Microbiota focus the colonic regulatory T cell repertoire

Key aspects of intestinal T cells including their antigen specificity, their selection by the microbiota and other intestinal antigens and the contribution of individual T cell clones to regulatory and effector functions are unresolved. We have modified the adoptive transfer colitis model based on the transfer of clonally defined effector (Teff) (PMID: 34582747) and T regulatory (Treg) populations, i.e. different recipients were transferred with collections of T cells comprising identical T cell clones. T cell populations accumulating in the recipient colon were analyzed by flow cytometry, TCR repertoire analysis and single cell sequencing. Accumulation of in vitro expanded Teff and Treg clones was harmonized in independent recipients, i.e. expanded clones detected in one recipient were also expanded in other recipients resulting in highly similar T cell repertoires shared between individual mice. To explore the impact of the microbiota on colonic T cell repertoires, clonally defined regulatory T cells were transferred into recipients colonized with different microbiota composition. We compared recipients colonized with the microbiota present in SPF mice housed in RWTH Aachen animal facility (AA, Aachen microbiota), mice colonized with Hamburg (HH) microbiota and mice colonized with Hamburg microbiota and additionally gavaged with Yale (YY) microbiota 3-4 week before adoptive T cell transfers. Microbiota composition was analyzed by 16S rRNA gen amplicon sequencing of mice before adoptive T cell transfers. We observed that differences in the recipients microbiota composition forced selection of different regulatory T cell repertoires in the colon. Focusing of the repertoire was more apparent in Aachen (AA) and Yale (YY) microbiota, whereas recipients colonized with Hamburg (HH) microbiota showed overall lower repertoire similarity between recipient (yet unpublished). We speculate that dominant T cell clones might provide a therapeutic target in human inflammatory bowel disease.