Transcriptional profiling of distinct fibroblast populations in the pancreatic tumor microenvironment

Pancreatic stellate cells are thought to be the predominant source of cancer-associated fibroblasts (CAFs) in pancreatic cancer. We developed a mouse model which allows us to track and analyze stellate cells and stellate cell-derived CAFs in vivo during pancreatic tumorigenesis for the first time. We find that stellate cells in fact give rise to a minority of all CAFs. Here, we have used lineage reporters to isolate stellate cell-derived and non-stellate cell-derived CAFs and compared them by RNA-seq. Rosa-mTmG; Fabp4-Cre mice at 8 weeks of age were injected with FC1199 murine pancreatic cancer cells orthotopically. After 4 weeks, tumors were harvested, single cell suspensions generated, and FACS performed to isolate GFP+ (stellate cell-derived) and Tomato+ (non-stellate cell-derived) CAFs. RNA was isolated and RNA-seq performed on both cell populations.