RNA splicing junction landscape reveals abundant tumor-specific transcripts in human cancer
Summary: RNA splicing is a critical process governing gene expression and transcriptomic diversity. Despite its importance, a detailed examination of transcript variation at the splicing junction level remains scarce. Here, we perform a thorough analysis of RNA splicing junctions in 34,775 samples a...
Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2024-11-01
|
| Series: | Cell Reports |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124724012440 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850266133258567680 |
|---|---|
| author | Qin Li Ziteng Li Bing Chen Jingjing Zhao Hongwu Yu Jia Hu Hongyan Lai Hena Zhang Yan Li Zhiqiang Meng Zhixiang Hu Shenglin Huang |
| author_facet | Qin Li Ziteng Li Bing Chen Jingjing Zhao Hongwu Yu Jia Hu Hongyan Lai Hena Zhang Yan Li Zhiqiang Meng Zhixiang Hu Shenglin Huang |
| author_sort | Qin Li |
| collection | DOAJ |
| description | Summary: RNA splicing is a critical process governing gene expression and transcriptomic diversity. Despite its importance, a detailed examination of transcript variation at the splicing junction level remains scarce. Here, we perform a thorough analysis of RNA splicing junctions in 34,775 samples across multiple sample types. We identified 29,051 tumor-specific transcripts (TSTs) in pan-cancer, with a majority of these TSTs being unannotated. Our findings show that TSTs are positively correlated with tumor stemness and linked to unfavorable outcomes in cancer patients. Additionally, TSTs display mutual exclusivity with somatic mutations and are overrepresented in transposable-element-derived transcripts possessing oncogenic functions. Importantly, TSTs can generate putative neoantigens for immunotherapy. Moreover, TSTs can be detected in blood extracellular vesicles from cancer patients. Our results shed light on the intricacies of RNA splicing and offer promising avenues for cancer diagnosis and therapy. |
| format | Article |
| id | doaj-art-a614c04e998f41fbae9f973e3d07285a |
| institution | OA Journals |
| issn | 2211-1247 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj-art-a614c04e998f41fbae9f973e3d07285a2025-08-20T01:54:15ZengElsevierCell Reports2211-12472024-11-01431111489310.1016/j.celrep.2024.114893RNA splicing junction landscape reveals abundant tumor-specific transcripts in human cancerQin Li0Ziteng Li1Bing Chen2Jingjing Zhao3Hongwu Yu4Jia Hu5Hongyan Lai6Hena Zhang7Yan Li8Zhiqiang Meng9Zhixiang Hu10Shenglin Huang11Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, and Institute of Pathology, Fudan University, Shanghai 200032, ChinaDepartment of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, ChinaDepartment of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, ChinaDepartment of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, ChinaDepartment of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, ChinaDepartment of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, ChinaDepartment of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, ChinaDepartment of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, ChinaDepartment of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, ChinaDepartment of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Corresponding authorDepartment of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Corresponding authorDepartment of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Corresponding authorSummary: RNA splicing is a critical process governing gene expression and transcriptomic diversity. Despite its importance, a detailed examination of transcript variation at the splicing junction level remains scarce. Here, we perform a thorough analysis of RNA splicing junctions in 34,775 samples across multiple sample types. We identified 29,051 tumor-specific transcripts (TSTs) in pan-cancer, with a majority of these TSTs being unannotated. Our findings show that TSTs are positively correlated with tumor stemness and linked to unfavorable outcomes in cancer patients. Additionally, TSTs display mutual exclusivity with somatic mutations and are overrepresented in transposable-element-derived transcripts possessing oncogenic functions. Importantly, TSTs can generate putative neoantigens for immunotherapy. Moreover, TSTs can be detected in blood extracellular vesicles from cancer patients. Our results shed light on the intricacies of RNA splicing and offer promising avenues for cancer diagnosis and therapy.http://www.sciencedirect.com/science/article/pii/S2211124724012440CP: Cell biologyCP: Molecular biology |
| spellingShingle | Qin Li Ziteng Li Bing Chen Jingjing Zhao Hongwu Yu Jia Hu Hongyan Lai Hena Zhang Yan Li Zhiqiang Meng Zhixiang Hu Shenglin Huang RNA splicing junction landscape reveals abundant tumor-specific transcripts in human cancer Cell Reports CP: Cell biology CP: Molecular biology |
| title | RNA splicing junction landscape reveals abundant tumor-specific transcripts in human cancer |
| title_full | RNA splicing junction landscape reveals abundant tumor-specific transcripts in human cancer |
| title_fullStr | RNA splicing junction landscape reveals abundant tumor-specific transcripts in human cancer |
| title_full_unstemmed | RNA splicing junction landscape reveals abundant tumor-specific transcripts in human cancer |
| title_short | RNA splicing junction landscape reveals abundant tumor-specific transcripts in human cancer |
| title_sort | rna splicing junction landscape reveals abundant tumor specific transcripts in human cancer |
| topic | CP: Cell biology CP: Molecular biology |
| url | http://www.sciencedirect.com/science/article/pii/S2211124724012440 |
| work_keys_str_mv | AT qinli rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer AT zitengli rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer AT bingchen rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer AT jingjingzhao rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer AT hongwuyu rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer AT jiahu rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer AT hongyanlai rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer AT henazhang rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer AT yanli rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer AT zhiqiangmeng rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer AT zhixianghu rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer AT shenglinhuang rnasplicingjunctionlandscaperevealsabundanttumorspecifictranscriptsinhumancancer |