Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is classified into epithelial and mesenchymal subtypes based on transcriptional profiling, and these subtypes are associated with varied patient outcomes. Differences in the tumor microenvironment (TME), particularly in cancer-associated fibroblasts (CAFs), may contribute to this variation. scRNA-seq studies have observed heterogeneous CAF populations in PDAC, although the relationship between tumor subtype and CAF phenotype is not well understood. To investigate this relationship, we utilized epithelial and mesenchymal PDAC cell lines in a xenograft model to examine whether these subtypes influence CAF phenotypes. Methods: Xenograft models were generated by subcutaneously injecting BALB/c nude mice with PDAC cell lines of either the epithelial subtype (BxPC-3) or the mesenchymal subtype (MIA PaCa-2). Tumors were then harvested and dissociated for scRNA-seq to investigate the TME. Human tumor (graft) and murine stromal (host) cells were computationally separated using the Xenocell tool. Subsequent analyses focused on fibroblasts within the TME, which were subclustered to assess CAF heterogeneity between PDAC subtypes. To characterize transcriptional programs and identify CAF features, we performed high-dimensional weighted gene co-expression network analysis (hdWGCNA) and analyzed differentially expressed genes. Finally, spatial transcriptomics was conducted on tumor sections from BxPC-3 and MIA PaCa-2 xenografts to validate CAF clusters observed in scRNA-seq. Results: Distinct CAF clusters were identified in the xenograft tumors, including LRRC15+ CAFs, RGS5+ CAFs, and inflammatory CAFs (iCAFs). LRRC15+ CAFs were predominant in tumors derived from the epithelial subtype (BxPC-3), while RGS5+ CAFs were enriched in tumors from the mesenchymal subtype (MIA PaCa-2). LRRC15+ CAFs exhibited a myofibroblastic CAF (myCAF) phenotype characterized by extracellular matrix production, with high expression of Lrrc15, Postn, and Fbln1. RGS5+ CAFs expressed canonical pericyte markers such as Rgs5 and Cox4i2, along with CAF-associated genes including Acta2. These CAF clusters also showed distinct expression patterns of collagens and secreted factors. In particular, Col11a1, Col12a1, and Wnt5a were upregulated in LRRC15+ CAFs, while Col4a1, Col10a1, and Tgfb1 were upregulated in RGS5+ CAFs. Spatial transcriptomics confirmed that gene modules associated with Lrrc15 and Rgs5, inferred from hdWGCNA, were differentially expressed between Acta2-positive stromal regions of epithelial and mesenchymal PDACs. Conclusions: These results suggest that epithelial and mesenchymal PDAC subtypes directly shape distinct CAF populations. Notably, the enrichment of RGS5+ CAFs in mesenchymal tumors may underlie their metastatic potential and poor clinical outcomes. Citation Format: Kyu Min Lim, Soo Been Park, Jung-hwan Park, Yoo Keung Tae, Hee Won Choi, In Rae Cho, Hee Seung Lee, Jung Hyun Jo. Distinct cancer-associated fibroblast populations induced by epithelial and mesenchymal PDAC subtypes in a xenograft model abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research—Emerging Science Driving Transformative Solutions; Boston, MA; 2025 Sep 28-Oct 1; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85 (18Suppl₃): Abstract nr B105.
Lim et al. (2025) studied this question.