Immunopeptidomics can inform the design of mRNA vaccines for the delivery of <i>Mycobacterium tuberculosis</i> MHC class II antigens

No currently licensed vaccine reliably prevents pulmonary tuberculosis (TB), a leading cause of infectious disease mortality. Developing effective new vaccines requires identifying which <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) proteins are presented on major histocompatibility complex class II (MHC-II) by infected human phagocytes (target cells) and defining their capacity for recognition by CD4⁺ T cells. Vaccine designs must elicit T cell responses recognizing the same peptide-MHC complexes presented by infected cells. Although many human CD4⁺ T cell <i>Mtb</i> epitopes have been described, presentation on MHC-II by infected cells in most cases has not been directly evaluated. Using mass spectrometry (MS), we demonstrated that <i>Mtb</i> type VII secretion system (T7SS) substrates are enriched in the MHC-II repertoire of <i>Mtb</i>-infected human monocyte-derived phagocytes and that many of these antigens are immunogenic in people with prior evidence of <i>Mtb</i> infection. We next used MS to guide TB messenger RNA (mRNA) vaccine design, increasing the presentation of target MHC-II epitopes by orders of magnitude by incorporating design features that mirror aspects of antigen presentation dynamics in infected phagocytes. Our results provide a strategy for TB vaccine design that is guided by bottom-up unbiased discovery. Our approach combines targeted evaluation of antigen presentation in human cells paired with rapid iterative testing of mRNA vaccine designs to optimize antigen presentation before animal studies or human clinical trials.