肝胆肿瘤中肿瘤特异性CircRNA衍生抗原肽的鉴定  

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

作　　者：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 王红阳 高栋 王鹏 陈磊 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(Fudan University Shanghai Cancer Center,Shanghai 200032,China;Bio-Med Big Data Center,CAS Key Laboratory of Computational Biology,Shanghai Institute of Nutrition and Health,Chinese Academy of Sciences,Shanghai 200031,China;University of Chinese Academy of Sciences,Beijing 100049,China;School of Life Science and Technology,ShanghaiTech University,Shanghai 201210,China;State Key Laboratory of Pharmaceutical Biotechnology&Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animal for Disease Study,Nanjing University,Nanjing 210061,China;School of Medicine,Nanjing University,Nanjing 210093,China;The International Cooperation Laboratory on Signal Transduction,Eastern Hepatobiliary Surgery Hospital,Second Military Medical University,Shanghai 200438,China;National Center for Liver Cancer,Shanghai 200441,China;Institute of Metabolism and Integrative Biology,Fudan University,Shanghai 200433,China;State Key Laboratory of Cell Biology&Shanghai Key Laboratory of Molecular Andrology,Center for Excellence in Molecular Cell Science,Chinese Academy of Sciences,Shanghai 200031,China;Institute for Stem Cell and Regeneration,Chinese Academy of Sciences,Beijing 100101,China;Faculty of Health Sciences,University of Macao,Macao 999078,China;Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer(SMMU),Ministry of Education&Shanghai Key Laboratory of Hepatobiliary Tumor Biology(EHBH),Eastern Hepatobiliary Surgery Hospital,Second Military Medical University,Shanghai 200438,China)

机构地区：[1]Fudan University Shanghai Cancer Center,Shanghai 200032,China [2]Bio-Med Big Data Center,CAS Key Laboratory of Computational Biology,Shanghai Institute of Nutrition and Health,Chinese Academy of Sciences,Shanghai 200031,China [3]University of Chinese Academy of Sciences,Beijing 100049,China [4]School of Life Science and Technology,ShanghaiTech University,Shanghai 201210,China [5]State Key Laboratory of Pharmaceutical Biotechnology&Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animal for Disease Study,Nanjing University,Nanjing 210061,China [6]School of Medicine,Nanjing University,Nanjing 210093,China [7]The International Cooperation Laboratory on Signal Transduction,Eastern Hepatobiliary Surgery Hospital,Second Military Medical University,Shanghai 200438,China [8]National Center for Liver Cancer,Shanghai 200441,China [9]Institute of Metabolism and Integrative Biology,Fudan University,Shanghai 200433,China [10]State Key Laboratory of Cell Biology&Shanghai Key Laboratory of Molecular Andrology,Center for Excellence in Molecular Cell Science,Chinese Academy of Sciences,Shanghai 200031,China [11]Institute for Stem Cell and Regeneration,Chinese Academy of Sciences,Beijing 100101,China [12]Faculty of Health Sciences,University of Macao,Macao 999078,China [13]Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer(SMMU),Ministry of Education&Shanghai Key Laboratory of Hepatobiliary Tumor Biology(EHBH),Eastern Hepatobiliary Surgery Hospital,Second Military Medical University,Shanghai 200438,China

出　　处：《Engineering》2023年第3期159-170,共12页工程（英文）

基　　金：the National Natural Science Foundation of China(U21A20376,82102871,81988101,81903184,81790633,and 81830054);the Innovation Program of Shanghai Municipal Education Commission(2019-01-07-00-07E00065);the National Science Foundation of Shanghai(21XD1404600,21JC1406600,and 22140901000);the China Postdoctoral Science Foundation(2020M671007).

摘　　要：基于肿瘤抗原的免疫治疗的应用受到验证免疫原性肽稀缺性的阻碍。本研究旨在研究环状RNA(circRNA)在肝胆肿瘤类器官中作为肿瘤抗原肽新来源的潜力。使用RNA测序(RNA-seq)和基于算法的评分工具,预测3950个翻译的肿瘤特异性环状RNA在27个类器官中产生18971个抗原肽。从抗原格局来看,11个氨基酸长度(mer)肽和人白细胞抗原(HLA)-A结合肽具有最高的免疫原性相关评分。在分析的3/5类器官中,有13个预测抗原肽通过质谱(MS)免疫肽组学被直接确认为HLA-A、HLA-B和HLA-C(HLA-ABC)结合肽。在流式细胞术和酶联免疫吸附试验(ELISA)中,由HLA-ABC分子呈递的circRNA衍生的肿瘤特异性肽刺激CD8(CD8)T细胞,显示CD107a干扰素γ(IFNγ)共表达和IFNγ分泌增加。免疫原性环状RNA衍生肽诱导的靶向类器官的细胞毒性T细胞活性在杀伤实验中得到验证。值得注意的是,来自circTBC1D15的抗原肽YGFNEILKK不仅被认为是类器官的HLA-ABC呈递肽,而且还显著降低了肿瘤类器官的存活率。本研究的发现强调了产生肿瘤抗原的一个关键亚群,这对靶向肿瘤特异性circRNA具有重要意义。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 18971 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 interferonγ(IFNγ)co-expressions and IFNγsecretion 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.

关 键 词：Tumor antigen Patient-derived hepatobiliary tumor organoid Circular RNA Mass-spectrometry-based immunopeptidomics 

分 类 号：R735[医药卫生—肿瘤]