Intraepithelial T lymphocytes (T-IEL) are a large population of cytotoxic T cells that protect the small intestinal epithelium against pathogens. Based on ontogeny, T-IEL can be categorized into two major subsets: induced and natural. Natural T-IEL are agonistically selected in the thymus on self-antigens before migrating directly to the small intestine. Despite having self-reactive T cell antigen receptors (TCR), natural T-IEL are maintained in a tolerized state in the gut by unknown mechanisms. We therefore investigated TCR signaling in T-IEL using multiplexed fluorescent cell barcoding, phosphoproteomics and TCR signaling reporter mouse models, which revealed that TCR signaling is intrinsically suppressed in natural, but not induced, T-IEL. Unexpectedly, we discover that this cell intrinsic suppression was mediated through altered TCR signalosome components. Specifically, downregulation of the key signaling adaptor, Linker for activation of T cells (LAT) during thymic selection is a vital checkpoint for the development and tolerization of natural IELs. Thus, TCR signaling is rewired in self-reactive natural T-IEL to promote tolerance and prevent inappropriate inflammation in the gut.

One sentence summary Self-reactive natural intestinal intraepithelial T lymphocytes are developmentally tolerized by rewiring the T cell antigen receptor signaling pathway through the downregulation of the adaptor protein, LAT.