Single Cell Sequence Analysis Reveals Mouse Mait Cell Diversity At Steady State And After Infection

Abstract Mucosal-associated invariant T (MAIT) cells are innate-like T lymphocytes that recognize vitamin B metabolites. We have performed single-cell RNA (sc-RNA) sequencing of MAIT cells from thymus, liver, spleen and lung using 10× single-cell genomics, where we sequenced more than 7,000 cells and identified 10 clusters by unbiased clustering. MAIT cells from the different organs are distributed in most of the clusters; except two clusters were lung MAIT cell specific and another consisted of cells exclusively from thymus. The lung specific cluster reveals a tissue residency gene signature. We compared the gene expression profile of MAIT cells with iNKT (invariant natural killer T) cells. Our data reveal that most mouse MAIT cells have a Th17/NKT17–like gene signature (MAIT17), although there are some with Th1/ NKT1-like transcriptomes (MAIT1), particularly in liver and spleen. A Th2/NKT2 gene expression profile was not observed. The thymus specific cluster showed a gene expression profile similar to the most immature or progenitor iNKT cells (NKT0), consistent with other data suggesting a unique thymus differentiation pathway for mouse MAIT that is similar to iNKT cells. We also performed scRNA sequencing of MAIT cells after bacterial infection in the lung. Our results indicate that after infection the transcriptome of lung MAIT cells changes significantly at day 6 and remains altered at day 40. Therefore, our study reveals that although mouse MAIT cells are predominantly Th17 cells and to a lesser extent Th1 cells, there is some heterogeneity and there are profound and relatively long-term changes in transcriptional signatures after infection.