SUMMARY
Bulk transcriptomic studies have defined classical and basal-like gene expression subtypes in pancreatic ductal adenocarcinoma (PDAC) that correlate with survival and response to chemotherapy; however, the underlying mechanisms that govern these subtypes and their heterogeneity remain elusive. Here, we performed single-cell RNA-sequencing of 23 metastatic PDAC needle biopsies and matched organoid models to understand how tumor cell-intrinsic features and extrinsic factors in the tumor microenvironment (TME) shape PDAC cancer cell phenotypes. We identify a novel cancer cell state that co-expresses basal-like and classical signatures, demonstrates upregulation of developmental and KRAS-driven gene expression programs, and represents a transitional intermediate between the basal-like and classical poles. Further, we observe structure to the metastatic TME supporting a model whereby reciprocal intercellular signaling shapes the local microenvironment and influences cancer cell transcriptional subtypes. In organoid culture, we find that transcriptional phenotypes are plastic and strongly skew toward the classical expression state, irrespective of genotype. Moreover, we show that patient-relevant transcriptional heterogeneity can be rescued by supplementing organoid media with factors found in the TME in a subtype-specific manner. Collectively, our study demonstrates that distinct microenvironmental signals are critical regulators of clinically relevant PDAC transcriptional states and their plasticity, identifies the necessity for considering the TME in cancer modeling efforts, and provides a generalizable approach for delineating the cell-intrinsic versus -extrinsic factors that govern tumor cell phenotypes.
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, KSQ Therapeutics, Jubilant Therapeutics, RAPPTA Therapeutics, and Paraxel. 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, Bayer, and Esperas Pharma, has served as a consultant to Bristol Myers Squib, and has received travel funding from Bristol Myers Squib. A.R. is an employee of AstraZeneca and an equity holder in Celsius Therapeutics and NucleAI. 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.
Footnotes
↵¶ Equal senior contribution