Diverse MR1-restricted T cells in mice and humans

Hui-Fern Koay,Daniel G Pellicci,Calvin Xu,David P Fairlie,Dale I Godfrey,Zhe Zhao,Zhenjun Chen,Nicholas A Gherardin,Rebecca Seneviratna,James Mccluskey,Adam P Uldrich

doi:10.1038/s41467-019-10198-w

Abstract

Mucosal-associated invariant T (MAIT) cells express an invariant TRAV1/TRAJ33 TCR-α chain and are restricted to the MHC-I-like molecule, MR1. Whether MAIT cell development depends on this invariant TCR-α chain is unclear. Here we generate Traj33-deficient mice and show that they are highly depleted of MAIT cells; however, a residual population remains and can respond to exogenous antigen in vitro or pulmonary Legionella challenge in vivo. These residual cells include some that express Trav1+ TCRs with conservative Traj-gene substitutions, and others that express Trav1- TCRs with a broad range of Traj genes. We further report that human TRAV1-2- MR1-restricted T cells contain both MAIT-like and non-MAIT-like cells, as judged by their TCR repertoire, antigen reactivity and phenotypic features. These include a MAIT-like population that expresses a public, canonical TRAV36+ TRBV28+ TCR. Our findings highlight the TCR diversity and the resulting potential impact on antigen recognition by MR1-restricted T cells.

Highlights

Mucosal-associated invariant T (MAIT) cells express an invariant TRAV1/TRAJ33 T cell receptor (TCR)-α chain and are restricted to the major histocompatibility class (MHC)-I-like molecule, MR1
Traj33+/− mice were backcrossed to inhouse wild-type (WT) C57BL/6 mice for 2 generations and intercrossed to generate Traj33+/+ WT, Traj33+/− heterozygous and Traj33−/− homozygous KO littermates. These were tested for heterozygosity or homozygosity using PCR (Supplementary Fig. 1B) and showed the expected Mendelian inheritance ratio. As it was previously reported[28] that genetic deletion of Traj[18] via PGK-neor cassette insertion to generate Traj18−/− mice[29] inadvertently disrupted TCR rearrangements using genes encoding Jα regions upstream of Traj1828, we examined the Traj usage in CD4+CD8+ double positive (DP) thymocytes from Traj33−/− mice to determine whether this deletion impacted on other Traj gene usage
Through TCR sequencing studies of in vitro expanded cells, direct ex vivo analysis of residual MR1-restricted T cells and examination of in vivo microbial responsive cells, we have determined the presence of two groups of MR1-reactive T cells in Traj[33] KO mice: (i) TRAV1+ cells that used a small number of alternate TRAJ genes (TRAJ6, TRAJ9, TRAJ12, TRA30 and TRAJ40), allowing the formation of the conserved CDR3α loop comprising exactly 12 amino acids and tyrosine at position 95 (Y95α), and (ii) TRAV1− cells that used a broad range of TRAV and TRAJ genes, with variable CDR3α length and no tyrosine at position 95

Summary

Introduction

Mucosal-associated invariant T (MAIT) cells express an invariant TRAV1/TRAJ33 TCR-α chain and are restricted to the MHC-I-like molecule, MR1. We generate Traj33-deficient mice and show that they are highly depleted of MAIT cells; a residual population remains and can respond to exogenous antigen in vitro or pulmonary Legionella challenge in vivo These residual cells include some that express Trav1+ TCRs with conservative Traj-gene substitutions, and others that express Trav1- TCRs with a broad range of Traj genes. MAIT cells are typically defined by their expression of an invariant T cell receptor (TCR)-α chain[7] In humans, this consists of TRAV1-2 joined to TRAJ338,9, TRAJ12 or TRAJ2010,11 with little to no n nucleotide additions at the TCR-α complementarity determining region 3 (CDR3α) junction[9]. Like the MAIT TCR, MR1 is highly evolutionarily conserved with approximately 90% sequence homology between the MR1 α1 and α2 domains of humans and mice[17], further suggesting an important physiological role for the MAIT TCR–MR1 axis

Methods

Results

Conclusion