MHC II immunogenicity shapes the neoepitope landscape in human tumors
Menée notamment à partir de données du projet "The Cancer Genome Atlas" et d'échantillons tumoraux fixés au formaldéhyde et inclus en paraffine après prélèvement sur 335 patients atteints d'un cancer du poumon non à petites cellules traité par anti-PD1/PDL-1, cette étude présente une approche méthodologique pour prédire l'immunogénicité des néo-épitopes, en particulier ceux associés au complexe majeur d'histocompatibilité II (CMH II), et met en évidence le rôle du CMH II dans la sélection immunitaire
Despite advances in predicting physical peptide-major histocompatibility complex I (pMHC I) binding, it remains challenging to identify functionally immunogenic neoepitopes, especially for MHC II. By using the results of >36,000 immunogenicity assay, we developed a method to identify pMHC whose structural alignment facilitates T cell reaction. Our method predicted neoepitopes for MHC II and MHC I that were responsive to checkpoint blockade when applied to >1,200 samples of various tumor types. To investigate selection by spontaneous immunity at the single epitope level, we analyzed the frequency spectrum of >25 million mutations in >9,000 treatment-naive tumors with >100 immune phenotypes. MHC II immunogenicity specifically lowered variant frequencies in tumors under high immune pressure, particularly with high TCR clonality and MHC II expression. A similar trend was shown for MHC I neoepitopes, but only in particular tissue types. In summary, we report immune selection imposed by MHC II-restricted natural or therapeutic T cell reactivity.
Nature Genetics , résumé, 2023