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

Tissue-resident memory T (T) cells provide key adaptive immune responses in infection, cancer, and autoimmunity. However, transcriptional heterogeneity of human intestinal T cells remains undefined. Here, we investigate transcriptional and functional heterogeneity of human T cells through study of donor-derived T cells from intestinal transplant recipients. Single-cell transcriptional profiling identifies two transcriptional states of CD8 T 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 phenotypes. CD8 CD69CD103 T cells produce interleukin-2 (IL-2) and demonstrate greater polyfunctional cytokine production, whereas β2-integrinCD69CD103 T 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 cells.