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Chan JJ, Zhang B, Chew XH, Salhi A, Kwok ZH, Lim CY, Desi N, Subramaniam N, Siemens A, Kinanti T, Ong S, Sanchez-Mejias A, Ly PT, An O, Sundar R, Fan X, Wang S, Siew BE, Lee KC, Chong CS, Lieske B, Cheong WK, Goh Y, Fam WN, Ooi MG, Koh BTH, Iyer SG, Ling WH, Chen J, Yoong BK, Chanwat R, Bonney GK, Goh BKP, Zhai W, Fullwood MJ, Wang W, Tan KK, Chng WJ, Dan YY, Pitt JJ, Roca X, Guccione E, Vardy LA, Chen L, Gao X, Chow PKH, Yang H, Tay Y. Pan-cancer pervasive upregulation of 3' UTR splicing drives tumourigenesis. Nat Cell Biol 2022; 24:928-939. [PMID: 35618746 PMCID: PMC9203280 DOI: 10.1038/s41556-022-00913-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/07/2022] [Indexed: 11/15/2022]
Abstract
Most mammalian genes generate messenger RNAs with variable untranslated regions (UTRs) that are important post-transcriptional regulators. In cancer, shortening at 3′ UTR ends via alternative polyadenylation can activate oncogenes. However, internal 3′ UTR splicing remains poorly understood as splicing studies have traditionally focused on protein-coding alterations. Here we systematically map the pan-cancer landscape of 3′ UTR splicing and present this in SpUR (http://www.cbrc.kaust.edu.sa/spur/home/). 3′ UTR splicing is widespread, upregulated in cancers, correlated with poor prognosis and more prevalent in oncogenes. We show that antisense oligonucleotide-mediated inhibition of 3′ UTR splicing efficiently reduces oncogene expression and impedes tumour progression. Notably, CTNNB1 3′ UTR splicing is the most consistently dysregulated event across cancers. We validate its upregulation in hepatocellular carcinoma and colon adenocarcinoma, and show that the spliced 3′ UTR variant is the predominant contributor to its oncogenic functions. Overall, our study highlights the importance of 3′ UTR splicing in cancer and may launch new avenues for RNA-based anti-cancer therapeutics. Chan et al. report that 3′ UTR splicing is widespread and enhanced across different cancer types and is associated with more advanced tumour progression.
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Affiliation(s)
- Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xiao Hong Chew
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Adil Salhi
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zhi Hao Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, MA, USA
| | - Chun You Lim
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ng Desi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Nagavidya Subramaniam
- A*STAR Skin Research Labs and Skin Research Institute of Singapore, A*STAR, Immunos, Singapore, Singapore
| | - Angela Siemens
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,The University of British Columbia, Vancouver, British Columbia, Canada
| | - Tyas Kinanti
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shane Ong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Avencia Sanchez-Mejias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Integra Therapeutics S.L., Barcelona, Spain
| | - Phuong Thao Ly
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Raghav Sundar
- Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
| | - Xiaonan Fan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shi Wang
- Department of Pathology, National University Health System, Singapore, Singapore
| | - Bei En Siew
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kuok Chung Lee
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Choon Seng Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Bettina Lieske
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wai-Kit Cheong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Yufen Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wee Nih Fam
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Melissa G Ooi
- Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bryan T H Koh
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shridhar Ganpathi Iyer
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Hepatobiliary & Pancreatic Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wen Huan Ling
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Boon-Koon Yoong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Rawisak Chanwat
- Hepato-Pancreato-Biliary Surgery Unit, Department of Surgery, National Cancer Institute, Bangkok, Thailand
| | - Glenn Kunnath Bonney
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Hepatobiliary & Pancreatic Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Brian K P Goh
- Department of Hepatopancreatobiliary and Transplantation Surgery, Singapore General Hospital and National Cancer Center Singapore, Singapore, Singapore
| | - Weiwei Zhai
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Melissa J Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wilson Wang
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Colorectal Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yock Young Dan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ernesto Guccione
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Leah A Vardy
- A*STAR Skin Research Labs and Skin Research Institute of Singapore, A*STAR, Immunos, Singapore, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,BioMap, Beijing, China
| | - Pierce K H Chow
- Program in Clinical and Translational Liver Cancer Research, National Cancer Center Singapore, Singapore, Singapore.,Department of Hepatopancreatobiliary and Transplantation Surgery, Singapore General Hospital and National Cancer Center Singapore, Singapore, Singapore.,Academic Clinical Programme for Surgery, SingHealth Duke-NUS Academic Medical Centre (AMC), Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore. .,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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Ly PT, Tan YS, Koe CT, Zhang Y, Xie G, Endow S, Deng WM, Yu F, Wang H. CRL4Mahj E3 ubiquitin ligase promotes neural stem cell reactivation. PLoS Biol 2019; 17:e3000276. [PMID: 31170139 PMCID: PMC6553684 DOI: 10.1371/journal.pbio.3000276] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 05/02/2019] [Indexed: 12/22/2022] Open
Abstract
The ability of neural stem cells (NSCs) to transit between quiescence and proliferation is crucial for brain development and homeostasis. Drosophila Hippo pathway maintains NSC quiescence, but its regulation during brain development remains unknown. Here, we show that CRL4Mahj, an evolutionarily conserved E3 ubiquitin ligase, is essential for NSC reactivation (exit from quiescence). We demonstrate that damaged DNA-binding protein 1 (DDB1) and Cullin4, two core components of Cullin4-RING ligase (CRL4), are intrinsically required for NSC reactivation. We have identified a substrate receptor of CRL4, Mahjong (Mahj), which is necessary and sufficient for NSC reactivation. Moreover, we show that CRL4Mahj forms a protein complex with Warts (Wts/large tumor suppressor [Lats]), a kinase of the Hippo signaling pathway, and Mahj promotes the ubiquitination of Wts. Our genetic analyses further support the conclusion that CRL4Mahj triggers NSC reactivation by inhibition of Wts. Given that Cullin4B mutations cause mental retardation and cerebral malformation, similar regulatory mechanisms may be applied to the human brain. During the transition from quiescence to reactivation of neural stem cells, the E3 ubiquitin ligase CRL4Mahj promotes their reactivation by inhibiting Wts, a core kinase of Hippo signalling pathway.
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Affiliation(s)
- Phuong Thao Ly
- Neuroscience and Behavioural Disorders Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Ye Sing Tan
- Neuroscience and Behavioural Disorders Programme, Duke-NUS Medical School, Singapore, Singapore
| | | | - Yingjie Zhang
- Neuroscience and Behavioural Disorders Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Gengqiang Xie
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Sharyn Endow
- Neuroscience and Behavioural Disorders Programme, Duke-NUS Medical School, Singapore, Singapore
- Department of Cell Biology, Duke University Medical Centre, Durham, North Carolina, United States of America
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Fengwei Yu
- Neuroscience and Behavioural Disorders Programme, Duke-NUS Medical School, Singapore, Singapore
- Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Hongyan Wang
- Neuroscience and Behavioural Disorders Programme, Duke-NUS Medical School, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail:
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