MAIT and NKT cells are innate-like T cells that are selected by double-positive thymocytes to become memory (CD44hi) type-1 (T-bet+) or type-17 (Rorgt+) cells. Despite this common development pathway, mature MAIT and NKT cells differ in subset distribution and tissue location in mice. Moreover, MAIT cells are abundant in human and scarce in mice while the opposite is true for NKT cells. We previously showed that TCR specificity is not involved in the choice of type 1 or 17 fate suggesting the existence of other mechanisms that may account for their distinct distribution, localization, and relative abundance across species.
To investigate the factor(s) underlying the differences between MAIT and NKT development, we analyzed Collaborative Cross (CC) mouse strains looking for an uncoupling between MAIT and NKT cell features. Comparative analysis across multiple CC strains revealed variability in both the number and maturation status of MAIT and NKT cells. Notably, in one particular CC strain, MAIT cell maturation was defective, while NKT development remained largely unaffected, suggesting that distinct genetic factors regulate MAIT and NKT cell maturation. Bone marrow transplantation from this strain into irradiated host mice demonstrated the hematopoietic-intrinsic nature of the defect in MAIT cell maturation. Subsequent quantitative trait locus (QTL) analysis identified a specific genomic region strongly correlated with this phenotype. A maturation defect in MAIT, but not NKT, cells was also found in NOD mice. Comparative scRNA-seq analysis of thymic MAIT cells from these strains revealed that several genes encoded in the previously identified chromosomal region were differentially expressed at the immature stages. Further analysis of common polymorphisms correlating with the MAIT cell maturation defect identified several candidate genes, which will be tested through CRISPR/Cas9 genetic modification. Thus, analysis of the CC strains unraveled unexpected mechanisms involved in the development of innate-like T cells.