Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation (RNA-seq)

A highly aggressive subset of pancreatic ductal adenocarcinomas undergo trans-differentiation into the squamous lineage during disease progression. While the tumorigenic consequences of this aberrant cell fate transition are poorly understood, recent studies have identified a role for the master regulator TP63 in this process. Here, we investigated whether squamous trans- differentiation of pancreatic cancer cells can influence the phenotype of non-neoplastic cells in the tumor microenvironment. Conditioned media experiments revealed that squamous-subtype pancreatic cancer cells secrete factors that convert quiescent pancreatic stellate cells into a specialized subtype of cancer-associated fibroblasts (CAFs) that express inflammatory genes at high levels. We use gain- and loss-of-function approaches in vivo to show that squamous-subtype pancreatic tumor models become enriched with inflammatory CAFs and neutrophils in a TP63- dependent manner. These non cell-autonomous effects occur, at least in part, through TP63- mediated activation of enhancers at pro-inflammatory cytokine loci, which includes IL1A as a key target. Taken together, our findings reveal enhanced tissue inflammation as a consequence of squamous trans-differentiation in pancreatic cancer, thus highlighting an instructive role of tumor cell lineage in reprogramming the stromal microenvironment. For RNA-seq performed in cells harvested from in vivo experiments (flow sorted or xenograft RNA-seq), four biological repeats were used for each experimental group. For RNA-seq performed following dox-inducible knockout of TP63 in T3M4 and KLM1 cells, three technical repeats were performed for each condition. For RNA-seq performed in human PDA cell lines or mouse PSCs following treatment with conditioned media, 1 technical repeat for each cell line was used.