Selection of Mucosal associated invariant T cells (MAIT cells) by CD4+CD8+ thymocytes expressing both MR1 and Slam molecules leads to a specific differentiation program linked to expression of the transcription factor PLZF, hallmark of innate like T cells. In mice, MAIT cells undergo subsequent differentiation into MAIT1 (T-bet+) or MAIT17 (RORγt+) subsets. The molecular mechanisms of MAIT cell differentiation and subset choice are poorly known.
We are studying this issue through four complementary approaches: 1) Using scRNAseq we compared the development of 5-OP-RU:MR1 tetramer+ thymocytes in 6 mammalian species to evidence the commonalities and differences in gene expression during MAIT cell development. 2) Using coupled snRNAseq and snATACseq of 5-OP-RU:MR1 tetramer+ murine thymocytes, we precisely defined the chronology of chromatin opening and gene expression along MAIT subset development. 3) scVDJ analysis of 5-OP-RU specific murine thymocytes allowed us to show that the characteristics of the TCRs are not involved in the MAIT1 vs MAIT17 subset choice. 4) Analysis of MAIT and NKT development in the thymocytes of mice from the collaborative cross evidenced variable numbers of MAIT and NKT cells which were linked to different genomic regions. Type 1 and type 17 subsets were found in all strains. However, the proportions were variable from one strain to another and were also associated with distinct genomic regions. Interestingly, MAIT cells did not mature to a CD44hi memory phenotype in the CC19 strain. Mixed bone-marrow chimeras indicated that the absence of maturation was intrinsic to the CC19 progenitors. The phenotype was mapped to chromosome 17. A similar phenotype was observed in the NOD strain as 5-OP-RU:MR1 tetramer+ also did not mature to a memory phenotype in the thymus as further confirmed using scRNAseq analysis. The exact mechanisms are being deciphered.