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

Summary 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.