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Tuning of human MAIT cell activation by commensal bacteria species and MR1-dependent T-cell presentation

Mucosal Immunology (2018) | Download Citation



Human mucosal-associated invariant T (MAIT) cell receptors (TCRs) recognize bacterial riboflavin pathway metabolites through the MHC class 1-related molecule MR1. However, it is unclear whether MAIT cells discriminate between many species of the human microbiota. To address this, we developed an in vitro functional assay through human T cells engineered for MAIT-TCRs (eMAIT-TCRs) stimulated by MR1-expressing antigen-presenting cells (APCs). We then screened 47 microbiota-associated bacterial species from different phyla for their eMAIT-TCR stimulatory capacities. Only bacterial species that encoded the riboflavin pathway were stimulatory for MAIT-TCRs. Most species that were high stimulators belonged to Bacteroidetes and Proteobacteria phyla, whereas low/non-stimulator species were primarily Actinobacteria or Firmicutes. Activation of MAIT cells by high- vs low-stimulating bacteria also correlated with the level of riboflavin they secreted or after bacterial infection of macrophages. Remarkably, we found that human T-cell subsets can also present riboflavin metabolites to MAIT cells in a MR1-restricted fashion. This T–T cell-mediated signaling also induced IFNγ, TNF and granzyme B from MAIT cells, albeit at lower level than professional APC. These findings suggest that MAIT cells can discriminate and categorize complex human microbiota through computation of TCR signals depending on antigen load and presenting cells, and fine-tune their functional responses.

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We thank Dr. David Mellert (Jackson Laboratory) for critical reading and critiques, Dr. Victor Torres (NYU School of Medicine) and Dr. Bo Shopsin (NYU School of Medicine) for insightful discussions and suggestions, Drs. Victor Torres, Bo Shopsin, Michael Otto (NIH) and George Weinstock (Jackson Laboratory) for several bacteria strains, and NIH tetramer facility for the MR1 tetramers. The research in this study was supported by the National Institute of Health (NIH) grant R01AI121920 to D.U, NIH Grant U54NS105539 to D.U., J.O. and X.Y. and the Jackson Laboratory Director’s Innovation Fund to D.U and J.O.

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  1. Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA

    • Cihan Tastan
    • , Ece Karhan
    • , Wei Zhou
    • , Elizabeth Fleming
    • , Anita Y. Voigt
    • , Meghan Horne
    • , Lindsey Placek
    • , Lina Kozhaya
    • , Julia Oh
    •  & Derya Unutmaz
  2. Department of Microbiology, NYU School of Medicine, New York, NY, 10016, USA

    • Cihan Tastan
  3. Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA

    • Xudong Yao
    •  & Lei Wang


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C.T. designed, performed and analyzed the experiments. W.Z. and J.O. performed bioinformatics studies. A.Y.V. performed CRISPR-repression experiments in E. coli. E.K. helped T–T interaction assays and performed intracellular staining. M.H., L.P., E.K. and L.K. prepared human primary T cells for the experiments. E.F. performed growth of the bacterial species. M.H. and L.K. isolated and prepared healthy human adult PBMCs. X.Y and L.W. performed mass spec analysis of riboflavin in bacteria supernatants. W.Z., A.Y.V, M.H., E.F., L.P., E.K. and L.K. provided helpful discussions in experimental design. C.T., J.O. and D.U. wrote the manuscript. J.O. and D.U. led the investigation and contributed to the design and interpretation of the data.

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The authors declare no competing interests.

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Correspondence to Derya Unutmaz.

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