Koay, Hui-FernGherardin, Nicholas AEnders, AnselmLoh, LiyenMackay, Laura KAlmeida, Catarina FRuss, Brendan ENold-Petry, Claudia ANold, Marcel FBedoui, SammyChen, ZhenjunCorbett, Alexandra JEckle, Sidonia B GMeehan, Bronwynd'Udekem, YvesKonstantinov, Igor ELappas, MarthaLiu, LigongGoodnow, Chris CFairlie, David PRossjohn, JamieChong, Mark MKedzierska, KatherineBerzins, Stuart PBelz, Gabrielle TMcCluskey, JamesUldrich, Adam PGodfrey, Dale IPellicci, Daniel G2019-02-141529-2908http://hdl.handle.net/1885/155714Mucosal-associated invariant T cells (MAIT cells) detect microbial vitamin B2 derivatives presented by the antigen-presenting molecule MR1. Here we defined three developmental stages and checkpoints for the MAIT cell lineage in humans and mice. Stage 1 and stage 2 MAIT cells predominated in thymus, while stage 3 cells progressively increased in abundance extrathymically. Transition through each checkpoint was regulated by MR1, whereas the final checkpoint that generated mature functional MAIT cells was controlled by multiple factors, including the transcription factor PLZF and microbial colonization. Furthermore, stage 3 MAIT cell populations were expanded in mice deficient in the antigen-presenting molecule CD1d, suggestive of a niche shared by MAIT cells and natural killer T cells (NKT cells). Accordingly, this study maps the developmental pathway and checkpoints that control the generation of functional MAIT cells.Supported by the National Health and Medical Research Council of Australia (1083942, 1013667 and 1016629; CDF 1035858 to A.E.; ECF 1054431 to D.G.P.; Senior Principal Research Fellowships 1020770 and 1027369 to D.I.G. and D.P.F.; Australia Fellowship AF50 to J.R.; CDF2 Fellowship 1047025 to M.C.; CDF2 Fellowship 1023294 to K.K.; and CDF1 Fellowship 1106004 to L.K.M.), the Australian Research Council (CE140100011 and LE110100106; Future Fellowship FT140100278 to A.P.U.), the Leukaemia Foundation of Australia (Postgraduate Scholarship for N.A.G.), the National Heart Foundation of Australia (Future Leader Fellowship for C.A.N.-P.), the Hudson Institute (Star Recruitment Fellowship for M.F.N.) and the Ritchie Centre (Victor Yu Fellowship for M.F.N.).application/pdfen-AU© 2016 Nature Americaanimalsantigens, cd1dbiomarkerscell differentiationgene expression profilinggene expression regulationhumansimmunophenotypinglymphoid progenitor cellsmalemicemice, knockoutmicrornasmucosal-associated invariant t cellsthymus gland2016-1110.1038/ni.3565