Global Analysis of the Mammalian MHC class I Immunopeptidome at the Organism-Wide Scale

Kubiniok, Peter; Marcu, Ana; Bichmann, Leon; Kuchenbecker, Leon; Schuster, Heiko; Hamelin, David; Despault, Jérome; Kovalchik, Kevin; Wessling, Laura; Kohlbacher, Oliver; Stevanovic, Stefan; Rammensee, Hans-Georg; Neidert, Marian C.; Sirois, Isabelle; Caron, Etienne

Understanding the molecular principles that govern the composition of the mammalian MHC-I immunopeptidome (MHC-Ii) across different primary tissues is fundamentally important to predict how T cell respond in different contexts in vivo. Here, we performed a global analysis of the mammalian MHC-Ii from 29 and 19 primary human and mouse tissues, respectively. First, we observed that different HLA-A, -B and -C allotypes do not contribute evenly to the global composition of the MHC-Ii across multiple human tissues. Second, we found that peptides that are presented in a tissue-dependent and -independent manner share very distinct properties. Third, we discovered that proteins that are evolutionarily hyperconserved represent the primary source of the MHC-Ii at the organism-wide scale. Finally, we uncovered new components of the antigen processing and presentation network that may drive the high level of heterogeneity of the MHC-Ii across different tissues in mammals. This study opens up new avenues toward a system-wide understanding of antigen presentation in vivo and may serve as ground work to understand tissue-dependent T cell responses in autoimmunity, infectious diseases and cancer.