Immunopeptidomics reveals determinants of <i>Mycobacterium tuberculosis</i> antigen presentation on MHC class I.

Abstract

CD8+ T cell recognition of <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>)-specific peptides presented on major histocompatibility complex class I (MHC-I) contributes to immunity to tuberculosis (TB), but the principles that govern presentation of <i>Mtb</i> antigens on MHC-I are incompletely understood. In this study, mass spectrometry (MS) analysis of the MHC-I repertoire of <i>Mtb</i>-infected primary human macrophages reveals that substrates of <i>Mtb</i>'s type VII secretion systems (T7SS) are overrepresented among <i>Mtb</i>-derived peptides presented on MHC-I. Quantitative, targeted MS shows that ESX-1 activity is required for presentation of <i>Mtb</i> 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 <i>Mtb</i> antigens on MHC-I, suggesting involvement of other proteolytic pathways or redundancy among multiple pathways. Our study identifies <i>Mtb</i> 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 <i>Mtb</i> antigens on MHC-I.