Tumour circular RNAs elicit anti-tumour immunity by encoding cryptic peptides

Di Huang, Xiaofeng Zhu, Shuying Ye, Jiahui Zhang, Jianyou Liao, Ning Zhang, Xin Zeng, Jiawen Wang, Bing Yang, Yin Zhang, Liyan Lao, Jianing Chen, Min Xin, Yan Nie, Phei Er Saw, Shicheng Su () and Erwei Song ()
Additional contact information
Di Huang: Sun Yat-Sen University
Xiaofeng Zhu: Sun Yat-Sen University
Shuying Ye: Sun Yat-Sen University
Jiahui Zhang: Sun Yat-Sen University
Jianyou Liao: Sun Yat-Sen University
Ning Zhang: Sun Yat-Sen University
Xin Zeng: Sun Yat-Sen University
Jiawen Wang: Sun Yat-Sen University
Bing Yang: Sun Yat-Sen University
Yin Zhang: Sun Yat-Sen University
Liyan Lao: Sun Yat-Sen University
Jianing Chen: Sun Yat-Sen University
Min Xin: Sun Yat-Sen University
Yan Nie: Sun Yat-Sen University
Phei Er Saw: Sun Yat-Sen University
Shicheng Su: Sun Yat-Sen University
Erwei Song: Sun Yat-Sen University

Nature, 2024, vol. 625, issue 7995, 593-602

Abstract: Abstract Emerging data have shown that previously defined noncoding genomes might encode peptides that bind human leukocyte antigen (HLA) as cryptic antigens to stimulate adaptive immunity1,2. However, the significance and mechanisms of action of cryptic antigens in anti-tumour immunity remain unclear. Here mass spectrometry of the HLA class I (HLA-I) peptidome coupled with ribosome sequencing of human breast cancer samples identified HLA-I-binding cryptic antigenic peptides that were noncanonically translated by a tumour-specific circular RNA (circRNA): circFAM53B. The cryptic peptides efficiently primed naive CD4+ and CD8+ T cells in an antigen-specific manner and induced anti-tumour immunity. Clinically, the expression of circFAM53B and its encoded peptides was associated with substantial infiltration of antigen-specific CD8+ T cells and better survival in patients with breast cancer and patients with melanoma. Mechanistically, circFAM53B-encoded peptides had strong binding affinity to both HLA-I and HLA-II molecules. In vivo, administration of vaccines consisting of tumour-specific circRNA or its encoded peptides in mice bearing breast cancer tumours or melanoma induced enhanced infiltration of tumour-antigen-specific cytotoxic T cells, which led to effective tumour control. Overall, our findings reveal that noncanonical translation of circRNAs can drive efficient anti-tumour immunity, which suggests that vaccination exploiting tumour-specific circRNAs may serve as an immunotherapeutic strategy against malignant tumours.

Date: 2024
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DOI: 10.1038/s41586-023-06834-7

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