22Mucosal-associated invariant T (MAIT) cells are MR1-restricted innate-like T cells 23 conserved across mammalian species, including mice and humans. By sequencing RNA 24 from sorted MR1-5-OP-RU tetramer + cells derived from either human blood or murine 25 lungs, we define the basic transcriptome of an activated MAIT cell in both species and 26 demonstrate how this profile changes during resolution and reinfection phases of infection. 27We observe strong similarities between MAIT cells in humans and mice. Compared with 28 previously published T cell transcriptomes, MAIT cells displayed most similarity to iNKT 29 cells when activated, but to gd T cells, after resolution of infection. In both species 30 activation leads to strong expression of pro-inflammatory cytokines and chemokines, and 31 also a strong tissue repair signature, recently described in murine commensal-specific H2-32 M3-restricted T cells. These data define the requirements for, and consequences of, MAIT 33 cell activation, revealing a tissue repair phenotype expressed upon MAIT cell activation in 34 both species. 35 36 Key words 37 Mucosal-associated invariant T cell, T cell, transcriptome, MHC-related protein 1, 38 activation, lung, human, mouse, riboflavin. 39 40 3 Mucosal-associated invariant T (MAIT) cells are innate-like T cells which express a 'semi-41 invariant' ab T cell receptor (TCR) and recognise metabolic derivatives of riboflavin 42 biosynthesis 1-3 presented on the restriction molecule major histocompatibility complex 43 (MHC)-related protein-1 (MR1) 4,5 . These antigens, which include the potent MAIT cell 44 ligand 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU) 6 , are produced by a 45 wide variety of bacteria, mycobacteria and yeasts 1,7 , but are absent from mammals, and 46 therefore allows host -pathogen discrimination. MAIT cells have a strong pro-47 Our data reveal strong similarities between MAIT cells in humans and in mice at a 64 transcriptional level, show that MAIT cells displayed the closest similarities to invariant 65 natural killer T (iNKT) cells when activated, but after resolution of infection were more 66 comparable to gd T cells, and reveal a previously unknown tissue repair phenotype 67 expressed upon MAIT cell activation in both species. 68 69
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Activation requirements of MAIT cells in vivo 71First we aimed to test, systematically, the activation requirements of MAIT cells in vivo in 72 mouse lungs. We have previously shown that pulmonary MAIT cell frequencies in mice 73 can be markedly enhanced by intranasal administration of 5-OP-RU if it is co-administered 74 with S-[2,3-bis(palmitoyloxy)propyl] cysteine (Pam2Cys), CpG ODN 1668 or 75 polyinosinic:polycytidylic acid (poly I:C), which are agonists for TLR2/6, TLR9 and 76 TLR3, respectively. We therefore investigated agonists for each of the murine TLRs, using 77 the maximum doses presented in a literature review of previous studies of these 78 compounds. All animals received the relevant TLR intranasally on day 0. In experimental 79 animals...