Small intestine and colon tissue-resident memory CD8+ T cells exhibit molecular heterogeneity and differential dependence on Eomesodermin

Abstract Tissue-resident memory CD8+T (TRM) cells are a subset of memory T cells positioned at barrier sites, critical for host defense against infection. Recent studies have begun to reveal substantial heterogeneity in CD8+ TRM populations across different tissues. The gut consists of four anatomically distinct compartments, the epithelia and lamina propria in the small intestine (siIEL, siLPL) and colon (cIEL, cLPL). While CD8+ TRM in the small intestine epithelia are well-described, findings are often generalized to the whole gut, thus obscuring potential differences in CD8+ TRM in the much-less studied small intestine lamina propria and colon compartments. We thereby characterized CD8+ TRM in the four intestinal layers using single cell RNA-sequencing and flow cytometry. We show that CD8+ TRM across the intestinal compartments exhibit differences in the expression of surface molecules, cytokines, granzymes, and transcription factors. For example, small intestine intraepithelial CD8+ TRM produce the highest levels of granzymes, whereas colon intraepithelial CD8+ TRM have the greatest capacity for cytokine production. We also uncover an unexpected, tissue-specific role for the T-box transcription factor Eomesodermin (Eomes), known to suppress TRM formation in the skin, liver, and kidney. Our data demonstrate that Eomes is dispensable for CD8+ TRM formation in both the small intestine and colon. By contrast, following CD8+ TRM formation, Eomes plays a critical role in promoting the maintenance of established CD8+ TRM in the small intestine, but not in the colon. Together, our study provides new insights into intestinal CD8+ TRM heterogeneity and differential transcriptional regulation of intestinal TRM formation vs. maintenance. Presenting author Y.H.L. is supported by the Canadian Institutes of Health Research (CIHR) Doctoral Foreign Study Award. This study is supported by grants from NIH (P01 AI132122).