{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T17:04:17Z","timestamp":1778173457431,"version":"3.51.4"},"reference-count":74,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,10,14]],"date-time":"2024-10-14T00:00:00Z","timestamp":1728864000000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Chinese Institute for Brain Research","award":["2020-NKX-XM-11"],"award-info":[{"award-number":["2020-NKX-XM-11"]}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2019YFA0801801"],"award-info":[{"award-number":["2019YFA0801801"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFA0801405"],"award-info":[{"award-number":["2018YFA0801405"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Recent advances in neoantigen research have accelerated the development of immunotherapies for cancers, such as glioblastoma (GBM). Neoantigens resulting from genomic mutations and dysregulated alternative splicing have been studied in GBM. However, these studies have primarily focused on annotated alternatively-spliced transcripts, leaving non-annotated transcripts largely unexplored. Circular ribonucleic acids (circRNAs), abnormally regulated in tumors, are correlated with the presence of non-annotated linear transcripts with exon skipping events. But the extent to which these linear transcripts truly exist and their functions in cancer immunotherapies remain unknown. Here, we found the ubiquitous co-occurrence of circRNA biogenesis and alternative splicing across various tumor types, resulting in large amounts of long-range alternatively-spliced transcripts (LRs). By comparing tumor and healthy tissues, we identified tumor-specific LRs more abundant in GBM than in normal tissues and other tumor types. This may be attributable to the upregulation of the protein quaking in GBM, which is reported to promote circRNA biogenesis. In total, we identified 1057 specific and recurrent LRs in GBM. Through in silico translation prediction and MS-based immunopeptidome analysis, 16 major histocompatibility complex class I-associated peptides were identified as potential immunotherapy targets in GBM. This study revealed long-range alternatively-spliced transcripts specifically upregulated in GBM may serve as recurrent, immunogenic tumor-specific antigens.<\/jats:p>","DOI":"10.1093\/bib\/bbae503","type":"journal-article","created":{"date-parts":[[2024,10,14]],"date-time":"2024-10-14T15:28:06Z","timestamp":1728919686000},"source":"Crossref","is-referenced-by-count":4,"title":["Long-range alternative splicing contributes to neoantigen specificity in glioblastoma"],"prefix":"10.1093","volume":"25","author":[{"given":"Mingjun","family":"Ji","sequence":"first","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]},{"name":"Peking University , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qing","family":"Yu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]},{"name":"Peking University , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin-Zhuang","family":"Yang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics , National Infrastructures for Translational Medicine, Institute of Clinical Medicine and Peking Union Medical College Hospital,"},{"name":"Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dongdan Santiao, Dongcheng District, Beijing 100730, China , National Infrastructures for Translational Medicine, Institute of Clinical Medicine and Peking Union Medical College Hospital,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xianhong","family":"Yu","sequence":"additional","affiliation":[{"name":"Academic Department, Shanghai MobiDrop Co., Ltd. , Room 308, Building 1, No. 351 Guoshoujing Road, Shanghai Free Trade Pilot Zone, Shanghai 200000 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiaxin","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]},{"name":"Peking University , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunfu","family":"Xiao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]},{"name":"Peking University , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ni A","family":"An","sequence":"additional","affiliation":[{"name":"Institute of Genetics and Developmental Biology, Chinese Academy of Sciences , No. 1 West Beichen Road, Chaoyang District, Beijing 100101 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chuanhui","family":"Han","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Peking University , No. 38 Xueyuan Road, Haidian District, Beijing 100191 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8008-8430","authenticated-orcid":false,"given":"Chuan-Yun","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]},{"name":"Peking University , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]},{"name":"Chinese Institute for Brain Research , No. 26 Science Park Road, Changping District, Beijing 102206 ,","place":["China"]},{"name":"Southwest United Graduate School , 121 Dajie, Wuhua District, Kunming 650092 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6650-8662","authenticated-orcid":false,"given":"Wanqiu","family":"Ding","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]},{"name":"Peking University , Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]},{"name":"Bioinformatics Core Facility , Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]},{"name":"Peking University , Institute of Molecular Medicine, College of Future Technology, , No. 5 Yiheyuan Road, Haidian District, Beijing 100871 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,10,14]]},"reference":[{"key":"2024101709172792300_ref1","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1001\/jamanetworkopen.2019.2535","article-title":"Estimation of the percentage of US patients with cancer who are eligible for and respond to checkpoint inhibitor immunotherapy drugs","volume":"2","author":"Haslam","year":"2019","journal-title":"JAMA Netw Open"},{"key":"2024101709172792300_ref2","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1007\/s11060-020-03448-1","article-title":"A review of glioblastoma 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