Cognate antigen recognition defines intestinal Treg specialization and stability

Regulatory CD4 T cells (Treg) confer non-overlapping functions in intestinal immune tolerance, tissue maintenance, repair, and regeneration. Cytokines and T cell receptor (TCR) signals, in combination with environmental cues, direct Treg proliferation and differentiation. However, how intestinal antigens shape intestinal Treg populations, their specialization and stability remain unknown. Here we show that only Treg bearing specific TCRs expand in the colon, resulting in highly oligoclonal Treg populations. Treg TCR repertoires are private, but crucially, when the same repertoire of polyclonal Treg was transferred into different recipients, the same clones expanded in each recipient, suggesting that cognate TCR-antigen interactions drive colonic Treg accumulation. Expanded Treg clones were correlated with Treg stability and individual transcriptional states that were maintained in different recipients irrespective of the presence or absence of intestinal inflammation. Our data suggest a role for antigen recognition in the selection and functional specialization of intestinal Treg. We speculate that the therapeutic use of Treg must take into account TCR context-mediated properties to optimise Treg stability and function in vivo. To investigate how the Treg TCR repertoire is connected with Treg function in the murine large intestine, the adoptive T cell transfer model of colitis, in which naive CD4+ T cells are either transfered with or without Treg was combined with scVDJ sequencing. To follow the same Treg clone in multiple Rag2 KO recipients, the Treg cells were previously expanded in vitro.