Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I

  1. Owen Leddy
  2. Forest M White
  3. Bryan D Bryson  Is a corresponding author
  1. Massachusetts Institute of Technology, United States

Abstract

CD8+ T cell recognition of Mycobacterium tuberculosis (Mtb)-specific peptides presented on major histocompatibility complex class I (MHC-I) contributes to immunity to tuberculosis (TB), but the principles that govern presentation of Mtb antigens on MHC-I are incompletely understood. In this study, mass spectrometry (MS) analysis of the MHC-I repertoire of Mtb-infected primary human macrophages reveals that substrates of Mtb's type VII secretion systems (T7SS) are overrepresented among Mtb-derived peptides presented on MHC-I. Quantitative, targeted MS shows that ESX-1 activity is required for presentation of Mtb peptides derived from both ESX-1 substrates and ESX-5 substrates on MHC-I, consistent with a model in which proteins secreted by multiple T7SSs access a cytosolic antigen processing pathway via ESX-1-mediated phagosome permeabilization. Chemical inhibition of proteasome activity, lysosomal acidification, or cysteine cathepsin activity did not block presentation of Mtb antigens on MHC-I, suggesting involvement of other proteolytic pathways or redundancy among multiple pathways. Our study identifies Mtb antigens presented on MHC-I that could serve as targets for TB vaccines, and reveals how the activity of multiple T7SSs interacts to contribute to presentation of Mtb antigens on MHC-I.

Data availability

The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2022) partner repository with the dataset identifiers PXD037837 (DDA data) and PXD037843 (SureQuant data). Microscopy data analysis scripts are available on GitHub at https://github.com/oleddy/local_correlation_analysis.

The following data sets were generated

Article and author information

Author details

  1. Owen Leddy

    Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Forest M White

    Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1545-1651
  3. Bryan D Bryson

    Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
    For correspondence
    bryand@mit.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1716-6712

Funding

National Institutes of Health (R35GM142900-01)

  • Owen Leddy
  • Bryan D Bryson

National Institutes of Health (R01A1022553)

  • Owen Leddy
  • Bryan D Bryson

National Institute of Environmental Health Sciences (P42 ES027707)

  • Owen Leddy
  • Forest M White

Center for Precision Cancer Medicine

  • Owen Leddy
  • Forest M White

National Institutes of Health (P30 AI06035)

  • Owen Leddy
  • Bryan D Bryson

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Bavesh D Kana, University of the Witwatersrand, South Africa

Version history

  1. Preprint posted: August 30, 2022 (view preprint)
  2. Received: October 10, 2022
  3. Accepted: April 17, 2023
  4. Accepted Manuscript published: April 19, 2023 (version 1)
  5. Version of Record published: May 4, 2023 (version 2)

Copyright

© 2023, Leddy et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Owen Leddy
  2. Forest M White
  3. Bryan D Bryson
(2023)
Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I
eLife 12:e84070.
https://doi.org/10.7554/eLife.84070

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https://doi.org/10.7554/eLife.84070

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