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Yu Q, Wu T, Xu W, Wei J, Zhao A, Wang M, Li M, Chi G. PTBP1 as a potential regulator of disease. Mol Cell Biochem 2023:10.1007/s11010-023-04905-x. [PMID: 38129625 DOI: 10.1007/s11010-023-04905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) is a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, which plays a key role in alternative splicing of precursor mRNA and RNA metabolism. PTBP1 is universally expressed in various tissues and binds to multiple downstream transcripts to interfere with physiological and pathological processes such as the tumor growth, body metabolism, cardiovascular homeostasis, and central nervous system damage, showing great prospects in many fields. The function of PTBP1 involves the regulation and interaction of various upstream molecules, including circular RNAs (circRNAs), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). These regulatory systems are inseparable from the development and treatment of diseases. Here, we review the latest knowledge regarding the structure and molecular functions of PTBP1 and summarize its functions and mechanisms of PTBP1 in various diseases, including controversial studies. Furthermore, we recommend future studies on PTBP1 and discuss the prospects of targeting PTBP1 in new clinical therapeutic approaches.
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Affiliation(s)
- Qi Yu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Tongtong Wu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Wenhong Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Junyuan Wei
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Anqi Zhao
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Miaomiao Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Meiying Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China.
| | - Guangfan Chi
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China.
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Jun Y, Suh YS, Park S, Lee J, Kim JI, Lee S, Lee WP, Anczuków O, Yang HK, Lee C. Comprehensive Analysis of Alternative Splicing in Gastric Cancer Identifies Epithelial-Mesenchymal Transition Subtypes Associated with Survival. Cancer Res 2022; 82:543-555. [PMID: 34903603 PMCID: PMC9359730 DOI: 10.1158/0008-5472.can-21-2117] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/25/2021] [Accepted: 12/03/2021] [Indexed: 01/07/2023]
Abstract
Alternatively spliced RNA isoforms are a hallmark of tumors, but their nature, prevalence, and clinical implications in gastric cancer have not been comprehensively characterized. We systematically profiled the splicing landscape of 83 gastric tumors and matched normal mucosa, identifying and experimentally validating eight splicing events that can classify all gastric cancers into three subtypes: epithelial-splicing (EpiS), mesenchymal-splicing (MesS), and hybrid-splicing. These subtypes were associated with distinct molecular signatures and epithelial-mesenchymal transition markers. Subtype-specific splicing events were enriched in motifs for splicing factors RBM24 and ESRP1, which were upregulated in MesS and EpiS tumors, respectively. A simple classifier based only on RNA levels of RBM24 and ESRP1, which can be readily implemented in the clinic, was sufficient to distinguish gastric cancer subtypes and predict patient survival in multiple independent patient cohorts. Overall, this study provides insights into alternative splicing in gastric cancer and the potential clinical utility of splicing-based patient classification. SIGNIFICANCE This study presents a comprehensive analysis of alternative splicing in the context of patient classification, molecular mechanisms, and prognosis in gastric cancer.
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Affiliation(s)
- Yukyung Jun
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul, Korea.,Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, Korea
| | - Yun-Suhk Suh
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Department of Surgery, Seoul National University College of Medicine, Seoul, Korea.,Department of Surgery, Seoul National University Hospital, Seoul, Korea.,Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Jieun Lee
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Sanghyuk Lee
- Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Wan-Ping Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,School of Cyber Science and Engineering, Xi'an Jiaotong University, Xi'an, China.,Corresponding Authors: Charles Lee, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032. Phone: 860-837-2458; E-mail: ; Han-Kwang Yang, ; Olga Anczuków, ; and Wan-Ping Lee,
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Corresponding Authors: Charles Lee, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032. Phone: 860-837-2458; E-mail: ; Han-Kwang Yang, ; Olga Anczuków, ; and Wan-Ping Lee,
| | - Han-Kwang Yang
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea.,Department of Surgery, Seoul National University Hospital, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.,Corresponding Authors: Charles Lee, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032. Phone: 860-837-2458; E-mail: ; Han-Kwang Yang, ; Olga Anczuków, ; and Wan-Ping Lee,
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.,Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea.,The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Corresponding Authors: Charles Lee, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032. Phone: 860-837-2458; E-mail: ; Han-Kwang Yang, ; Olga Anczuków, ; and Wan-Ping Lee,
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Ray D, Yun YC, Idris M, Cheng S, Boot A, Iain TBH, Rozen SG, Tan P, Epstein DM. A tumor-associated splice-isoform of MAP2K7 drives dedifferentiation in MBNL1-low cancers via JNK activation. Proc Natl Acad Sci U S A 2020; 117:16391-16400. [PMID: 32601196 PMCID: PMC7368273 DOI: 10.1073/pnas.2002499117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Master splicing regulator MBNL1 shapes large transcriptomic changes that drive cellular differentiation during development. Here we demonstrate that MBNL1 is a suppressor of tumor dedifferentiation. We surveyed MBNL1 expression in matched tumor/normal pairs across The Cancer Genome Atlas and found that MBNL1 was down-regulated in several common cancers. Down-regulation of MBNL1 predicted poor overall survival in breast, lung, and stomach adenocarcinomas and increased relapse and distant metastasis in triple-negative breast cancer. Down-regulation of MBNL1 led to increased tumorigenic and stem/progenitor-like properties in vitro and in vivo. A discrete set of alternative splicing events (ASEs) are shared between MBNL1-low cancers and embryonic stem cells including a MAP2K7∆exon2 splice variant that leads to increased stem/progenitor-like properties via JNK activation. Accordingly, JNK inhibition is capable of reversing MAP2K7∆exon2-driven tumor dedifferentiation in MBNL1-low cancer cells. Our work elucidates an alternative-splicing mechanism that drives tumor dedifferentiation and identifies biomarkers that predict enhanced susceptibility to JNK inhibition.
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Affiliation(s)
- Debleena Ray
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 165897 Singapore, Singapore;
| | - Yu Chye Yun
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 165897 Singapore, Singapore
| | - Muhammad Idris
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 165897 Singapore, Singapore
| | - Shanshan Cheng
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 165897 Singapore, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, 165897 Singapore, Singapore
| | - Arnoud Boot
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 165897 Singapore, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, 165897 Singapore, Singapore
| | - Tan Bee Huat Iain
- Division of Medical Oncology, National Cancer Centre, 169610 Singapore, Singapore
| | - Steven G Rozen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 165897 Singapore, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, 165897 Singapore, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 165897 Singapore, Singapore
| | - David M Epstein
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 165897 Singapore, Singapore;
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