1. Epstein-Barr virus and immune status imprint the immunogenomics of non-Hodgkin lymphomas occurring in immune-suppressed environments.
- Author
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Baron M, Labreche K, Veyri M, Désiré N, Bouzidi A, Seck-Thiam F, Charlotte F, Rousseau A, Morin V, Nakid-Cordero C, Abbar B, Picca A, Le Cann M, Balegroune N, Gauthier N, Theodorou I, Touat M, Morel V, Bielle F, Samri A, Alentorn A, Sanson M, Roos-Weil D, Haioun C, Poullot E, De Septenville AL, Davi F, Guihot A, Boelle PY, Leblond V, Coulet F, Spano JP, Choquet S, and Autran B
- Subjects
- Humans, Male, Female, Middle Aged, Adult, Aged, Immunocompromised Host, Immunogenetics, Young Adult, Herpesvirus 4, Human immunology, Herpesvirus 4, Human genetics, Lymphoma, Non-Hodgkin immunology, Lymphoma, Non-Hodgkin genetics, Lymphoma, Non-Hodgkin virology, Epstein-Barr Virus Infections immunology, Epstein-Barr Virus Infections complications, Epstein-Barr Virus Infections genetics, Epstein-Barr Virus Infections virology, Tumor Microenvironment immunology, Mutation
- Abstract
Non-Hodgkin lymphomas (NHL) commonly occur in immunodeficient patients, both those infected by human immunodeficiency virus (HIV) and those who have been transplanted, and are often driven by Epstein-Barr virus (EBV) with cerebral localization, raising the question of tumor immunogenicity, a critical issue for treatment responses. We investigated the immunogenomics of 68 lymphoproliferative disorders from 51 immunodeficient (34 post-transplant, 17 HIV+) and 17 immunocompetent patients. Overall, 72% were large B-cell lymphoma and 25% were primary central nervous system lymphoma, while 40% were EBV+. Tumor whole-exome and RNA sequencing, along with a bioinformatics pipeline allowed analysis of tumor mutational burden, tumor landscape and tumor microenvironment and prediction of tumor neoepitopes. Both tumor mutational burden (2.2 vs. 3.4/Mb, P=0.001) and numbers of neoepitopes (40 vs. 200, P=0.00019) were lower in EBV+ than in EBV- NHL, regardless of the immune status. In contrast both EBV and the immune status influenced the tumor mutational profile, with HNRNPF and STAT3 mutations observed exclusively in EBV+ and immunodeficient NHL, respectively. Peripheral blood T-cell responses against tumor neoepitopes were detected in all EBV- cases but in only half of the EBV+ ones, including responses against IgH-derived MHC-class-II restricted neoepitopes. The tumor microenvironment analysis showed higher CD8 T-cell infiltrates in EBV+ versus EBV- NHL, together with a more tolerogenic profile composed of regulatory T cells, type-M2 macrophages and an increased expression of negative immune-regulators. Our results highlight that the immunogenomics of NHL in patients with immunodeficiency primarily relies on the tumor EBV status, while T-cell recognition of tumor- and IgH-specific neoepitopes is conserved in EBV- patients, offering potential opportunities for future T-cell-based immune therapies.
- Published
- 2024
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