HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy [RNA-Seq_QJ9511]

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 HIF-responsive ERVs by RNA-Seq in A-498 cells. We generated three isogenic comparisons to create HIF2 high and low status, for which cells 1) were stably infected with a virus encoding pVHL (VHL) or the empty vector (EV), 2) were treated with 2 uM PT2399 (PT) or vehicle (Veh) for 72 hours, 3) underwent CRISPR-based gene editing with a HIF2a sgRNA or a contrl sgRNA (sgCtrl). We then performed RNA-Seq experiments to quantify ERV amount for each condition in triplicates.