SUMMARY Prognostically relevant RNA expression states exist in pancreatic ductal adenocarcinoma (PDAC), but our understanding of their drivers, stability, and relationship to therapeutic response is limited. To examine these attributes systematically, we profiled metastatic biopsies and matched organoid models at single-cell resolution. In vivo , we identify a new intermediate PDAC transcriptional cell state and uncover distinct site- and state-specific tumor microenvironments (TMEs). Benchmarking models against this reference map, we reveal strong culture-specific biases in cancer cell transcriptional state representation driven by altered TME signals. We restore expression state heterogeneity by adding back in vivo -relevant factors and show plasticity in culture models. Further, we prove that non-genetic modulation of cell state can strongly influence drug responses, uncovering state-specific vulnerabilities. This work provides a broadly applicable framework for aligning cell states across in vivo and ex vivo settings, identifying drivers of transcriptional plasticity and manipulating cell state to target associated vulnerabilities.

Highlights d Obesity accelerates oncogenic Kras-driven pancreatic ductal tumorigenesis in mice d Genetic or dietary weight loss intercepts pancreatic cancer progression d Obesity is associated with aberrant pancreatic islet cholecystokinin expression d Islet cholecystokinin overexpression drives pancreatic ductal cancer development

248 Word count, text (from the beginning of Introduction to the end of Discussion): 4,467 Reference count: 48 Table count: 3 Figure count: 3 Supplementary online material: 12 figures and 8 tables Disclosure of Potential Conflicts of Interest: M.C.L., J.B., S.O., and J.A.N. are listed as co-inventors on a provisional application for a patent titled "System for and Method of Discovering Spatially-Derived Signatures of Tumor-Immune Cell Interactions through Tumor-Immune Partitioning and Clustering" regarding novel methods for characterizing immune cell distributions in solid tumors that has been filed through Partners Healthcare. J.L.G. is a consultant for GlaxoSmithKline, Codagenix, Array BioPharma, and Verseau Therapeutics; and receives research support from GlaxoSmithKline, Eli Lilly and Array BioPharma for the study of the breast tumor microenvironment. A.T.