Abstract B49: Human Endogenous Retroviruses represent a source of shared tumor epitopes inducing high-avidity cytotoxic T cells for cancer immunotherapy
Authors: Bonaventura Paola , Alcazer Vincent , Mutez Virginie , Tonon Laurie , Martin Juliette , Chuvin Nicolas , Michel Emilie , Boulos Rasha , Estornes Yann , Valladeau-Guilemond Jenny , Viari Alain , Wang Quing , Caux Christophe , Depil Stephane 
Published: December 2022

Abstract
Human endogenous retroviruses (HERVs) represent 8% of the human genome. HERVs are silenced by epigenetic mechanisms in normal cells but are aberrantly expressed by tumor cells. Given their viral origin, HERV products may represent tumor antigens relevant for cancer immunotherapy. We developed a systematic bioinformatics-based approach to identify shared CD8+ T cell epitopes derived from cancer-associated HERVs in solid tumors. Six HLA-A2 epitopes among the most shared epitope candidates with evidence of translation were selected for further immunological evaluation. In vitro priming assays showed the induction of specific CD8+ T cells leading to polyfunctional T cell responses. The functionality of the sorted T cell clones was confirmed by Elispot (GrzB+ IFN-γ+) before TCR sequencing. Interestingly, these TCRs were predicted to interact with a high affinity with their respective MHC-peptide complexes in 3D models. This was confirmed by measurement of the functional avidity, which was in the same order as CMV-specific T cell clones. HERV-specific CD8+ T cells induced specific cell death of HLA-A2+ cancer cell lines presenting HERV epitopes on HLA molecules, as demonstrated by mass spectrometry. Furthermore, HERV-specific CD8+ T cells were identified by dextramer-staining among tumor infiltrating lymphocytes (TILs) from HLA-A2+ breast and ovarian cancer patients. Finally, we showed that HERV-specific T cells can lyse patient-derived organoids (Bonaventura et al. Sci Adv 2022). Synthetic long peptides containing these HERV epitopes have been validated for the development of a cancer vaccine. TCR engineered T cells specific to these HERV epitopes have been generated and their functionality and specificity have been confirmed. In parallel, we also evaluated HERV expression in Acute Myeloid Leukemia (AML). We used a complete database of 14,968 HERVs functional units to provide a thorough analysis of HERVs in normal and AML bone marrow cells. We found that HERV retrotranscriptome characterizes normal and leukemic cell subpopulations and HERV expression separates distinct AML subtypes of different prognosis. We showed that patients’ bone marrow infiltrating lymphocytes at diagnosis also contain naturally occurring CD8+ T cells against AML-specific HERV epitopes. Furthermore, we demonstrated that HERV-specific CD8+ T cells specifically recognize AML cells (Alcazer et al. Am J Hematol 2022). Our bioinformatic approach allowed us to identify shared HERV-derived CD8+ T cell epitopes specifically expressed by tumor cells and inducing high-avidity T cell clones able to kill tumor cells in a class I-restricted manner. The detection of TILs recognizing HERV peptides suggests natural presentation of these epitopes in the tumors. These HERV-derived epitopes may thus represent relevant targets for the development of new immunotherapeutic approaches, especially in tumors with a low or moderate mutational burden. We are currently developing a therapeutic vaccine as well as TCR engineered T cells specific to these HERV epitopes.
Citation Format: Paola Bonaventura, Vincent Alcazer, Virginie Mutez, Laurie Tonon, Juliette Martin, Nicolas Chuvin, Emilie Michel, Rasha Boulos, Yann Estornes, Jenny Valladeau-Guilemond, Alain Viari, Quing Wang, Christophe Caux, Stephane Depil. Human Endogenous Retroviruses represent a source of shared tumor epitopes inducing high-avidity cytotoxic T cells for cancer immunotherapy [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr B49.