Abstract 7641: Decoding the spatial architecture of the immune microenvironment in mismatch repair-deficient colorectal carcinogenesis

Abstract Introduction: Lynch Syndrome (LS) is the most common hereditary colorectal cancer syndrome and is secondary to germline mutations in the mismatch repair (MMR) genes. Upon acquiring a second somatic hit, epithelial cells become MMR-deficient (MMRd) and accumulate high number of indel mutations in microsatellite loci, generating frameshift peptides (mutated neo-antigens). These neo-antigens activate robust immune responses and promote the expansion of specific T-cell clonotypes. However, the spatial organization of immune-epithelial compartments, and how MMR loss shapes early immune surveillance and escape, remains unclear. Methods: We dissected the immune microenvironment across the LS carcinogenesis axis using spatial transcriptomics to interrogate over 5,000 genes and 27 LS neoantigen-specific TCR clonotypes from our LS cohort at MD Anderson. We studied a total of 41 colorectal biopsies from 23 LS and 15 sporadic cases that were arranged in tissue microarrays and analyzed according to MMR status and malignancy, thus representing the largest spatial transcriptomic dataset generate to date in the context of LS. Results: Spatial profiling using Xenium platform identified distinct epithelial, immune, and stromal domains across LS and sporadic samples. Relative to normal mucosa, adenomas showed expansion of proliferating transit-amplifying epithelium, cancer stem-like cells, REG4+ epithelia, and a shift toward M2b-enriched macrophages, consistent with signs of early immune modulation. Neo-antigen-specific TCRs increased along the pathology axis and localized near dysplastic glands. MMRd adenomas displayed enrichment of activated monocytes/macrophages, plasma cells, inflammatory epithelium, and broad induction of interferon-responsive and cytokine-mediated pathways, thus reflecting strong innate and adaptative immunity. CD8+ T cells in MMRd lesions also expressed higher CTLA-4 levels, indicating activation-induced inhibitory signaling and early exhaustion. Compared to sporadic samples, LS tissues showed stronger immune activation, larger inflammatory and remodeling neighborhoods, and increased macrophage and plasma-cell infiltration. Multiple neo-antigen-specific TCR clones appeared exclusively in LS lesions, supporting enhanced immune surveillance. Conclusions: Spatial transcriptomics reveals coordinated remodeling of epithelial, immune, and stromal neighborhoods driven by pathology progression, MMR loss, and LS background. These spatial patterns provide insights into immune-epithelial interactions during LS neoplasm progression, establishing spatial biomarkers that may inform surveillance and immune interception strategies in hereditary gastrointestinal syndromes, such neo-antigen-based vaccination for boosting the expansion, infiltration, and effector function of tumor-specific T cells in MMRd cancers. Citation Format: Abel Martel-Martel, Nan Deng, Melissa W. Taggart, Araceli Garcia-Gonzalez, Jacklyn V. Thompson, Luigi Ricciardiello, Y. Nancy You, Selvi Thirumurthi, Krishna M. Sinha, Eduardo Vilar. Decoding the spatial architecture of the immune microenvironment in mismatch repair-deficient colorectal carcinogenesis [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 7641.