Abstract 4989: SIPA1 deficiency reprograms mesenchymal stromal cells differentiaion and enhance the T cell immunity in the tumor microenvironment

Abstract Background: Sipa1 (Signal-induced proliferation-associated gene 1) is a Rap1 GTPase-activating protein implicated in cellular adhesion and immune regulation. However, its functions within the tumor microenvironment (TME) remain unclear. Sipa1-/- mice resistant to Bcr-Abl+ leukemia by coordinated interplay between MSCs and immune T cells. Methods: In this research, we clearly demonstrated that Sipa1-/- mice also showed increased resistance to different epithelial cancer cells such as MC38 intestinal and IPmN pancreatic cancers accompanied with increased stromal reaction and T cells infiltration. To clarify the stromal response in the anti-tumor mechanism, tumor resident mesenchymal stromal cells (MSCs) were sorted and subjected to Single cell RNA sequencing (scRNA-seq). Results: Three major MSCs subsets which have distinct gene expression profiles were identified: αSMA+ myofibroblast CAFs(myCAF), inflammatory CAFs(iCAF), and antigen-presenting CAFs(apCAFs). In Sipa1-/- tumor, iCAFs were significantly enriched, whereas the proportion of myCAFs decreased relative to WT tumors. Sipa1 expression levels across MSCs subsets followed the hierarchy myCAF > apCAFs > iCAF, suggesting a role for Sipa1 in MSCs lineage determination. These findings indicate that Sipa1 is required for MSCs differentiation into myCAF, and that Sipa1 deficient MSCs transdifferentiate from myCAF to iCAF. Functionally, MSCs from Sipa1-/- tumors exhibited significant upregulation of CXCL9 and immunohistochemical analyses demonstrated enhanced IFNγ-STAT1signaling in Sipa1-/- MSCs. In vitro experiments using MC38 cells and other stromal cells revealed that Sipa1 interacted directly with STAT1/pSTAT1 and suppresses its activation, suggesting that Sipa1 negatively regulates the IFNγ-STAT1 axis. Conclusion: All of the results demonstrate that Sipa1 is a critical regulator of MSCs-to-CAF differentiation and CAF functional programming in the TME. Sipa1 deficiency drives MSCs toward an iCAF-like, CXCL9 producing, immunostimulatory phenotype, which promoting enhanced T cell recruitment and anti-tumor immunity. These findings identify Sipa1 as a previously unrecognized stromal checkpoint controlling T cell responses against tumors and highlight Sipa1 as a potential therapeutic target to improve cancer immunotherapy. Citation Format: Yan Xu, Kentaro Sumida, Ryuhei Kawakami, Masakazu Hattori, Nagahiro Minato, . SIPA1 deficiency reprograms mesenchymal stromal cells differentiaion and enhance the T cell immunity in the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 4989.