Human MAIT cells undergo clonal selection and expansion during thymic maturation and aging

Abstract Mucosal-associated invariant T (MAIT) cells harbor conserved T cell receptors (TCRs) recognizing riboflavin metabolites, yet exhibit substantial diversity similar to conventional memory T cells. However, the mechanisms shaping this diversity related to their thymic ontogeny remain unclear. Here we analyze 37 samples of human thymic MAIT cells across ages and compare them with other unconventional T cells, such as iNKT and γδ T cells. We find that CD27 and CD161 serve as common markers distinguishing the maturation stages of unconventional T cells such as MAIT, iNKT and Vγ9+Vδ2+ γδ T cells. Notably, CD161+ mature MAIT cells clonally expand proportionally to aging with the upregulation of genes associated with tissue residency. MAIT cell diversity is initially determined by diverse CDR3β sequences, which become reduced upon maturation. Furthermore, 25% of MAIT cells express polyclonal dual TCRα transcripts, suggesting they arise from double-positive thymocytes with random TCRα rearrangement. Collectively, these findings show that thymic MAIT cells undergo dynamic regulation of repertoire selection, similar to conventional T cells.