Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation

we compare the TCR repertoires of MAIT1 and MAIT17 cells from the mouse thymus using 5’ scRNAseq and scTCRseq of MR1:5-OP-RU tetramer positive thymocytes. A thorough analysis of TCR features between MAIT sub-populations did not show any difference between the repertoires of MAIT1 and MAIT17 subsets. Quantitative simulation of clonotype distributions of MAIT1 and MAIT17 cells allowed us to investigate the role of TCR characteristics in MAIT fate choice, and to pinpoint the stage at which lineage commitment occurs. Our results indicate that the TCR characteristics are not instructive in MAIT lineage choice and that MAIT1/17 commitment takes place during MAIT cell proliferation in the thymus. Finally, we performed analogous analysis of a published scRNA-seq and scTCR-seq dataset of iNKT from mouse thymus and demonstrated that our conclusions are also relevant for iNKT1 vs iNKT17 fate commitment. Cd3e-/-Mr1-/- mice were sublethally irradiated (420 rads) and reconstituted intravenously with 1 million bone marrow cells from B6-MAITCast RorcGFP mice. Seven weeks after reconstitution, thymus was harvested for further analysis of MR1:5-OP-RU restricted thymocytes. Single-cell suspension of thymus was obtained