Human intestinal tissue-resident memory CD8+ T cells comprise transcriptionally and functionally distinct subsets

Tissue-resident memory T (T RM ) cells provide key adaptive immune responses in infection, cancer, and autoimmunity. However transcriptional heterogeneity of human intestinal T RM cells remains undefined, and definitive markers of CD103-T RM cells are lacking. Here, we investigated transcriptional and functional heterogeneity of human T RM cells through the study of donor-derived intestinal T RM cells from intestinal transplant recipients. Single-cell transcriptional profiling identified four conventional T RM populations, with two distinct transcriptional states of CD8+ T RM cells, delineated by ITGAE and ITGB2 expression. We defined a transcriptional signature discriminating the two CD8+ populations, including differential expression of key residency-associated genes and cytotoxic molecules. Flow cytometry of recipient-derived cells infiltrating the graft and intestinal lymphocytes from healthy gut confirmed the two CD8+ T RM phenotypes, with β2-integrin acting as a CD103-CD8+ T RM marker. CD103+ CD8+ T RM cells produced IL-2, and demonstrated greater polyfunctional cytokine production, while β2-integrin+ CD69+ CD103-T RM cells had higher granzyme expression. Phenotypic and functional analysis of intestinal CD4+ T cells identified many parallels, including a distinct β2-integrin+ population. Together, these results describe the transcriptional, phenotypic, and functional heterogeneity of human intestinal T RM cells, and suggest a role for β2-integrin in T RM development. Summary Heterogeneity within human tissue-resident memory T (T RM ) cells is poorly understood. We show that transcriptionally, phenotypically, and functionally distinct CD4+ and CD8+ T RM subsets exist in the human intestine, and that β2-integrin expression identifies a distinct population of CD8+ T RM cells.