A conserved transcriptional program for MAIT cells across mammalian evolution [Mdomestica_thymus_MAIT]
Mucosal-Associated Invariant T (MAIT) cells recognize the riboflavin pathway-derived metabolite 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU) presented by the MHC-Ib molecule MR1. Both MR1 and the T cell receptor genes used by MAIT cells are under strong evolutionary pressure in mammals, suggesting an important role of 5-OP-RU-specific T cells across species. In humans and mice, MAIT cells acquire distinctive effector functions linked to the expression of the master transcription factor ZBTB16 (PLZF) during thymic development. Conservation of a unique differentiation program in 5-OP-RU-specific T cells from other species is unclear. Here, we used single-cell RNA sequencing to characterize the development of 5-OP-RU-specific T cells in 6 species spanning 110 million years of mammalian evolution. Cross-species comparative analyses revealed a conserved sequence of transcriptional events underlying the maturation of 5-OP-RU-specific thymocytes, marked by the early expression of ZBTB16 in all species. MAIT cells also co-expressed the transcription factors TBX21 (Tbet) and RORC (RORgt) in human, sheep, cattle and opossum. By contrast, Tbet and RORgt were expressed by distinct subsets of MAIT cells in the thymus of rodents, including pet mice and >30 genetically diverse mouse strains, dismissing a laboratory mouse artifact. In mice, RORgt+ MAIT cells further matured in the mesenteric lymph nodes and intestines to acquire a transcriptional program remarkably conserved in MAIT cells from non-rodent species and characterized by co-expression of type 1 and type 17 effector genes, but also genes associated with cytotoxicity and tissue repair. Thus, we define a deeply conserved transcriptional program for 5-OP-RU-specific T cells, which may help understand their functions. Overall design: Mdomestica_thymus_MAIT