HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy [ChIP-seq]

Clear cell renal cell carcinoma (ccRCC), despite having a low mutational burden, is considered immunogenic because it occasionally undergoes spontaneous regressions and often responds to immunotherapies. The signature lesion in ccRCC is inactivation of the VHL tumor suppressor gene and consequent upregulation of the HIF transcription factor. An earlier case report described a ccRCC patient who was cured by an allogeneic stem cell transplant and later found to have donor-derived T cells that recognized a ccRCC-specific peptide encoded by a HIF-responsive endogenous retrovirus (ERVE-4). We report that ERVE-4 is one of many ERVs that are induced by HIF, translated into HLA-bound peptides in ccRCCs, and capable of generating antigen-specific T cell responses. Moreover, ERV expression can be induced in non-ccRCC tumors with clinical-grade HIF stabilizers. These findings have implications for leveraging ERVs for cancer immunotherapy. Overall design: We aim to systematically identify HIF2a binding sites genome-wide by ChIP-Seq. We performed ChIP-Seq experiments using an anti-HIF2a antibody and isogenic 786-O cells in which HIF2a was or was not eliminated using CRISPR/Cas9. To further enhance our ability to detect HIF2a-binding sites, we also performed ChIP-Seq using an anti-FLAG antibody and ccRCC cells (786-O, OS-RC-2, and RCC4) cells in which CRISPR/Cas9 was used to append a FLAG-HA epitope tag to the N-terminus of HIF2a expressed from the endogenous HIF2a locus. In order to identify additional HIF2a binding sites upon DNMT1i treatment, we also treated isogenic 786-O cells cells that underwent CRISPR-based gene editing with a HIF2a sgRNA or a control sgRNA (sgCtrl) with 0.5 uM GSK3685032 (DNMT1i) for 9 days.