Colon-Specific Signatures for Tissue Resident Memory T cells in Health and Colorectal Cancer 2258023

Abstract

Abstract Introduction Tissue-resident memory T cells (TRM) are one of the predominant T cell subsets in the human intestine, yet their role in intestinal anti-tumor immunity remains poorly defined. In colorectal cancer (CRC), TRM are positively prognostic. However, their baseline features during homeostasis are not well delineated, limiting our understanding of their behavior within and in response to CRC. Here, we leverage our unique human organ donor tissue resource spanning multiple mucosal and lymphoid tissues to define colon TRM signatures across diverse host variables (age, sex, BMI, CMV serostatus, etc.) and how these programs are altered in CRC. Methods We performed CITE-seq profiling of colon and blood samples from 8 human organ donors, integrated with a multi-tissue in-house single-cell dataset (24 donors) and publicly available datasets from healthy colon, CRC, and CRC-adjacent tissue (73 donors). We conducted differential gene expression (DE) analysis comparing colon TRM to those in the small intestine (jejunum) and other mucosal tissues. DE results, in combination with single-cell hierarchical Poisson factorization, were used to define homeostatic colon TRM gene signatures that were then queried in disease states. Results We found that colon CD4 and CD8 TRM express genes associated with tissue residency, stemness and quiescence (GPR15, LEF1, BACH2, IKZF2, ZEB1, TGFBR3) at significantly higher levels than jejunum TRM. We found that expression of these gene programs was lost in tumor-infiltrating TRM in both microsatellite stable and microsatellite instable CRC subtypes. Additionally, we identified several tumor-specific TRM gene co-expression programs, including an innate-cytotoxic program in CD8+ TRM enriched in tumor-adjacent tissue, and a CD4+ TEMRA-like program enriched in CRC but also present in tumor-adjacent and healthy tissue. Conclusion These data establish a comprehensive framework for dissecting how the tissue environment and tumor context shape features of human colon TRM. Funding Source Herbert Irving Comprehensive Cancer Center Human Tissue Immunity Initiative Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)