Human intestinal tissue-resident memory CD8+ T cells comprise transcriptionally and functionally distinct subsets
FitzPatrick MEB., Provine N., Garner L., Powell K., Amini A., Irwin S., Ferry H., Ambrose T., Friend P., Vrakas G., Reddy S., Soilleux E., Klenerman P., Allan P.
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.