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

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.

ESAT-6 undergoes self-association at phagosomal pH and an ESAT-6-specific nanobody restricts M. tuberculosis growth in macrophages

“…The second functional assay we performed was based on continuous growth measurement of luminescent LuxABCDE-expressing Mtb ( Andreu et al, 2010 ; Leddy et al, 2023 ). We prepared stable THP-1 cell lines with cytoplasmic expression of E11rv or an isotype nanobody.…”

“…Because E11rv showed functional effects both when added in the media and when expressed inside the cell cytoplasm, it suggests a significant amount of communication between Mtb inside the phagosome and other compartments of the cell. This is consistent with the findings of many other studies which show numerous putative activities for ESAT-6 such as induction of apoptosis ( Behura et al, 2019 ; Choi et al, 2010 ; Lim et al, 2016 ; Yang et al, 2015 ), inhibition of interferon-γ production ( Kumar et al, 2012 ; Peng et al, 2011 ), inhibition of autophagy ( Dong et al, 2016 ; Romagnoli et al, 2012 ; Yabaji et al, 2020 ), inhibition of antigen presentation ( Sreejit et al, 2014 ), induction of type I interferon ( Jang et al, 2018 ; Lienard et al, 2020 ), and a more recent study showing an ESX-1-dependent mechanism for incorporation of Mtb antigens into MHC-I presentation via cytosolic antigen processing ( Leddy et al, 2023 ). Most of these functions rely on ESAT-6 getting into the cytoplasm, and this may occur via disruptions in the phagosomal membrane to establish two-way communication between compartments, or by complete phagosomal escape of Mtb into the cytoplasm and subsequent secretion of ESAT-6 directly into the cytoplasm.…”

Birinapant Reshapes the Tumor Immunopeptidome and Enhances Antigen Presentation

“…Although most immunopeptides are derived from normal proteins originally existing in cells and unable to elicit an immune response, a small proportion of immunopeptides are derived from CTAs or TSAs; therefore, they are more easily recognized as non-self-antigens by T lymphocytes or antigen-presenting cells, thereby enhancing anti-tumor immunity. In the past, many excellent studies have taken advantage of immunopeptidomics to directly identify antigens as personalized therapeutic targets for clinical treatment [30,31,60,61]. However, our work pioneers the use of immunopeptidomics to explore the regulatory mechanism of Birinapant in anti-tumor immunity.…”

The functional response of human monocyte-derived macrophages to serum amyloid A and Mycobacterium tuberculosis infection

“…The adaptive immune response to Mtb is primarily mediated by CD4 + T-cells, which recognize tubercle bacilli antigens presented by antigen-presenting cells (APCs) e.g. Ag85B ( 8 ), a wide range of peptides from proteins of secretion systems ESX-1, ESX-3, ESX-5 and also membrane-bound protease FtsH and putative conserved ATPase ( 9 , 10 ). As for the group of Mtb non-protein components presented by APC, it has been shown to belong to it monoglycosolated mycolic acids, phospatydilinositols (e.g.…”