T cell Tolerance to Enteric Commensal Bacteria

PROJECT SUMMARY The gastrointestinal tract is colonized by an enormous collection of commensal bacteria living in harmony with the host. This poses a challenge for the immune system which must promote tolerance to beneficial bacteria species while still providing protection against pathogenic species. Indeed, a breakdown in

such discrimination is thought to be a major underlying cause of inflammatory bowel disease (IBD). Unlike self-antigens, antigens derived from commensal microbiota are unlikely to be presented in the thymus to impact central T cell tolerance. Rather, specific tolerance to these antigens must rely exclusively on

peripheral mechanisms acting within the immune environment of the gut. However, these mechanisms and the quality of the tolerance they mediate are unclear. To better investigate these processes, our lab has developed peptide:MHCII tetramer reagents that enable us to directly identify rare gut CD4+ T cells with

specificity to immunodominant epitopes from several different commensal bacteria species in mice. Our preliminary studies support varied roles for deletion, Treg, and Tr1 cell development depending on the bacteria species. To provide better resolution of commensal antigen-specific T cell phenotypes as well as the

heterogeneity of these phenotypes within the overall antigen-specific population, we are combining our use of tetramers with single cell RNA-seq transcriptomics to comprehensively define phenotypic and clonal heterogeneity within distinct commensal antigen-specific CD4+ T cell populations. The overarching goal of this project is to understand the mechanisms by which T cells maintain immune

tolerance to specific commensal bacteria of the gastrointestinal tract so that they may ultimately be manipulated for therapeutic benefit. We hypothesize that tolerance to commensal bacterial antigens is maintained by multiple CD4+ T cell fates, each making unique but overlapping functional contributions that

collectively establish durable tolerance in the face of the dynamic gut environment. We will test this hypothesis by 1) defining developmental fates for commensal bacterial antigen-specific CD4+ T cells that contribute to immune tolerance, and 2) characterizing the function of commensal antigen-specific regulatory T cell subsets.