Cancer associated fibroblasts drive epithelial to mesenchymal transition and classical to basal change in pancreatic ductal adenocarcinoma cells with loss of IL-8 expression

Abstract Pancreatic ductal adenocarcinoma (PDAC) carries an extremely poor prognosis, in part resulting from cellular heterogeneity that supports overall tumorigenicity. Cancer associated fibroblasts (CAF) are key determinants of PDAC biology and response to systemic therapy. While CAF subtypes have been defined, the effects of patient-specific CAF heterogeneity and plasticity on tumor cell behavior remain unclear. Here, multi-omics was used to characterize the tumor microenvironment (TME) in tumors from patients undergoing curative-intent surgery for PDAC. In these same patients, matched tumor organoid and CAF lines were established to functionally validate the impact of CAFs on the tumor cells. CAFs were found to drive epithelial-mesenchymal transition (EMT) and a switch in tumor cell classificiaton from classical to basal subtype. Furthermore, we identified CAF-specific interleukin 8 (IL-8) as an important modulator of tumor cell subtype. Finally, we defined neighborhood relationships between tumor cell and T cell subsets. Statement of Significance This multidimensional analysis highlights the diverse role CAFs have in influencing other cell types in the TME, including epithelial-derived tumor and infiltrating immune cells. Our methods provide a platform for evaluating emerging therapeutic approaches and for studying mechanisms that dictate tumor behavior in a manner that reflects patient-specific heterogeneity. Competing Interest Statement E.M.J is a paid consultant for Adaptive Biotech, Achilles, DragonFly, Candel Therapeutics, Genocea, and Roche. She receives funding from Lustgarten Foundation and Bristol Myer Squibb. She is the Chief Medical Advisor for Lustgarten and SAB advisor to the Parker Institute for Cancer Immunotherapy (PICI) and for the C3 Cancer Institute. She is a founding member of Abmeta. E.J.F is on the SAB for Resistance Biology, Consultant for Mestag Therapeutics and Merck. L.Z. reports personal fees from Biosion, Alphamab, NovaRock, Xilio, Ambrx, Novagenesis, and Snow Lake Capitals; and other support from Alphamab and Mingruizhiyao outside the submitted work. D.J.Z. reports grant support (to Johns Hopkins) and travel from Roche/Genentech, and honoraria from Omni Health Media, Sermo, Atheneum, Escientiq, Deerfield Institute, ZoomRx, and NeuCore Bio.W.J.H. reports patent royalties from Rodeo/Amgen; grants from Sanofi, NeoTX, and Riboscience; speaking/travel honoraria from Exelixis and Standard BioTools. J.W.Z. report grant funding support (to Johns Hopkins) and travel from Roche/Genentch outside the submitted work. Footnotes Conflict of Interest Statement E.M.J is a paid consultant for Adaptive Biotech, Achilles, DragonFly, Candel Therapeutics, Genocea, and Roche. She receives funding from Lustgarten Foundation and Bristol Myer Squibb. She is the Chief Medical Advisor for Lustgarten and SAB advisor to the Parker Institute for Cancer Immunotherapy (PICI) and for the C3 Cancer Institute. She is a founding member of Abmeta. E.J.F is on the SAB for Resistance Biology, Consultant for Mestag Therapeutics and Merck. L.Z. reports personal fees from Biosion, Alphamab, NovaRock, Xilio, Ambrx, Novagenesis, and Snow Lake Capitals; and other support from Alphamab and Mingruizhiyao outside the submitted work. D.J.Z. reports grant support (to Johns Hopkins) and travel from Roche/Genentech, and honoraria from Omni Health Media, Sermo, Atheneum, Escientiq, Deerfield Institute, ZoomRx, and NeuCore Bio.W.J.H. reports patent royalties from Rodeo/Amgen; grants from Sanofi, NeoTX, and Riboscience; speaking/travel honoraria from Exelixis and Standard BioTools. J.W.Z. report grant funding support (to Johns Hopkins) and travel from Roche/Genentch outside the submitted work. Data and code availability Raw reads for the RNA-seq data are being submitted to dbGAP and processed read counts are being submitted to GEO. IMC data are available at Zenodo (10.5281/zenodo.14219608). All scripts from analysis will be made available through Github.