Overall, our study provides novel insights on the biology of Dclk1+ cells in normal pancreas and also unveils a protective axis against pancreatic neoplasia involving Dclk1+ tuft-like cells, ILC2 and CAFs, which ultimately results in angiotensinogen release. Overall design: In order to dissect the identity of Dclk1 cells in normal pancreas and early pancreatic neoplasia we performed a scRNA-seq analysis. Specifically, we used a droplet-based scRNA-seq to profile Dclk1 cells isolated from Dclk1-DTR-ZSGreen, Mist1-Kras-TdTomato-Dclk1-DTR-ZSGreen mice at 2 weeks after KRAS activation and Mist1-Kras-TdTomato-Dclk1-DTR-ZSGreen mice 16 weeks after KRAS activation. To better identify the genetic programs controlled by SPIB in pancreatic neoplasia, we performed a RNA-seq analysis of pancreatic organoids grown from single cells obtained from normal murine pancreas, in which we overexpressed SPIB as well as mutant KRAS.