Using immunopeptidomics and exome and transcriptome sequencing, Wang et al. analyzed 22 RCC samples and identified HLA-I-presented non-canonical tumor-specific antigens (TSA) derived from human endogenous retroviruses and long non-coding RNAs, with some shared across patients. TSA-reactive T cells in the TIME primarily expressed an exhausted phenotype. T cells expressing TSA-reactive TCRs isolated using scRNA seq mediated tumor cell killing/ regression in vitro in RCC patient-derived tumor-like cell clusters cocultured with autologous peripheral lymphocytes and in mouse xenograft models, particularly combined with anti-PD-1.
Contributed by Paula Hochman
(1) Wang J (2) Zhu Y (3) He X (4) Yin S (5) He Y (6) Yao P (7) Li J (8) Li X (9) Shi P (10) Qian R (11) Xiao Z (12) Ye X (13) Xi JJ (14) Ye B
Using immunopeptidomics and exome and transcriptome sequencing, Wang et al. analyzed 22 RCC samples and identified HLA-I-presented non-canonical tumor-specific antigens (TSA) derived from human endogenous retroviruses and long non-coding RNAs, with some shared across patients. TSA-reactive T cells in the TIME primarily expressed an exhausted phenotype. T cells expressing TSA-reactive TCRs isolated using scRNA seq mediated tumor cell killing/ regression in vitro in RCC patient-derived tumor-like cell clusters cocultured with autologous peripheral lymphocytes and in mouse xenograft models, particularly combined with anti-PD-1.
Contributed by Paula Hochman
BACKGROUND: Renal cell carcinoma (RCC) frequently exhibits favorable responses to immunotherapy, despite a low tumor mutational burden, suggesting a critical role for non-mutational antigens presented by human leukocyte antigen class I in activating CD8(+) T cells. METHODS: To systematically identify non-canonical tumor-specific antigens, we developed an integrated proteogenomic approach to RCC samples by combining immunopeptidomics with exome and transcriptome sequencing. We subsequently primed and expanded antigen-reactive T cells in vitro, isolated a panel of antigen-specific T-cell receptors, and characterized their functionality. Finally, we investigated the tumor-killing and regression of non-canonical antigen-reactive T cells using patient-derived tumor-like cell clusters and mouse models. RESULTS: We discovered a diverse repertoire of non-canonical tumor-specific antigens derived from human endogenous retroviruses (hERVs) and long non-coding RNAs (lncRNAs), many of which were shared across patients. Single-cell RNA sequencing further revealed that T cells reactive to these antigens were enriched within exhausted subsets in the tumor microenvironment, indicative of persistent antigen-specific stimulation. Functionally, T cells engineered to recognize these non-canonical antigens mediated potent tumor cell killing both in vitro and in vivo. Our findings establish hERV-derived and lncRNA-derived antigens as key drivers of RCC immunogenicity and highlight their strong potential as targets for T-cell-based immunotherapy. CONCLUSIONS: Our work is the first to demonstrate that non-canonical antigens drive immunogenicity in low-mutation RCC, thereby resolving a key question in cancer immunology-how tumors with low mutational burden can provoke robust T-cell responses.
Author Info:
(1) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future T
echnology, Peking University, Beijing, China. (2) Department of Urology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. (3) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (4) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (5) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (6) Innovative Vaccine and Immunotherapy Research Center, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. (7) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (8) Department of Urology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. (9) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (10) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (11) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. (12) Department of Urology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China jzxi@pku.edu.cn bqye@pku.edu.cn yexiongjun@cicams.ac.cn. (13) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China jzxi@pku.edu.cn bqye@pku.edu.cn yexiongjun@cicams.ac.cn. (14) State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Tumor Organoid and Digital Tumor Twin, Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China jzxi@pku.edu.cn bqye@pku.edu.cn yexiongjun@cicams.ac.cn.
Citation: J Immunother Cancer 2026 Jun 24 14: Epub06/24/2026
