T cell receptors and gene expression from intestinal intraepithelial lymphocytes

Intestinal intraepithelial lymphocytes (IELs) form an unconventional T cell population delineated by agonistic selection in the thymus, after which they reside in the gut where it is thought they contribute in the surveillance, homeostasis, and repair of the mucosal epithelium. We utilized genetic models and various interventions (special diets, germ free housing, antibiotic treatment) to identify the specificity determinants that recruit T cells into the IEL lineage. Integrating T cell receptor (TCR) repertoire sequencing and transcriptional profiling, this study identifies characteristic TCR features of induced CD4-, CD8-, and natural-IEL subsets in mice and humans.