Tumor-Specific CircRNA-Derived Antigen Peptide Identification for Hepatobiliary Tumors

Wenwen Wang; Lili Ma; Zheng Xing; Tinggan Yuan; Jinxia Bao; Yanjing Zhu; Xiaofang Zhao; Yan Zhao; Yali Zong; Yani Zhang; Siyun Shen; Xinyao Qiu; Shuai Yang; Hongyang Wang; Dong Gao; Peng Wang; Lei Chen

doi:10.1016/j.eng.2022.06.008

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Engineering ›› 2023, Vol. 22 ›› Issue (3) : 159-170. DOI: 10.1016/j.eng.2022.06.008

Research

Article

Tumor-Specific CircRNA-Derived Antigen Peptide Identification for Hepatobiliary Tumors

Wenwen Wang^a^,^* ,
Lili Ma^b^,^c^,^* ,
Zheng Xing^b^,^c^,^* ,
Tinggan Yuan^b^,^c^,^d ,
Jinxia Bao^e^,^f ,
Yanjing Zhu^g^,^h ,
Xiaofang Zhao^a ,
Yan Zhaoⁱ ,
Yali Zongⁱ ,
Yani Zhangⁱ ,
Siyun Shen^g^,^h ,
Xinyao Qiu^a ,
Shuai Yang^a ,
Hongyang Wang^a^,^g^,^h ,
Dong Gao^c^,^j^,^k ,
Peng Wang^b^,^c^,^l ,
Lei Chen^a^,^h^,^m

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Abstract

The application of tumor antigen-based immunotherapy is hindered by the rarity of validated immunogenic peptides. In this study, we aimed to investigate the potential of circular RNAs (circRNAs) as a novel source of tumor antigen peptides in hepatobiliary tumor organoids. Using RNA-sequencing (RNA-seq) with an algorithm-based score tool, 3950 translated tumor-specific circRNAs were predicted to generate 18 971 antigen peptides in 27 organoids. In view of the antigen landscape, 11 amino acid length (mer) peptides and human leukocyte antigen (HLA)-A binding peptides harbored the highest immunogenicity-related scores. In three out of five analyzed organoids, 13 predicted antigen peptides were directly confirmed as HLA-A, -B, and -C (HLA-ABC) binding peptides with mass spectrometry (MS)-based immunopeptidomics. CircRNA-derived tumor-specific peptides presented by the HLA-ABC molecules stimulated cluster of differentiation 8 (CD8) T cells to exhibit increased CD107a interferon γ (IFNγ) co-expressions and IFNγ secretion in flow cytometry and enzyme-linked immunosorbent assay (ELISA). Cytotoxic T cell activity targeting the organoids, induced by the immunogenic circRNA-derived peptides, was verified in a killing assay. Notably, the antigen peptide YGFNEILKK from circTBC1D15 was not only recognized as an HLA-ABC-presented peptide of the organoids but also drastically reduced the tumor organoid survival rate. Our findings highlight a crucial subset for generating tumor antigens, which has implications for targeting tumor-specific circRNAs in cancers.

Keywords

Tumor antigen / Patient-derived hepatobiliary tumor organoid / Circular RNA / Mass-spectrometry-based immunopeptidomics

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Wenwen Wang, Lili Ma, Zheng Xing, Tinggan Yuan, Jinxia Bao, Yanjing Zhu, Xiaofang Zhao, Yan Zhao, Yali Zong, Yani Zhang, Siyun Shen, Xinyao Qiu, Shuai Yang, Hongyang Wang, Dong Gao, Peng Wang, Lei Chen. Tumor-Specific CircRNA-Derived Antigen Peptide Identification for Hepatobiliary Tumors. Engineering, 2023, 22(3): 159‒170 https://doi.org/10.1016/j.eng.2022.06.008

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