Abstract B009: Characterization and CRISPR perturbation of cancer-associated fibroblast heterogeneity in vitro models
Authors: Saputra Elysia , Vellarikkal Shamsudheen Karuthedath , Li Lixia , Sun Hong , Natarajan Suchitra , Piccioni Federica , Tamburino Alex M. , Yu Xin , Olow Aleksandra K. 
Published: November 2024

Cancer-associated fibroblasts (CAFs) are attractive therapeutic targets for cancer due to their abundance in the tumor microenvironment (TME) and extensive pro- and antitumorigenic functions. However, formulating CAF-targeting strategies remains challenging due to the complexity of CAF biology. CAFs specialize into phenotypically and functionally distinct subtypes that may respond differently to specific treatments. Thus, designing CAF-targeting therapies necessitates a thorough understanding of CAF heterogeneity and preclinical model systems that can reliably prototype CAF biology observed in tumors. However, CAF heterogeneity is still not well-understood for many solid tumors, including the stroma-rich pancreatic ductal adenocarcinoma (PDAC), and the translatability of stroma models has not been comprehensively evaluated. In this work, we developed in vitro cell lines of tumor-CAF cocultures using primary CAFs derived from PDAC and used single-cell transcriptomics and CRISPR perturbation to investigate CAF heterogeneity and subtype-specific responses. We found that coculturing primary CAFs with the BxPC3 PDAC cell line could capture the tumor-CAF crosstalks underlying CAF activation. We characterized eight subtypes, including myofibroblastic, inflammatory, extracellular matrix (ECM)-like, and interferon CAFs, which could be preserved with immortalization. We also delineated the trajectories of CAF subtype interconvertibility, highlighting inflammatory CAFs as the likely initial diseased state and ECM CAFs as a “reservoir” that seeded the later states. By correlating the in vitro subtypes with clinical data of immunotherapy responses, we established that the in vitro cell lines could model the immuno-modulatory and immunoresistant phenotypes of CAFs. Finally, using an immortalized tumor-CAF coculture line, we performed Perturb-seq single-cell perturbation to perturb several stroma genes of interest, including TGFBR1, SPATS2L, AEBP1, and PTGS1, and evaluated the subtype-specific effects of the perturbations. We found that perturbing TGFBR1 resulted in the expected eradication of myofibroblastic CAFs, while the other perturbations resulted in subtype-specific modulations of metabolic and extracellular matrix related pathways. Overall, our findings underscored that in vitro tumor-CAF coculture models could serve as a translatable system that effectively captured CAF biology and heterogeneity observed in tumors and highlighted some similarities between PDAC CAFs and previously characterized breast cancer CAFs. We also demonstrated that single-cell perturbation could be a useful approach for interrogating the distinct responses of different CAF subtypes to perturbations.

Citation Format: Elysia Saputra, Shamsudheen Karuthedath Vellarikkal, Lixia Li, Hong Sun, Suchitra Natarajan, Federica Piccioni, Alex M. Tamburino, Xin Yu, Aleksandra K. Olow. Characterization and CRISPR perturbation of cancer-associated fibroblast heterogeneity in vitro models [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr B009.