Abstract PR001: Exploiting HIF-driven endogenous retroviral neoantigens to advance kidney cancer immunotherapy

Abstract Background Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer. Despite therapeutic advances including VEGF pathway inhibitors, immune checkpoint inhibitors (ICIs), and a recently approved HIF2 inhibitor, metastatic ccRCC often relapses, with overall survival below 50%. While ccRCC is immunogenic, the specific antigenic drivers remain largely unknown. Loss of the VHL gene, a hallmark of ccRCC, stabilizes HIF2, a transcription factor that drives tumor growth. Analysis of a patient who achieved a complete remission after allogeneic stem cell transplantation (allo-SCT) identified donor T cells that recognized a peptide derived from a HIF2-induced endogenous retrovirus (ERV), ERVE-4. This was the first evidence that HIF2-activated ERVs in ccRCC can generate tumor-specific epitopes capable of eliciting potent antitumor immunity. Methods We employed a multi-omics approach to systematically identify HIF-regulated ERVs. Targeted long-read DNA sequencing resolved locus-specific sequence variants, critical for accurate open reading frame (ORF) prediction and mass spectrometry (MS) search database construction at ERV loci. Translation of ERV transcripts was assessed by Polysome-seq, while HLA-bound peptides were identified through HLA immunoprecipitation (endogenous or tagged exogenous HLA) followed by MS. Immunogenicity of ERV-derived peptides was evaluated using IFNγ ELISpot assays with immune cells from ccRCC patients who responded to allo-SCT. Using the TScan discovery platform, expanded tumor-infiltrating T-cell clones were subjected to a genome-wide screen to identify HIF-regulated ERV-derived peptides they recognize. Additionally, ex vivo priming and expansion of healthy donor PBMCs enabled identifications of TCRs recognizing ERV-derived peptides. Results Transcriptomic and immunopeptidomic analyses identified dozens of HIF2-induced ERVs that are presented as HLA-bound peptides in ccRCC but absent in matched normal tissues. Many of these ERV-derived peptides were recognized by T cells from archival specimens of ccRCC patients who responded to allo-SCT or ICI therapy. Targeted long-read sequencing revealed numerous DNA variants relative to the reference genome, enabling accurate ORF prediction and incorporation of these sequences into cell line-specific MS databases. Immunopeptidomic profiling of engineered ccRCC cell lines expressing tagged prevalent HLA alleles facilitated creation of a reference peptide library for ERV-derived HLA ligands across common HLA types. Finally, dozens of TCRs recognizing ERV-derived peptides were identified. Conclusions HIF2 induces tumor-specific, immunogenic ERVs in ccRCCs. These ERVs are actively translated and presented on tumor cells by HLA complexes across multiple prevalent alleles. Their recognition by T cells highlights their potential as promising targets for future immunotherapies. Citation Format: Qinqin Jiang, David Braun, Karl Clauser, Vijyendra Ramesh, Gurcan Gunaydin, Justin Becker, Nitin Shirole, Joseph Duke-Cohan, Nancy Nabilsi, Nicholas Kramer, Cleo Forman, Isabelle Lippincott, Sudarsana Addepalli, Susan Klaeger, Kshiti Phulphagar, Vipheaviny Chea, Nawoo Kim, Allison Vanasse, Eddy Saad, Melissa Carr-Reynolds, Teagan Parsons, Isabel Carulli, Yijia Jiang, Rong Li, Sudeepa Syamala, Suzanna Rachimi, Eva Verzani, Jonathan Stevens, Sabrina Camp, William Lane, Kevin Meli, Melissa Pappalardi, Zachary Herbert, Xintao Qiu, Paloma Cejas, Henry Long, Sachet Shukla, Eliezer Van Allen, Toni Choueiri, L. Stirling Churchman, Jennifer Abelin, Cagan Gurer, Gavin MacBeath, Richard Childs, Bradley Bernstein, William Freed-Pastor, Steven Carr, Derin Keskin, Catherine Wu, William Kaelin Jr.. Exploiting HIF-driven endogenous retroviral neoantigens to advance kidney cancer immunotherapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Kidney Cancer Research: From Molecular Insights to Therapeutic Breakthroughs; 2026 Mar 13-16; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(5_Suppl_2):Abstract nr PR001.