GSE209599
Systematic comparison of pancreatic ductal adenocarcinoma models identifies a conserved highly plastic basal cell state
Pancreatic ductal adenocarcinoma (PDAC) portends a dire prognosis. Intra-tumoral heterogeneity and cellular plasticity have emerged as hallmarks of cancer, including PDAC. Yet, our understanding of the mechanisms underpinning cellular diversity in PDAC remains limited. Here, we investigate cellular heterogeneity of PDAC cancer cells across a range of in vitro and in vivo growth conditions using single-cell genomics. We find heterogeneity contracts significantly in 2D and 3D cell culture models but becomes restored upon orthotopic transplantation. Orthotopic transplants reproducibly acquire cell states identified in autochthonous PDAC tumors, including a basal state exhibiting co-expression and co-accessibility of epithelial and mesenchymal genes. Using linage-tracing combined with single-cell transcriptomics, we demonstrate basal cells display high plasticity in situ. This work defines the impact of cellular growth conditions on phenotypic diversity and uncovers a highly plastic cell state with the capacity to facilitate state transitions and promote intra-tumoral heterogeneity in PDAC. Overall design: Single-cell RNA-sequencing data of pancreatic ductal adenocarcinoma was generated on the 10X Chromium platform from either autochthonous  KPCT mice or from orthotopic pancreas transplants. Autochthonous KPCT mice were generated by crossing previously published KrasLSL-G12D/+ , Trp53flox/flox , Pdx1-Cre, and Rosa26LSL-tdTomato mice. For Lgr5 co-expression studies, the KPCT mice above were crossed with Lgr5GFP-IRES-CreER/+ reporter mice. To generate various orthotopic PDAC transplant models we have implanted into pancreas of NSG recipient mice either: ~3mm PDAC fragments generated from KPCT primary tumors; or  tumor cells derived from KPCT primary PDAC tumors.