Single-cell transcriptomics of human gut T cells identifies cytotoxic CD4⁺CD8A⁺ T cells related to mouse CD4 cytotoxic T cells

Cytotoxic CD4⁺ T cells (CD4-CTLs) show the presence of cytolytic granules, which include the enzymes granzyme and perforin. The cells have a pathogenic and protective role in various diseases, including cancer, viral infection, and autoimmune disease. In mice, cytotoxic CD4⁺ T cells express CD8αα⁺ and reside in the intestine (mouse CD4⁺CTLs; mCD4-CTLs). The population of cytotoxic CD4⁺ T cells in the human intestine is currently unknown. Moreover, it is unclear how cytotoxic CD4 T cells change in patients with inflammatory bowel disease (IBD). Here, we aimed to identify cytotoxic CD4⁺ T cells in the human intestine and analyze the characteristics of the population in patients with IBD using single-cell RNA-seq (scRNA-seq). In CD4⁺ T cells, granzyme and perforin expression was high in humanMAIT (hMAIT) cells and hCD4⁺CD8A⁺ T cell cluster. Both CD4 and CD8A were expressed in hTreg, hMAIT, and hCD4⁺CD8A⁺ T cell clusters. Next we performed fast gene set enrichment analysis to identify cell populations that showed homology to mCD4CTLs. The analysis identified the hCD4⁺CD8A⁺ T cell cluster (hCTL-like population; hCD4-CTL) similar to mouse CTLs. The percentage of CD4⁺CD8A⁺ T cells among the total CD4⁺ T cells in the inflamed intestine of the patients with Crohn’s disease was significantly reduced compared with that in the noninflamed intestine of the patients. In summary, we identified cytotoxic CD4⁺CD8⁺ T cells in the small intestine of humans. The integration of the mouse and human sc-RNA-seq data analysis highlight an approach to identify human cell populations related to mouse cell populations, which may help determine the functional properties of several human cell populations in mice.