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

Abstract

Abstract Tissue-resident memory CD8 +T (T RM) 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 +T RMpopulations 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 +T RMin the small intestine epithelia are well-described, findings are often generalized to the whole gut, thus obscuring potential differences in CD8 +T RMin the much-less studied small intestine lamina propria and colon compartments. We thereby characterized CD8 +T RMin the four intestinal layers using single cell RNA-sequencing and flow cytometry. We show that CD8 +T RMacross the intestinal compartments exhibit differences in the expression of surface molecules, cytokines, granzymes, and transcription factors. For example, small intestine intraepithelial CD8 +T RMproduce the highest levels of granzymes, whereas colon intraepithelial CD8 +T RMhave 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 T RMformation in the skin, liver, and kidney. Our data demonstrate that Eomes is dispensable for CD8 +T RMformation in both the small intestine and colon. By contrast, following CD8 +T RMformation, Eomes plays a critical role in promoting the maintenance of established CD8 +T RMin the small intestine, but not in the colon. Together, our study provides new insights into intestinal CD8 +T RMheterogeneity and differential transcriptional regulation of intestinal T RMformation 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).