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

Abstract

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.

Keywords: cytotoxic CD4 T cells; human CD4+CD8A+ T cells; inflammatory bowel disease; intestinal inflammation; single-cell RNA sequencing.