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In pancreatic ductal adenocarcinoma (PDAC), the basal-like and classical transcriptional subtypes are associated with differential chemotherapy sensitivity and patient survival. These phenotypes have been defined using bulk transcriptional profiling, which can mask underlying cellular heterogeneity and the biologic mechanisms that distinguish these subtypes. Furthermore, few studies have interrogated metastases, which are the cause of mortality in most patients with this highly lethal disease. Using single-cell RNA-sequencing of metastatic needle biopsies and matched organoid models, we demonstrate intra-tumoral subtype heterogeneity at the single-cell level and define a continuum for the basal-like and classical phenotypes that includes hybrid cells that co-express features of both states. Basal-like tumors show enrichment of mesenchymal and stem-like programs, and demonstrate immune exclusion and tumor cell crosstalk with specific macrophage subsets. Conversely, classical tumors harbor greater immune infiltration and a relatively pro-angiogenic microenvironment. Matched organoid models exhibit a strong bias against the growth of basal-like cells in standard organoid media, but modification of culture conditions can rescue the basal-like phenotype. This study reframes the transcriptional taxonomy of PDAC, demonstrates how divergent transcriptional subtypes associate with unique tumor microenvironments, and highlights the importance of evaluating both genotype and transcriptional phenotype to establish high-fidelity patient-derived cancer models. ### Competing Interest Statement B.M.W. reports research support from Celgene, Eli Lilly and consulting for BioLineRx, Celgene, G1 Therapeutics, GRAIL. W.C.H. is a consultant for Thermo Fisher, Solasta Ventures, MPM Capital, Tyra Biosciences, iTeos, Frontier Medicines, and Paraxel. W.C.H. is a founder and a member of the scientific advisory board (SAB) for KSQ Therapeutics. A.K.S. reports compensation for consulting and/or SAB membership from Merck, Honeycomb Biotechnologies, Cellarity, Cogen Therapeutics, Orche Bio, and Dahlia Biosciences. A.J.A. has consulted for Oncorus, Inc., Arrakis Therapeutics, and Merck & Co., Inc, and has research funding from Mirati Therapeutics, Deerfield, Inc. and Novo Ventures that are unrelated to this project. S.R.M. is a founder of Travera. J.M.C. has received research funding from Merck, Tesaro, Astrazeneca, and Esperas Pharma, has served as a consultant to Bristol Myers Squib, and has received travel funding from Bristol Myers Squib. A.R. is a consultant to eGenesis, a member of the SAB for NucleAI, and an equity holder in Celsius Therapeutics. Y.Y.L. reports equity from g.Root Biomedical Services. A.D.C. reports research support from Bayer. K.N. reports research support from Revolution Medicines, Evergrande Group, Genentech, Gilead Sciences, Celgene, Trovagene, Pharmavite, and Tarrex Biopharma, is a member of SABs for Bayer, Seattle Genetics, and Array Biopharma, and has consulted for X-Biotix Therapeutics.

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  • Download rankings, all-time:
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