Circulating and Tissue-resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function is Altered During Inflammation

Background & Aims Interactions between commensal microbes and the immune system are tightly regulated and maintain intestinal homeostasis, but little is known about these interactions in humans. We investigated responses of human CD4+ T cells to the intestinal microbiota. We measured the abundance of T cells in circulation and intestinal tissues that respond to intestinal microbes and determined their clonal diversity. We also assessed their functional phenotypes and effects on intestinal resident cell populations, and studied alterations in microbe-reactive T cells in patients with chronic intestinal inflammation. Methods We collected samples of peripheral blood mononuclear cells (PBMC) and intestinal tissues from healthy individuals (controls, n=13–30) and patients with inflammatory bowel diseases (IBD, total n=119; 59 with UC and 60 with Crohn’s disease). We used 2 independent assays (CD154 detection and carboxy-fluorescein succinimidyl ester dilution assays) and 9 intestinal bacterial species (Escherichia coli, Lactobacillus acidophilus, Bifidobacterium animalis subsp. lactis, Faecalibacterium prausnitzii, Bacteroides vulgatus, Roseburia intestinalis, Ruminococcus obeum, Salmonella typhimurium and Clostridium difficile) to quantify, expand, and characterize microbe-reactive CD4+ T cells. We sequenced T-cell receptor vβ genes in expanded microbe-reactive T-cell lines to determine their clonal diversity. We examined the effects of microbe-reactive CD4+ T cells on intestinal stromal and epithelial cell lines. Cytokines, chemokines, and gene expression patterns were measured by flow cytometry and quantitative PCR. Results Circulating and gut-resident CD4+ T cells from controls responded to bacteria at frequencies of 40–4000 per million for each bacterial species tested. Microbiota-reactive CD4+ T cells were mainly of a memory phenotype, present in PBMCs and intestinal tissue, and had a diverse T-cell receptor vβ repertoire. These cells were functionally heterogeneous, produced barrier protective cytokines, and stimulated intestinal stromal and epithelial cells via interleukin 17A (IL17A), interferon gamma, and tumor necrosis factor. In patients with IBD, microbiota-reactive CD4+ T cells were reduced in the blood compared to intestine; T-cell responses we detected had an increased frequency of IL17A production compared to responses of T cells from blood or intestinal tissues of controls. Conclusions In an analysis of PBMC and intestinal tissues from patients with IBD vs controls, we found that reactivity to intestinal bacteria is a normal property of the human CD4+ T-cell repertoire, and does not necessarily indicate disrupted interactions between immune cells and the commensal microbiota. T-cell responses to commensals might support intestinal homeostasis, by producing barrier-protective cytokines and providing a large pool of T cells that react to pathogens.