HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy [PRO-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 direct transcriptional target of HIF2a by PRO-Seq in OS-RC-2 cells. OS-RC-2 cells were treated with 2 uM PT2399 (PT) or vehicle (Veh) for 2 hours, we then performed PRO-Seq experiments to quantify ERV amount for each condition in triplicates.

透明细胞肾细胞癌（Clear cell renal cell carcinoma, ccRCC）尽管突变负荷较低，但因偶尔发生自发消退且常对免疫治疗产生应答，故被认为具有免疫原性。该肿瘤的特征性病变为VHL抑癌基因（VHL tumor suppressor gene）失活，继而引发缺氧诱导因子（hypoxia-inducible factor, HIF）转录因子的表达上调。此前一项病例报告显示，一名透明细胞肾细胞癌患者经异基因干细胞移植后痊愈，后续研究发现其体内存在供体来源T细胞，可识别由缺氧诱导因子响应性内源性逆转录病毒（endogenous retrovirus, ERV）ERV-4编码的透明细胞肾细胞癌特异性肽段。本研究证实，ERV-4是众多受缺氧诱导因子诱导的内源性逆转录病毒之一：这类病毒在透明细胞肾细胞癌中可被翻译为与人类白细胞抗原（human leukocyte antigen, HLA）结合的肽段，并能够诱导抗原特异性T细胞应答。此外，使用临床级缺氧诱导因子稳定剂可在非透明细胞肾细胞癌肿瘤中诱导内源性逆转录病毒的表达。上述发现为利用内源性逆转录病毒开展癌症免疫治疗提供了潜在应用方向。实验设计：本研究旨在通过PRO-Seq技术系统鉴定OS-RC-2细胞中HIF2α的直接转录靶标。将OS-RC-2细胞用2 μM PT2399或溶剂对照处理2小时后，开展PRO-Seq实验，对各处理条件下的内源性逆转录病毒表达量进行三次生物学重复定量检测。