Human intestinal tissue-resident memory 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. Here, we investigate transcriptional and functional heterogeneity of human T(RM) cells through study of donor-derived T(RM) cells from intestinal transplant recipients. Single-cell transcriptional profiling identifies two transcriptional states of CD8(+) T(RM) cells, delineated by ITGAE and ITGB2 expression. We define a transcriptional signature discriminating these populations, including differential expression of cytotoxicity- and residency-associated genes. Flow cytometry of recipient-derived cells infiltrating the graft, and lymphocytes from healthy gut, confirm these CD8(+) T(RM) phenotypes. CD8(+) CD69(+)CD103(+) T(RM) cells produce interleukin-2 (IL-2) and demonstrate greater polyfunctional cytokine production, whereas β2-integrin(+)CD69(+)CD103(−) T(RM) cells have higher granzyme expression. Analysis of intestinal CD4(+) T cells identifies several parallels, including a β2-integrin(+) population. Together, these results describe the transcriptional, phenotypic, and functional heterogeneity of human intestinal CD4(+) and CD8(+) T(RM) cells.