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Chauhan AS, Jhujh SS, Stewart GS. E3 ligases: a ubiquitous link between DNA repair, DNA replication and human disease. Biochem J 2024; 481:923-944. [PMID: 38985307 DOI: 10.1042/bcj20240124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Maintenance of genome stability is of paramount importance for the survival of an organism. However, genomic integrity is constantly being challenged by various endogenous and exogenous processes that damage DNA. Therefore, cells are heavily reliant on DNA repair pathways that have evolved to deal with every type of genotoxic insult that threatens to compromise genome stability. Notably, inherited mutations in genes encoding proteins involved in these protective pathways trigger the onset of disease that is driven by chromosome instability e.g. neurodevelopmental abnormalities, neurodegeneration, premature ageing, immunodeficiency and cancer development. The ability of cells to regulate the recruitment of specific DNA repair proteins to sites of DNA damage is extremely complex but is primarily mediated by protein post-translational modifications (PTMs). Ubiquitylation is one such PTM, which controls genome stability by regulating protein localisation, protein turnover, protein-protein interactions and intra-cellular signalling. Over the past two decades, numerous ubiquitin (Ub) E3 ligases have been identified to play a crucial role not only in the initiation of DNA replication and DNA damage repair but also in the efficient termination of these processes. In this review, we discuss our current understanding of how different Ub E3 ligases (RNF168, TRAIP, HUWE1, TRIP12, FANCL, BRCA1, RFWD3) function to regulate DNA repair and replication and the pathological consequences arising from inheriting deleterious mutations that compromise the Ub-dependent DNA damage response.
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Affiliation(s)
- Anoop S Chauhan
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Satpal S Jhujh
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
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2
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Chen H, Ferguson CJ, Mitchell DC, Titus A, Paulo JA, Hwang A, Lin TH, Yano H, Gu W, Song SK, Yuede CM, Gygi SP, Bonni A, Kim AH. The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.24.563880. [PMID: 37961719 PMCID: PMC10634808 DOI: 10.1101/2023.10.24.563880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Precise control of protein ubiquitination is essential for brain development, and hence, disruption of ubiquitin signaling networks can lead to neurological disorders. Mutations of the deubiquitinase USP7 cause the Hao-Fountain syndrome (HAFOUS), characterized by developmental delay, intellectual disability, autism, and aggressive behavior. Here, we report that conditional deletion of USP7 in excitatory neurons in the mouse forebrain triggers diverse phenotypes including sensorimotor deficits, learning and memory impairment, and aggressive behavior, resembling clinical features of HAFOUS. USP7 deletion induces neuronal apoptosis in a manner dependent of the tumor suppressor p53. However, most behavioral abnormalities in USP7 conditional mice persist despite p53 loss. Strikingly, USP7 deletion in the brain perturbs the synaptic proteome and dendritic spine morphogenesis independently of p53. Integrated proteomics analysis reveals that the neuronal USP7 interactome is enriched for proteins implicated in neurodevelopmental disorders and specifically identifies the RNA splicing factor Ppil4 as a novel neuronal substrate of USP7. Knockdown of Ppil4 in cortical neurons impairs dendritic spine morphogenesis, phenocopying the effect of USP7 loss on dendritic spines. These findings reveal a novel USP7-Ppil4 ubiquitin signaling link that regulates neuronal connectivity in the developing brain, with implications for our understanding of the pathogenesis of HAFOUS and other neurodevelopmental disorders.
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3
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Liu J, Cao L, Wang Y, Zou Y, Guo Q, Chen S, Jiang B, Wu X, Zheng L, Zhang S, Lu S, Zhou K, Jiang P, Xiao Y, Yang R, Dong S, Li Z, Chen D, Zhang Y, Zhang N, Sun G, Xing C, Song X, Wang Z, Cao L. The phosphorylation-deubiquitination positive feedback loop of the CHK2-USP7 axis stabilizes p53 under oxidative stress. Cell Rep 2024; 43:114366. [PMID: 38879877 DOI: 10.1016/j.celrep.2024.114366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/20/2024] [Accepted: 05/31/2024] [Indexed: 06/18/2024] Open
Abstract
p53 regulates multiple signaling pathways and maintains cell homeostasis under conditions of DNA damage and oxidative stress. Although USP7 has been shown to promote p53 stability via deubiquitination, the USP7-p53 activation mechanism has remained unclear. Here, we propose that DNA damage induces reactive oxygen species (ROS) production and activates ATM-CHK2, and CHK2 then phosphorylates USP7 at S168 and T231. USP7 phosphorylation is essential for its deubiquitination activity toward p53. USP7 also deubiquitinates CHK2 at K119 and K131, increasing CHK2 stability and creating a positive feedback loop between CHK2 and USP7. Compared to peri-tumor tissues, thyroid cancer and colon cancer tissues show higher CHK2 and phosphorylated USP7 (S168, T231) levels, and these levels are positively correlated. Collectively, our results uncover a phosphorylation-deubiquitination positive feedback loop involving the CHK2-USP7 axis that supports the stabilization of p53 and the maintenance of cell homeostasis.
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Affiliation(s)
- Jingwei Liu
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China; Department of Anus and Intestine Surgery, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province 110001, China
| | - Liangzi Cao
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Yubang Wang
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Yu Zou
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Qiqiang Guo
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Shu Chen
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Bo Jiang
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Xuan Wu
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Lixia Zheng
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Siyi Zhang
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Songming Lu
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Keshen Zhou
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Pengcheng Jiang
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Yutong Xiao
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Ruohan Yang
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Shiyuan Dong
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Ziwei Li
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Di Chen
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Ying Zhang
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Naijin Zhang
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Guozhe Sun
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang 110001, China.
| | - Chengzhong Xing
- Department of Anus and Intestine Surgery, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province 110001, China.
| | - Xiaoyu Song
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China.
| | - Zhenning Wang
- Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China.
| | - Liu Cao
- The College of Basic Medical Science, Health Sciences Institute, China Medical University, Shenyang, Liaoning Province 110122, China; Key Laboratory of Cell Biology of the Ministry of Public Health, Key Laboratory of Medical Cell Biology of the Ministry of Education, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors of the Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging-Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province 110122, China.
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4
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Vogt M, Classen S, Krause AK, Peter NJ, Petersen C, Rothkamm K, Borgmann K, Meyer F. USP7 Deregulation Impairs S Phase Specific DNA Repair after Irradiation in Breast Cancer Cells. Biomedicines 2024; 12:762. [PMID: 38672118 PMCID: PMC11047985 DOI: 10.3390/biomedicines12040762] [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: 02/15/2024] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
The ubiquitin specific protease 7 (USP7) is a deubiquitinating enzyme with numerous substrates. Aberrant expression of USP7 is associated with tumor progression. This study aims to investigate how a deregulated USP7 expression affects chromosomal instability and prognosis of breast cancer patients in silico and radiosensitivity and DNA repair in breast cancer cells in vitro. The investigations in silico were performed using overall survival and USP7 mRNA expression data of breast cancer patients. The results showed that a high USP7 expression was associated with increased chromosomal instability and decreased overall survival. The in vitro experiments were performed in a luminal and a triple-negative breast cancer cell line. Proliferation, DNA repair, DNA replication stress, and survival after USP7 overexpression or inhibition and irradiation were analyzed. Both, USP7 inhibition and overexpression resulted in decreased cellular survival, distinct radiosensitization and an increased number of residual DNA double-strand breaks in the S phase following irradiation. RAD51 recruitment and base incorporation were decreased after USP7 inhibition plus irradiation and more single-stranded DNA was detected. The results show that deregulation of USP7 activity disrupts DNA repair in the S phase by increasing DNA replication stress and presents USP7 as a promising target to overcome the radioresistance of breast tumors.
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Affiliation(s)
| | | | | | | | | | | | | | - Felix Meyer
- Department of Radiotherapy & Radiation Oncology, Hubertus Wald Tumor Center—University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.V.); (S.C.); (A.K.K.); (N.-J.P.); (C.P.); (K.R.); (K.B.)
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5
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Bolhuis DL, Emanuele MJ, Brown NG. Friend or foe? Reciprocal regulation between E3 ubiquitin ligases and deubiquitinases. Biochem Soc Trans 2024; 52:BST20230454. [PMID: 38414432 DOI: 10.1042/bst20230454] [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: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/29/2024]
Abstract
Protein ubiquitination is a post-translational modification that entails the covalent attachment of the small protein ubiquitin (Ub), which acts as a signal to direct protein stability, localization, or interactions. The Ub code is written by a family of enzymes called E3 Ub ligases (∼600 members in humans), which can catalyze the transfer of either a single ubiquitin or the formation of a diverse array of polyubiquitin chains. This code can be edited or erased by a different set of enzymes termed deubiquitinases (DUBs; ∼100 members in humans). While enzymes from these distinct families have seemingly opposing activities, certain E3-DUB pairings can also synergize to regulate vital cellular processes like gene expression, autophagy, innate immunity, and cell proliferation. In this review, we highlight recent studies describing Ub ligase-DUB interactions and focus on their relationships.
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Affiliation(s)
- Derek L Bolhuis
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Care Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Care Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
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Su J, Huang F, Tian Y, Tian R, Qianqian G, Bello ST, Zeng D, Jendrichovsky P, Lau CG, Xiong W, Yu D, Tortorella M, Chen X, He J. Entorhinohippocampal cholecystokinin modulates spatial learning by facilitating neuroplasticity of hippocampal CA3-CA1 synapses. Cell Rep 2023; 42:113467. [PMID: 37979171 DOI: 10.1016/j.celrep.2023.113467] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 10/01/2023] [Accepted: 11/03/2023] [Indexed: 11/20/2023] Open
Abstract
The hippocampus is broadly impacted by neuromodulations. However, how neuropeptides shape the function of the hippocampus and the related spatial learning and memory remains unclear. Here, we discover the crucial role of cholecystokinin (CCK) in heterosynaptic neuromodulation from the medial entorhinal cortex (MEC) to the hippocampus. Systematic knockout of the CCK gene impairs CA3-CA1 LTP and space-related performance. The MEC provides most of the CCK-positive neurons projecting to the hippocampal region, which potentiates CA3-CA1 long-term plasticity heterosynaptically in a frequency- and NMDA receptor (NMDAR)-dependent manner. Selective inhibition of MEC CCKergic neurons or downregulation of their CCK mRNA levels also impairs CA3-CA1 LTP formation and animals' performance in the water maze. This excitatory extrahippocampal projection releases CCK upon high-frequency excitation and is active during animal exploration. Our results reveal the critical role of entorhinal CCKergic projections in bridging intra- and extrahippocampal circuitry at electrophysiological and behavioral levels.
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Affiliation(s)
- Junfeng Su
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China
| | - Fengwen Huang
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China; Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, P.R. China.
| | - Yu Tian
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China
| | - Ran Tian
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China
| | - Gao Qianqian
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China
| | - Stephen Temitayo Bello
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China; Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, P.R. China
| | - Dingxaun Zeng
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China
| | - Peter Jendrichovsky
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China
| | - C Geoffrey Lau
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China
| | - Wenjun Xiong
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China; City University of Hong Kong Shenzhen Research Institute, Shenzhen, P.R. China
| | - Daiguan Yu
- Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, P.R. China
| | - Micky Tortorella
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, P.R. China; Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, P.R. China
| | - Xi Chen
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China; City University of Hong Kong Shenzhen Research Institute, Shenzhen, P.R. China.
| | - Jufang He
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China; Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China; City University of Hong Kong Shenzhen Research Institute, Shenzhen, P.R. China.
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7
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Park HB, Baek KH. Current and future directions of USP7 interactome in cancer study. Biochim Biophys Acta Rev Cancer 2023; 1878:188992. [PMID: 37775071 DOI: 10.1016/j.bbcan.2023.188992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
The ubiquitin-proteasome system (UPS) is an essential protein quality controller for regulating protein homeostasis and autophagy. Ubiquitination is a protein modification process that involves the binding of one or more ubiquitins to substrates through a series of enzymatic processes. These include ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligases (E3). Conversely, deubiquitination is a reverse process that removes ubiquitin from substrates via deubiquitinating enzymes (DUBs). Dysregulation of ubiquitination-related enzymes can lead to various human diseases, including cancer, through the modulation of protein ubiquitination. The most structurally and functionally studied DUB is the ubiquitin-specific protease 7 (USP7). Both the TRAF and UBL domains of USP7 are known to bind to the [P/A/E]-X-X-S or K-X-X-X-K motif of substrates. USP7 has been shown to be involved in cancer pathogenesis by binding with numerous substrates. Recently, a novel substrate of USP7 was discovered through a systemic analysis of its binding motif. This review summarizes the currently discovered substrates and cellular functions of USP7 in cancer and suggests putative substrates of USP7 through a comprehensive systemic analysis.
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Affiliation(s)
- Hong-Beom Park
- Department of Convergence, CHA University, Gyeonggi-Do 13488, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Convergence, CHA University, Gyeonggi-Do 13488, Republic of Korea; International Ubiquitin Center(,) CHA University, Gyeonggi-Do 13488, Republic of Korea.
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8
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Ananthapadmanabhan V, Shows KH, Dickinson AJ, Litovchick L. Insights from the protein interaction Universe of the multifunctional "Goldilocks" kinase DYRK1A. Front Cell Dev Biol 2023; 11:1277537. [PMID: 37900285 PMCID: PMC10600473 DOI: 10.3389/fcell.2023.1277537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
Human Dual specificity tyrosine (Y)-Regulated Kinase 1A (DYRK1A) is encoded by a dosage-dependent gene located in the Down syndrome critical region of human chromosome 21. The known substrates of DYRK1A include proteins involved in transcription, cell cycle control, DNA repair and other processes. However, the function and regulation of this kinase is not fully understood, and the current knowledge does not fully explain the dosage-dependent function of this kinase. Several recent proteomic studies identified DYRK1A interacting proteins in several human cell lines. Interestingly, several of known protein substrates of DYRK1A were undetectable in these studies, likely due to a transient nature of the kinase-substrate interaction. It is possible that the stronger-binding DYRK1A interacting proteins, many of which are poorly characterized, are involved in regulatory functions by recruiting DYRK1A to the specific subcellular compartments or distinct signaling pathways. Better understanding of these DYRK1A-interacting proteins could help to decode the cellular processes regulated by this important protein kinase during embryonic development and in the adult organism. Here, we review the current knowledge of the biochemical and functional characterization of the DYRK1A protein-protein interaction network and discuss its involvement in human disease.
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Affiliation(s)
- Varsha Ananthapadmanabhan
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, United States
| | - Kathryn H. Shows
- Department of Biology, Virginia State University, Petersburg, VA, United States
| | - Amanda J. Dickinson
- Department of Biology, Virginia Commonwealth University, Richmond, VA, United States
| | - Larisa Litovchick
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, United States
- Massey Cancer Center, Richmond, VA, United States
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9
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Lee SY, Kim MY, Han JH, Park SS, Yun Y, Jee SC, Han JJ, Lee JH, Seok H, Choi BY. Ramifications of POU4F3 variants associated with autosomal dominant hearing loss in various molecular aspects. Sci Rep 2023; 13:12584. [PMID: 37537203 PMCID: PMC10400627 DOI: 10.1038/s41598-023-38272-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
POU4F3, a member of the POU family of transcription factors, commonly causes autosomal dominant deafness. Exome sequencing was used to identify four novel variants in POU4F3 (NM_002700.2), including c.564dupA: p.Ala189SerfsTer26, c.743T > C:p.Leu248Pro, c.879C > A:p.Phe293Leu, and c.952G > A:p.Val318Met, and diverse aspects of the molecular consequences of their protein expression, stability, subcellular localization, and transcriptional activity were investigated. The expression of three mutant proteins, encoded by missense variants, was reduced compared to the wild-type protein, demonstrating that the mutants were unstable and vulnerable to degradation. Additionally, all the mutant proteins had distinct subcellular localization patterns. A mutant protein carrying p.Ala189SerfsTer26, in which both mono- and bi-partite nuclear localization signals were disrupted, showed abnormal subcellular localization. Resultantly, all the mutant proteins significantly reduced the transcriptional activity required to regulate the downstream target gene expression. Furthermore, we identified the altered expression of 14 downstream target genes associated with inner ear development using patient-derived lymphoblastoid cell lines. There was a significant correlation of the expression profile between patient-derived cells and the cochlear hair cells, which provided a breakthrough for cases where the collection of human cochlear samples for transcriptome studies was unfeasible. This study expanded the genotypic spectrum of POU4F3 in DFNA15, and further refined the molecular mechanisms underlying POU4F3-associated DFNA15.
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Affiliation(s)
- Sang-Yeon Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Min Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Republic of Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Republic of Korea
| | - Sang Soo Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yejin Yun
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung-Cheol Jee
- Department of Transdisciplinary Research and Collaboration, Genomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jae Joon Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Heeyoung Seok
- Department of Transdisciplinary Research and Collaboration, Genomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Republic of Korea.
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea.
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10
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Kim EY, Basit A, Kim WJ, Ko EB, Lee JH. Multi-functional regulation of cGAS by the nuclear localization signal2 (NLS2) motif: Nuclear localization, enzyme activity and protein degradation. Biochem Biophys Res Commun 2023; 673:1-8. [PMID: 37352571 DOI: 10.1016/j.bbrc.2023.06.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/11/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS), which recognizes double-stranded DNA (dsDNA) and activates the innate immune system, is mainly localized in the cytosol, but also shows nuclear localization. Here, we sought to determine the role of nuclear cGAS by mutating known nuclear localization signal (NLS) motifs in cGAS and assessing its functionality by monitoring phosphorylation of the downstream target, interferon regulatory factor-3 (IRF3). Interestingly, NLS2-mutated cGAS failed to promote phosphorylation of IRF3, reflecting the loss of its ability to produce cyclic GMP-AMP (cGAMP). We further found that insertion of an NLS from SV40 large T antigen could not restore this loss of activity, indicating that this loss was attributable to the mutation of NLS2 itself, but not dependent on the inability of cGAS to enter the nucleus. NLS2-mutant cGAS protein also showed decreased stability dependent on polyubiquitination, an effect that was independent of both its loss of catalytic function and its inability to enter into the nucleus. Collectively, these findings indicate that the NLS2 motif of cGAS is not only involved in regulating the subcellular localization of cGAS protein but also influences its stability and enzymatic activity through independent mechanisms, highlighting the novel roles of NLS2 in regulating the intracellular functions of cGAS.
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Affiliation(s)
- Eui-Yun Kim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 443-721, South Korea; Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, 443-721, South Korea.
| | - Abdul Basit
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 443-721, South Korea; Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, 443-721, South Korea
| | - Won-Joo Kim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 443-721, South Korea; Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, 443-721, South Korea
| | - Eun-Bi Ko
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 443-721, South Korea; Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, 443-721, South Korea
| | - Jae-Ho Lee
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 443-721, South Korea; Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, 443-721, South Korea.
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11
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Chi L, Wang H, Yu F, Gao C, Dai H, Si X, Liu L, Wang Z, Zheng J, Ke Y, Liu H, Zhang Q. Recent Progress of Ubiquitin-Specific-Processing Protease 7 Inhibitors. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2023. [DOI: 10.1134/s1068162023020073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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12
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Al Adhami H, Vallet J, Schaal C, Schumacher P, Bardet AF, Dumas M, Chicher J, Hammann P, Daujat S, Weber M. Systematic identification of factors involved in the silencing of germline genes in mouse embryonic stem cells. Nucleic Acids Res 2023; 51:3130-3149. [PMID: 36772830 PMCID: PMC10123117 DOI: 10.1093/nar/gkad071] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 12/29/2022] [Accepted: 01/23/2023] [Indexed: 02/12/2023] Open
Abstract
In mammals, many germline genes are epigenetically repressed to prevent their illegitimate expression in somatic cells. To advance our understanding of the mechanisms restricting the expression of germline genes, we analyzed their chromatin signature and performed a CRISPR-Cas9 knock-out screen for genes involved in germline gene repression using a Dazl-GFP reporter system in mouse embryonic stem cells (mESCs). We show that the repression of germline genes mainly depends on the polycomb complex PRC1.6 and DNA methylation, which function additively in mESCs. Furthermore, we validated novel genes involved in the repression of germline genes and characterized three of them: Usp7, Shfm1 (also known as Sem1) and Erh. Inactivation of Usp7, Shfm1 or Erh led to the upregulation of germline genes, as well as retrotransposons for Shfm1, in mESCs. Mechanistically, USP7 interacts with PRC1.6 components, promotes PRC1.6 stability and presence at germline genes, and facilitates DNA methylation deposition at germline gene promoters for long term repression. Our study provides a global view of the mechanisms and novel factors required for silencing germline genes in embryonic stem cells.
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Affiliation(s)
- Hala Al Adhami
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Judith Vallet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Celia Schaal
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Paul Schumacher
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France.,Karlsruhe Institute of Technology (KIT), IAB, Department of Food Chemistry and Toxicology, 76131 Karlsruhe, Germany
| | - Anaïs Flore Bardet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, 67000 Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, 67000 Strasbourg, France
| | - Sylvain Daujat
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Michael Weber
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
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13
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Wang J, Chen H, Deng Q, Chen Y, Wang Z, Yan Z, Wang Y, Tang H, Liang H, Jiang Y. High expression of RNF169 is associated with poor prognosis in pancreatic adenocarcinoma by regulating tumour immune infiltration. Front Genet 2023; 13:1022626. [PMID: 36685833 PMCID: PMC9849556 DOI: 10.3389/fgene.2022.1022626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Background: Pancreatic adenocarcinoma (PAAD) is a highly deadly and aggressive tumour with a poor prognosis. However, the prognostic value of RNF169 and its related mechanisms in PAAD have not been elucidated. In this study, we aimed to explore prognosis-related genes, especially RNF169 in PAAD and to identify novel potential prognostic predictors of PAAD. Methods: The GEPIA and UALCAN databases were used to investigate the expression and prognostic value of RNF169 in PAAD. The correlation between RNF169 expression and immune infiltration was determined by using TIMER and TISIDB. Correlation analysis with starBase was performed to identify a potential regulatory axis of lncRNA-miRNA-RNF169. Results: The data showed that the level of RNF169 mRNA expression in PAAD tissues was higher than that in normal tissues. High RNF169 expression was correlated with poor prognosis in PAAD. In addition, analysis with the TISIDB and TIMER databases revealed that RNF169 expression was positively correlated with tumour immune infiltration in PAAD. Correlation analysis suggested that the long non-coding RNA (lncRNA) AL049555.1 and the microRNA (miRNA) hsa-miR-324-5p were involved in the expression of RNF169, composing a potential regulatory axis to control the progression of PAAD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that RNF169 plays a role in PAAD through pathways such as TNF, Hippo, JAK-STAT and Toll-like receptor signaling. Conclusion: In summary, the upregulation of RNF169 expression mediated by ncRNAs might influence immune cell infiltration in the microenvironment; thus, it can be used as a prognostic biomarker and a potential therapeutic target in PAAD.
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Affiliation(s)
- Jieyan Wang
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Hanghang Chen
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qiong Deng
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Yeda Chen
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Zhu Wang
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Zhengzheng Yan
- Dongguan Key Laboratory of Respiratory and Critical Care Medicine, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China
| | - Yinglin Wang
- Department of Pediatrics, The Second Hospital of Zhuzhou, Zhuzhou, Hunan, China
| | - Haoxuan Tang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hui Liang
- Department of Urology, The People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, Guangdong, China,*Correspondence: Hui Liang, ; Yong Jiang,
| | - Yong Jiang
- Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, Department of pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,Dongguan Key Laboratory of Respiratory and Critical Care Medicine, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, China,*Correspondence: Hui Liang, ; Yong Jiang,
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14
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Lu X, An L, Fan G, Zang L, Huang W, Li J, Liu J, Ge W, Huang Y, Xu J, Du S, Cao Y, Zhou T, Yin H, Yu L, Jiao S, Wang H. EGFR signaling promotes nuclear translocation of plasma membrane protein TSPAN8 to enhance tumor progression via STAT3-mediated transcription. Cell Res 2022; 32:359-374. [PMID: 35197608 PMCID: PMC8975831 DOI: 10.1038/s41422-022-00628-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/26/2022] [Indexed: 12/12/2022] Open
Abstract
TSPAN family of proteins are generally considered to assemble as multimeric complexes on the plasma membrane. Our previous work uncovered that TSPAN8 can translocate into the nucleus as a membrane-free form, a process that requires TSPAN8 palmitoylation and association with cholesterol to promote its extraction from the plasma membrane and subsequent binding with 14-3-3θ and importin-β. However, what upstream signal(s) regulate(s) the nuclear translocation of TSPAN8, the potential function of TSPAN8 in the nucleus, and the underlying molecular mechanisms all remain unclear. Here, we demonstrate that, epidermal growth factor receptor (EGFR) signaling induces TSPAN8 nuclear translocation by activating the kinase AKT, which in turn directly phosphorylates TSPAN8 at Ser129, an event essential for its binding with 14-3-3θ and importin ß1. In the nucleus, phosphorylated TSPAN8 interacts with STAT3 to enhance its chromatin occupancy and therefore regulates transcription of downstream cancer-promoting genes, such as MYC, BCL2, MMP9, etc. The EGFR-AKT-TSPAN8-STAT3 axis was found to be hyperactivated in multiple human cancers, and associated with aggressive phenotype and dismal prognosis. We further developed a humanized monoclonal antibody hT8Ab4 that specifically recognizes the large extracellular loop of TSPAN8 (TSPAN8-LEL), thus being able to block the extraction of TSPAN8 from the plasma membrane and consequently its nuclear localization. Importantly, both in vitro and in vivo studies demonstrated an antitumor effect of hT8Ab4. Collectively, we discovered an unconventional function of TSPAN8 and dissected the underlying molecular mechanisms, which not only showcase a new layer of biological complexity of traditional membrane proteins, but also shed light on TSPAN8 as a novel therapeutic target for refractory cancers.
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Affiliation(s)
- Xiaoqing Lu
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Breast Surgery, Shanxi Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, Shanxi, China
| | - Liwei An
- Department of Medical Ultrasound, Shanghai Tenth People's Hospital, Tongji University Cancer Center, School of Medicine, Tongji University, Shanghai, China
| | - Guangjian Fan
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lijuan Zang
- Department of Pathology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiyi Huang
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junjian Li
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Liu
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiyu Ge
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuwei Huang
- State Key Laboratory of Membrane Biology, Tsinghua-Peking University Joint Center for Life Sciences, School of Life Science, Tsinghua University, Beijing, China
| | - Jingxuan Xu
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaoqian Du
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuan Cao
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianhao Zhou
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huijing Yin
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking University Joint Center for Life Sciences, School of Life Science, Tsinghua University, Beijing, China
| | - Shi Jiao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongxia Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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15
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Zhou L, Ouyang T, Li M, Hong T, Mhs A, Meng W, Zhang N. Ubiquitin-Specific Peptidase 7: A Novel Deubiquitinase That Regulates Protein Homeostasis and Cancers. Front Oncol 2021; 11:784672. [PMID: 34869041 PMCID: PMC8640129 DOI: 10.3389/fonc.2021.784672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/26/2021] [Indexed: 12/23/2022] Open
Abstract
Ubiquitin-Specific Peptidase 7 (USP7), or herpes virus-associated protease (HAUSP), is the largest family of the deubiquitinating enzymes (DUBs). Recent studies have shown that USP7 plays a vital role in regulating various physiological and pathological processes. Dysregulation of these processes mediated by USP7 may contribute to many diseases, such as cancers. Moreover, USP7 with aberrant expression levels and abnormal activity are found in cancers. Therefore, given the association between USP7 and cancers, targeting USP7 could be considered as an attractive and potential therapeutic approach in cancer treatment. This review describes the functions of USP7 and the regulatory mechanisms of its expression and activity, aiming to emphasize the necessity of research on USP7, and provide a better understanding of USP7-related biological processes and cancer.
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Affiliation(s)
- Lin Zhou
- First Clinical Medical College, Nanchang University, Nanchang, China
| | - Taohui Ouyang
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Meihua Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tao Hong
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Alriashy Mhs
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Wei Meng
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Na Zhang
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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16
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Li S, Zhang H, Wei X. Roles and Mechanisms of Deubiquitinases (DUBs) in Breast Cancer Progression and Targeted Drug Discovery. Life (Basel) 2021; 11:life11090965. [PMID: 34575114 PMCID: PMC8467271 DOI: 10.3390/life11090965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 02/06/2023] Open
Abstract
Deubiquitinase (DUB) is an essential component in the ubiquitin—proteasome system (UPS) by removing ubiquitin chains from substrates, thus modulating the expression, activity, and localization of many proteins that contribute to tumor development and progression. DUBs have emerged as promising prognostic indicators and drug targets. DUBs have shown significant roles in regulating breast cancer growth, metastasis, resistance to current therapies, and several canonical oncogenic signaling pathways. In addition, specific DUB inhibitors have been identified and are expected to benefit breast cancer patients in the future. Here, we review current knowledge about the effects and molecular mechanisms of DUBs in breast cancer, providing novel insight into treatments of breast cancer-targeting DUBs.
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17
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Gao L, Zhu D, Wang Q, Bao Z, Yin S, Qiang H, Wieland H, Zhang J, Teichmann A, Jia J. Proteome Analysis of USP7 Substrates Revealed Its Role in Melanoma Through PI3K/Akt/FOXO and AMPK Pathways. Front Oncol 2021; 11:650165. [PMID: 33869052 PMCID: PMC8044529 DOI: 10.3389/fonc.2021.650165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/15/2021] [Indexed: 01/10/2023] Open
Abstract
The ubiquitin-specific protease 7 (USP7), as a deubiquitinating enzyme, plays an important role in tumor progression by various mechanisms and serves as a potential therapeutic target. However, the functional role of USP7 in melanoma remains elusive. Here, we found that USP7 is overexpressed in human melanoma by tissue microarray. We performed TMT-based quantitative proteomic analysis to evaluate the A375 human melanoma cells treated with siRNA of USP7. Our data revealed specific proteins as well as multiple pathways and processes that are impacted by USP7. We found that the phosphatidylinositol-3-kinases/Akt (PI3K-Akt), forkhead box O (FOXO), and AMP-activated protein kinase (AMPK) signaling pathways may be closely related to USP7 expression in melanoma. Moreover, knockdown of USP7 in A375 cells, particularly USP7 knockout using CRISPR-Cas9, verified that USP7 regulates cell proliferation in vivo and in vitro. The results showed that inhibition of USP7 increases expression of the AMPK beta (PRKAB1), caspase 7(CASP7), and protein phosphatase 2 subunit B R3 isoform (PPP2R3A), while attenuating expression of C subunit of vacuolar ATPase (ATP6V0C), and peroxisomal biogenesis factor 11 beta (PEX11B). In summary, these findings reveal an important role of USP7 in regulating melanoma progression via PI3K/Akt/FOXO and AMPK signaling pathways and implicate USP7 as an attractive anticancer target for melanoma.
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Affiliation(s)
- Lanyang Gao
- Sichuan Provincial Center for Gynaecology and Breast Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Danli Zhu
- Sichuan Provincial Center for Gynaecology and Breast Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qin Wang
- Sichuan Provincial Center for Gynaecology and Breast Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zheng Bao
- Sichuan Provincial Center for Gynaecology and Breast Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shigang Yin
- Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Nervous System Disease and Brain Functions, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Huiyan Qiang
- Department of Outpatient, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Heinrich Wieland
- Sichuan Provincial Center for Gynaecology and Breast Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinyue Zhang
- Sichuan Provincial Center for Gynaecology and Breast Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Alexander Teichmann
- Sichuan Provincial Center for Gynaecology and Breast Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jing Jia
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Anesthesiology, Southwest Medical University, Luzhou, China
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18
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Dong C, An L, Yu CH, Huen MSY. A DYRK1B-dependent pathway suppresses rDNA transcription in response to DNA damage. Nucleic Acids Res 2021; 49:1485-1496. [PMID: 33469661 PMCID: PMC7897492 DOI: 10.1093/nar/gkaa1290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/22/2020] [Accepted: 01/18/2021] [Indexed: 12/29/2022] Open
Abstract
DNA double-strand breaks (DSBs) at ribosomal gene loci trigger inhibition of ribosomal DNA (rDNA) transcription and extensive nucleolar reorganization, including the formation of nucleolar caps where rDNA DSBs engage with canonical DSB signaling and repair factors. While these nucleolar responses underlie maintenance of rDNA stability, the molecular components that drive each of these events remain to be defined. Here we report that full suppression of rRNA synthesis requires the DYRK1B kinase, a nucleolar DSB response that can be uncoupled from ATM-mediated DSB signaling events at the nucleolar periphery. Indeed, by targeting DSBs onto rDNA arrays, we uncovered that chemical inhibition or genetic inactivation of DYRK1B led to sustained nucleolar transcription. Not only does DYRK1B exhibit robust nucleolar accumulation following laser micro-irradiation across cell nuclei, we further showed that DYRK1B is required for rDNA DSB repair and rDNA copy number maintenance, and that DYRK1B-inactivated cells are hypersensitised to DSBs induced at the rDNA arrays. Together, our findings not only identify DYRK1B as a key signaling intermediate that coordinates DSB repair and rDNA transcriptional activities, but also support the idea of specialised DSB responses that operate within the nucleolus to preserve rDNA integrity.
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Affiliation(s)
- Chao Dong
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong S.A.R
| | - Liwei An
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong S.A.R
| | - Cheng-han Yu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong S.A.R
| | - Michael S Y Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong S.A.R
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, 5 Sassoon Road, Pokfulam, Hong Kong S.A.R
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19
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Ashton NW, Valles GJ, Jaiswal N, Bezsonova I, Woodgate R. DNA Polymerase ι Interacts with Both the TRAF-like and UBL1-2 Domains of USP7. J Mol Biol 2021; 433:166733. [PMID: 33279577 PMCID: PMC7873624 DOI: 10.1016/j.jmb.2020.166733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022]
Abstract
Reversible protein ubiquitination is an essential signaling mechanism within eukaryotes. Deubiquitinating enzymes are critical to this process, as they mediate removal of ubiquitin from substrate proteins. Ubiquitin-specific protease 7 (USP7) is a prominent deubiquitinating enzyme, with an extensive network of interacting partners and established roles in cell cycle activation, immune responses and DNA replication. Characterized USP7 substrates primarily interact with one of two major binding sites outside the catalytic domain. These are located on the USP7 N-terminal TRAF-like (TRAF) domain and the first and second UBL domains (UBL1-2) within the C-terminal tail. Here, we report that DNA polymerase iota (Pol ι) is a novel USP7 substrate that interacts with both TRAF and UBL1-2. Through the use of biophysical approaches and mutational analysis, we characterize both interfaces and demonstrate that bipartite binding to both USP7 domains is required for efficient Pol ι deubiquitination. Together, these data establish a new bipartite mode of USP7 substrate binding.
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Affiliation(s)
- Nicholas W Ashton
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Gabrielle J Valles
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA.
| | - Nancy Jaiswal
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA.
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA.
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
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20
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Molecular Mechanisms of DUBs Regulation in Signaling and Disease. Int J Mol Sci 2021; 22:ijms22030986. [PMID: 33498168 PMCID: PMC7863924 DOI: 10.3390/ijms22030986] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
The large family of deubiquitinating enzymes (DUBs) are involved in the regulation of a plethora of processes carried out inside the cell by protein ubiquitination. Ubiquitination is a basic pathway responsible for the correct protein homeostasis in the cell, which could regulate the fate of proteins through the ubiquitin–proteasome system (UPS). In this review we will focus on recent advances on the molecular mechanisms and specificities found for some types of DUBs enzymes, highlighting illustrative examples in which the regulatory mechanism for DUBs has been understood in depth at the molecular level by structural biology. DUB proteases are responsible for cleavage and regulation of the multiple types of ubiquitin linkages that can be synthesized inside the cell, known as the ubiquitin-code, which are tightly connected to specific substrate functions. We will display some strategies carried out by members of different DUB families to provide specificity on the cleavage of particular ubiquitin linkages. Finally, we will also discuss recent progress made for the development of drug compounds targeting DUB proteases, which are usually correlated to the progress of many pathologies such as cancer and neurodegenerative diseases.
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21
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Yang J, Lee SJ, Kwon Y, Ma L, Kim J. Tumor suppressive function of Matrin 3 in the basal-like breast cancer. Biol Res 2020; 53:42. [PMID: 32977861 PMCID: PMC7519516 DOI: 10.1186/s40659-020-00310-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Basal-like breast cancer (BLBC) or triple-negative breast cancer (TNBC) is an aggressive and highly metastatic subtype of human breast cancer. The present study aimed to elucidate the potential tumor-suppressive function of MATR3, an abundant nuclear protein, in BLBC/TNBC, whose cancer-relevance has not been characterized. METHODS We analyzed in vitro tumorigenecity by cell proliferation and soft agar colony formation assays, apoptotic cell death by flow cytometry and Poly (ADP-ribose) polymerase (PARP) cleavage, epithelial-mesenchymal transition (EMT) by checking specific EMT markers with real-time quantitative PCR and in vitro migration and invasion by Boyden Chamber assays. To elucidate the underlying mechanism by which MATR3 functions as a tumor suppressor, we performed Tandem affinity purification followed by mass spectrometry (TAP-MS) and pathway analysis. We also scrutinized MATR3 expression levels in the different subtypes of human breast cancer and the correlation between MATR3 expression and patient survival by bioinformatic analyses of publicly available transcriptome datasets. RESULTS MATR3 suppressed in vitro tumorigenecity, promoted apoptotic cell death and inhibited EMT, migration, and invasion in BLBC/TNBC cells. Various proteins regulating apoptosis were identified as MATR3-binding proteins, and YAP/TAZ pathway was suppressed by MATR3. MATR3 expression was inversely correlated with the aggressive and metastatic nature of breast cancer. Moreover, high expression levels of MATR3 were associated with a good prognosis of breast cancer patients. CONCLUSIONS Our data demonstrate that MATR3 functions as a putative tumor suppressor in BLBC/TNBC cells. Also, MATR3 potentially plays a role as a biomarker in predicting chemotherapy-sensitivity and patient survival in breast cancer patients.
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Affiliation(s)
- Jaehyuk Yang
- Department of Life Sciences, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul, Republic of Korea
| | - Seung Jun Lee
- Department of Life Sciences, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul, Republic of Korea
| | - Yongseok Kwon
- Department of Chemistry, Sogang University, Seoul, Republic of Korea
| | - Li Ma
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jongchan Kim
- Department of Life Sciences, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul, Republic of Korea.
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22
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Ning S, Wang L. The Multifunctional Protein p62 and Its Mechanistic Roles in Cancers. Curr Cancer Drug Targets 2020; 19:468-478. [PMID: 30332964 PMCID: PMC8052633 DOI: 10.2174/1568009618666181016164920] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/17/2018] [Accepted: 09/28/2018] [Indexed: 12/16/2022]
Abstract
The multifunctional signaling hub p62 is well recognized as a ubiquitin sensor and a selective autophagy receptor. As a ubiquitin sensor, p62 promotes NFκB activation by facilitating TRAF6 ubiquitination and aggregation. As a selective autophagy receptor, p62 sorts ubiquitinated substrates including p62 itself for lysosome-mediated degradation. p62 plays crucial roles in myriad cellular processes including DNA damage response, aging/senescence, infection and immunity, chronic inflammation, and cancerogenesis, dependent on or independent of autophagy. Targeting p62-mediated autophagy may represent a promising strategy for clinical interventions of different cancers. In this review, we summarize the transcriptional and post-translational regulation of p62, and its mechanistic roles in cancers, with the emphasis on its roles in regulation of DNA damage response and its connection to the cGAS-STING-mediated antitumor immune response, which is promising for cancer vaccine design.
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Affiliation(s)
- Shunbin Ning
- Division of Infectious Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, United States.,Center of Excellence for Inflammation, Infectious Diseases and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, United States
| | - Ling Wang
- Division of Infectious Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, United States.,Center of Excellence for Inflammation, Infectious Diseases and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, United States
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23
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Bojagora A, Saridakis V. USP7 manipulation by viral proteins. Virus Res 2020; 286:198076. [DOI: 10.1016/j.virusres.2020.198076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/14/2020] [Accepted: 06/24/2020] [Indexed: 01/27/2023]
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24
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Tang M, Feng X, Pei G, Srivastava M, Wang C, Chen Z, Li S, Zhang H, Zhao Z, Li X, Chen J. FOXK1 Participates in DNA Damage Response by Controlling 53BP1 Function. Cell Rep 2020; 32:108018. [PMID: 32783940 PMCID: PMC7458625 DOI: 10.1016/j.celrep.2020.108018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 06/09/2020] [Accepted: 07/17/2020] [Indexed: 01/28/2023] Open
Abstract
53BP1 plays a central role in dictating DNA repair choice between non-homologous end joining (NHEJ) and homologous recombination (HR), which is important for the sensitivity to poly(ADP-ribose) polymerase inhibitors (PARPis) of BRCA1-deficient cancers. In this study, we show that FOXK1 associates with 53BP1 and regulates 53BP1-dependent functions. FOXK1-53BP1 interaction is significantly enhanced upon DNA damage during the S phase in an ATM/CHK2-dependent manner, which reduces the association of 53BP1 with its downstream factors RIF1 and PTIP. Depletion of FOXK1 impairs DNA repair and induces compromised cell survival upon DNA damage. Overexpression of FOXK1 diminishes 53BP1 foci formation, which leads to resistance to PARPis and elevation of HR in BRCA1-deficient cells and decreased telomere fusion in TRF2-depleted cells. Collectively, our findings demonstrate that FOXK1 negatively regulates 53BP1 function by inhibiting 53BP1 localization to sites of DNA damage, which alters the DSB-induced protein complexes centering on 53BP1 and thus influences DNA repair choice.
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Affiliation(s)
- Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xu Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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25
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Valles GJ, Bezsonova I, Woodgate R, Ashton NW. USP7 Is a Master Regulator of Genome Stability. Front Cell Dev Biol 2020; 8:717. [PMID: 32850836 PMCID: PMC7419626 DOI: 10.3389/fcell.2020.00717] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/13/2020] [Indexed: 12/25/2022] Open
Abstract
Genetic alterations, including DNA mutations and chromosomal abnormalities, are primary drivers of tumor formation and cancer progression. These alterations can endow cells with a selective growth advantage, enabling cancers to evade cell death, proliferation limits, and immune checkpoints, to metastasize throughout the body. Genetic alterations occur due to failures of the genome stability pathways. In many cancers, the rate of alteration is further accelerated by the deregulation of these processes. The deubiquitinating enzyme ubiquitin specific protease 7 (USP7) has recently emerged as a key regulator of ubiquitination in the genome stability pathways. USP7 is also deregulated in many cancer types, where deviances in USP7 protein levels are correlated with cancer progression. In this work, we review the increasingly evident role of USP7 in maintaining genome stability, the links between USP7 deregulation and cancer progression, as well as the rationale of targeting USP7 in cancer therapy.
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Affiliation(s)
- Gabrielle J Valles
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Nicholas W Ashton
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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26
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Dong C, West KL, Tan XY, Li J, Ishibashi T, Yu CH, Sy SMH, Leung JWC, Huen MSY. Screen identifies DYRK1B network as mediator of transcription repression on damaged chromatin. Proc Natl Acad Sci U S A 2020; 117:17019-17030. [PMID: 32611815 PMCID: PMC7382216 DOI: 10.1073/pnas.2002193117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA double-strand breaks (DSBs) trigger transient pausing of nearby transcription, an emerging ATM-dependent response that suppresses chromosomal instability. We screened a chemical library designed to target the human kinome for new activities that mediate gene silencing on DSB-flanking chromatin, and have uncovered the DYRK1B kinase as an early respondent to DNA damage. We showed that DYRK1B is swiftly and transiently recruited to laser-microirradiated sites, and that genetic inactivation of DYRK1B or its kinase activity attenuated DSB-induced gene silencing and led to compromised DNA repair. Notably, global transcription shutdown alleviated DNA repair defects associated with DYRK1B loss, suggesting that DYRK1B is strictly required for DSB repair on active chromatin. We also found that DYRK1B mediates transcription silencing in part via phosphorylating and enforcing DSB accumulation of the histone methyltransferase EHMT2. Together, our findings unveil the DYRK1B signaling network as a key branch of mammalian DNA damage response circuitries, and establish the DYRK1B-EHMT2 axis as an effector that coordinates DSB repair on transcribed chromatin.
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Affiliation(s)
- Chao Dong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kirk L West
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - Xin Yi Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Junshi Li
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong SAR, China
| | - Cheng-Han Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Shirley M H Sy
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Justin W C Leung
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205;
| | - Michael S Y Huen
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China;
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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27
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Ubiquitylation-Mediated Fine-Tuning of DNA Double-Strand Break Repair. Cancers (Basel) 2020; 12:cancers12061617. [PMID: 32570875 PMCID: PMC7352447 DOI: 10.3390/cancers12061617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 01/04/2023] Open
Abstract
The proper function of DNA repair is indispensable for eukaryotic cells since accumulation of DNA damages leads to genome instability and is a major cause of oncogenesis. Ubiquitylation and deubiquitylation play a pivotal role in the precise regulation of DNA repair pathways by coordinating the recruitment and removal of repair proteins at the damaged site. Here, we summarize the most important post-translational modifications (PTMs) involved in DNA double-strand break repair. Although we highlight the most relevant PTMs, we focus principally on ubiquitylation-related processes since these are the most robust regulatory pathways among those of DNA repair.
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28
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Nielsen CP, MacGurn JA. Coupling Conjugation and Deconjugation Activities to Achieve Cellular Ubiquitin Dynamics. Trends Biochem Sci 2020; 45:427-439. [PMID: 32311336 DOI: 10.1016/j.tibs.2020.01.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 12/19/2022]
Abstract
In eukaryotic cells, proteome remodeling is mediated by the ubiquitin-proteasome system, which regulates protein degradation, trafficking, and signaling events in the cell. Interplay between the cellular proteome and ubiquitin is complex and dynamic and many regulatory features that support this system have only recently come into focus. An unexpected recurring feature in this system is the physical interaction between E3 ubiquitin ligases and deubiquitylases (DUBs). Recent studies have reported on the regulatory significance of DUB-E3 interactions and it is becoming clear that they play important but complicated roles in the regulation of diverse cellular processes. Here, we summarize the current understanding of interactions between ubiquitin conjugation and deconjugation machineries and we examine the regulatory logic of these enigmatic complexes.
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Affiliation(s)
- Casey P Nielsen
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
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29
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Beyond reversal: ubiquitin and ubiquitin-like proteases and the orchestration of the DNA double strand break repair response. Biochem Soc Trans 2020; 47:1881-1893. [PMID: 31769469 PMCID: PMC6925521 DOI: 10.1042/bst20190534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022]
Abstract
The cellular response to genotoxic DNA double strand breaks (DSBs) uses a multitude of post-translational modifications to localise, modulate and ultimately clear DNA repair factors in a timely and accurate manner. Ubiquitination is well established as vital to the DSB response, with a carefully co-ordinated pathway of histone ubiquitination events being a central component of DSB signalling. Other ubiquitin-like modifiers (Ubl) including SUMO and NEDD8 have since been identified as playing important roles in DSB repair. In the last five years ∼20 additional Ub/Ubl proteases have been implicated in the DSB response. The number of proteases identified highlights the complexity of the Ub/Ubl signal present at DSBs. Ub/Ubl proteases regulate turnover, activity and protein-protein interactions of DSB repair factors both catalytically and non-catalytically. This not only ensures efficient repair of breaks but has a role in channelling repair into the correct DSB repair sub-pathways. Ultimately Ub/Ubl proteases have essential roles in maintaining genomic stability. Given that deficiencies in many Ub/Ubl proteases promotes sensitivity to DNA damaging chemotherapies, they could be attractive targets for cancer treatment.
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30
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Gagarina V, Bojagora A, Lacdao IK, Luthra N, Pfoh R, Mohseni S, Chaharlangi D, Tan N, Saridakis V. Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2. J Mol Biol 2019; 432:897-912. [PMID: 31866294 DOI: 10.1016/j.jmb.2019.12.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/26/2019] [Accepted: 12/12/2019] [Indexed: 11/25/2022]
Abstract
USP7 is a deubiquitinase that regulates many diverse cellular processes, including tumor suppression, epigenetics, and genome stability. Several substrates, including GMPS, UHRF1, and ICP0, were shown to bear a specific KxxxK motif that interacts within the C-terminal region of USP7. We identified a similar motif in Enhancer of Zeste 2 (EZH2), the histone methyltransferase found within Polycomb Repressive Complex 2 (PRC2). PRC2 is responsible for the methylation of Histone 3 Lys27 (H3K27) leading to gene silencing. GST pull-down and coimmunoprecipitation experiments showed that USP7 interacts with EZH2. We determined the structural basis of interaction between USP7 and EZH2 and identified residues mediating the interaction. Mutations in these critical residues disrupted the interaction between USP7 and EZH2. Furthermore, USP7 silencing and knockout experiments showed decreased EZH2 levels in HCT116 carcinoma cells. Finally, we demonstrated decreased H3K27Me3 levels in HCT116 USP7 knockout cells. These results indicate that USP7 interacts with EZH2 and regulates both its stability and function.
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Affiliation(s)
- Varvara Gagarina
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, M3J1P3, Canada
| | - Anna Bojagora
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, M3J1P3, Canada
| | - Ira Kay Lacdao
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, M3J1P3, Canada
| | - Niharika Luthra
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, M3J1P3, Canada
| | - Roland Pfoh
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, M3J1P3, Canada
| | - Sadaf Mohseni
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, M3J1P3, Canada
| | - Danica Chaharlangi
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, M3J1P3, Canada
| | - Nadine Tan
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, M3J1P3, Canada
| | - Vivian Saridakis
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, M3J1P3, Canada.
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31
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Deng B, Xu W, Wang Z, Liu C, Lin P, Li B, Huang Q, Yang J, Zhou H, Qu L. An LTR retrotransposon-derived lncRNA interacts with RNF169 to promote homologous recombination. EMBO Rep 2019; 20:e47650. [PMID: 31486214 DOI: 10.15252/embr.201847650] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 08/10/2019] [Accepted: 08/14/2019] [Indexed: 01/10/2023] Open
Abstract
LTR retrotransposons are abundant repetitive elements in the human genome, but their functions remain poorly understood. Here, we report the function and regulatory mechanism of an ERV-9 LTR retrotransposon-derived lncRNA called p53-regulated lncRNA for homologous recombination (HR) repair 1 (PRLH1) in human cells. PRLH1 is highly expressed in p53-mutated hepatocellular carcinoma (HCC) samples and promotes cell proliferation in p53-mutated HCC cells, and its transcription is promoted by NF-Y and suppressed by p53. Mechanistically, PRLH1 specifically binds to an uncharacterized domain of RNF169 through two GCUUCA boxes in its 5' terminal region to form a DNA repair complex that supplants 53BP1 at double-strand break (DSB) sites and then promotes the initiation of HR repair. Notably, PRLH1 is essential for the stabilization of RNF169, acting as an RNA platform to recruit and assemble HR protein factors. This study characterizes PRLH1 as a novel HR-promoting factor and provides new insights into the function and mechanism of LTR retrotransposon-derived lncRNAs.
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Affiliation(s)
- Bing Deng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Wenli Xu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Zelin Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Chang Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Penghui Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Qiaojuan Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Hui Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, China
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32
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Guo X, Bai Y, Zhao M, Zhou M, Shen Q, Yun CH, Zhang H, Zhu WG, Wang J. Acetylation of 53BP1 dictates the DNA double strand break repair pathway. Nucleic Acids Res 2019; 46:689-703. [PMID: 29190394 PMCID: PMC5778472 DOI: 10.1093/nar/gkx1208] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/22/2017] [Indexed: 12/17/2022] Open
Abstract
P53-binding protein 1 (53BP1) plays critical roles in DNA double strand break (DSB) repair by promoting non-homologous end joining (NHEJ), and loss of 53BP1 abolishes PARPi sensitivity in BRCA1-deficient cells by restoring homologous recombination (HR). 53BP1 is one of the proteins initially recruited to sites of DSBs via recognition of H4K20me2 through the Tudor-UDR domain and H2AK15ub through the UDR motif. Although extensive studies have been conducted, it remains unclear how the post-translational modification of 53BP1 affects DSB repair pathway choice. Here, we identified 53BP1 as an acetylated protein and determined that acetylation of 53BP1 inhibit NHEJ and promote HR by negatively regulating 53BP1 recruitment to DSBs. Mechanistically, CBP-mediated acetylation of K1626/1628 in the UDR motif disrupted the interaction between 53BP1 and nucleosomes, subsequently blocking the recruitment of 53BP1 and its downstream factors PTIP and RIF1 to DSBs. Hyperacetylation of 53BP1, similar to depletion of 53BP1, restored PARPi resistance in BRCA1-deficient cells. Interestingly, 53BP1 acetylation was tightly regulated by HDAC2 to maintain balance between the HR and NHEJ pathways. Together, our results demonstrate that the acetylation status of 53BP1 plays a key role in its recruitment to DSBs and reveal how specific 53BP1 modification modulates the choice of DNA repair pathway.
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Affiliation(s)
- Xiang Guo
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yongtai Bai
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Meimei Zhao
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Mei Zhou
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Qinjian Shen
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Cai-Hong Yun
- Department of Biophysics, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Hongquan Zhang
- Department of Anatomy, Histology and Embryology, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Jiadong Wang
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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Episkopou H, Diman A, Claude E, Viceconte N, Decottignies A. TSPYL5 Depletion Induces Specific Death of ALT Cells through USP7-Dependent Proteasomal Degradation of POT1. Mol Cell 2019; 75:469-482.e6. [PMID: 31278054 DOI: 10.1016/j.molcel.2019.05.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 04/05/2019] [Accepted: 05/17/2019] [Indexed: 01/11/2023]
Abstract
A significant fraction (∼10%) of cancer cells maintain their telomere length via a telomerase-independent mechanism known as alternative lengthening of telomeres (ALT). There are no known molecular, ALT-specific, therapeutic targets. We have identified TSPYL5 (testis-specific Y-encoded-like protein 5) as a PML body component, co-localizing with ALT telomeres and critical for ALT+ cell viability. TSPYL5 was described as an inhibitor of the USP7 deubiquitinase. We report that TSPYL5 prevents the poly-ubiquitination of POT1-a shelterin component-and protects POT1 from proteasomal degradation exclusively in ALT+ cells. USP7 depletion rescued POT1 poly-ubiquitination and loss, suggesting that the deubiquitinase activates POT1 E3 ubiquitin ligase(s). Similarly, PML depletion suppressed POT1 poly-ubiquitination, suggesting an interplay between USP7 and PML to trigger POT1 degradation in TSPYL5-depleted ALT+ cells. We demonstrate that ALT telomeres need to be protected from POT1 degradation in ALT-associated PML bodies and identify TSPYL5 as an ALT+ cancer-specific therapeutic target.
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Affiliation(s)
- Harikleia Episkopou
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Faculty of Pharmacy and Biomedical Sciences, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Aurélie Diman
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Faculty of Pharmacy and Biomedical Sciences, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Eloïse Claude
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Faculty of Pharmacy and Biomedical Sciences, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Nikenza Viceconte
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Faculty of Pharmacy and Biomedical Sciences, Université Catholique de Louvain, Brussels 1200, Belgium
| | - Anabelle Decottignies
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Faculty of Pharmacy and Biomedical Sciences, Université Catholique de Louvain, Brussels 1200, Belgium.
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34
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Guard SE, Poss ZC, Ebmeier CC, Pagratis M, Simpson H, Taatjes DJ, Old WM. The nuclear interactome of DYRK1A reveals a functional role in DNA damage repair. Sci Rep 2019; 9:6539. [PMID: 31024071 PMCID: PMC6483993 DOI: 10.1038/s41598-019-42990-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/12/2019] [Indexed: 12/21/2022] Open
Abstract
The chromosome 21 encoded protein kinase DYRK1A is essential for normal human development. Mutations in DYRK1A underlie a spectrum of human developmental disorders, and increased dosage in trisomy 21 is implicated in Down syndrome related pathologies. DYRK1A regulates a diverse array of cellular processes through physical interactions with substrates and binding partners in various subcellular compartments. Despite recent large-scale protein-protein interaction profiling efforts, DYRK1A interactions specific to different subcellular compartments remain largely unknown, impeding progress toward understanding emerging roles for this kinase. Here, we used immunoaffinity purification and quantitative mass spectrometry to identify nuclear interaction partners of endogenous DYRK1A. This interactome was enriched in DNA damage repair factors, transcriptional elongation factors and E3 ubiquitin ligases. We validated an interaction with RNF169, a factor that promotes homology directed repair upon DNA damage, and found that DYRK1A expression and kinase activity are required for maintenance of 53BP1 expression and subsequent recruitment to DNA damage loci. Further, DYRK1A knock out conferred resistance to ionizing radiation in colony formation assays, suggesting that DYRK1A expression decreases cell survival efficiency in response to DNA damage and points to a tumor suppressive role for this kinase.
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Affiliation(s)
- Steven E Guard
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Zachary C Poss
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Christopher C Ebmeier
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Maria Pagratis
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Helen Simpson
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - William M Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA.
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO, USA.
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35
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Roewenstrunk J, Di Vona C, Chen J, Borras E, Dong C, Arató K, Sabidó E, Huen MSY, de la Luna S. A comprehensive proteomics-based interaction screen that links DYRK1A to RNF169 and to the DNA damage response. Sci Rep 2019; 9:6014. [PMID: 30979931 PMCID: PMC6461666 DOI: 10.1038/s41598-019-42445-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Dysregulation of the DYRK1A protein kinase has been associated with human disease. On the one hand, its overexpression in trisomy 21 has been linked to certain pathological traits of Down syndrome, while on the other, inactivating mutations in just one allele are responsible for a distinct yet rare clinical syndrome, DYRK1A haploinsufficiency. Moreover, altered expression of this kinase may also provoke other human pathologies, including cancer and diabetes. Although a few DYRK1A substrates have been described, its upstream regulators and downstream targets are still poorly understood, an information that could shed light on the functions of DYRK1A in the cell. Here, we carried out a proteomic screen using antibody-based affinity purification coupled to mass spectrometry to identify proteins that directly or indirectly bind to endogenous DYRK1A. We show that the use of a cell line not expressing DYRK1A, generated by CRISPR/Cas9 technology, was needed in order to discriminate between true positives and non-specific interactions. Most of the proteins identified in the screen are novel candidate DYRK1A interactors linked to a variety of activities in the cell. The in-depth characterization of DYRK1A's functional interaction with one of them, the E3 ubiquitin ligase RNF169, revealed a role for this kinase in the DNA damage response. We found that RNF169 is a DYRK1A substrate and we identified several of its phosphorylation sites. In particular, one of these sites appears to modify the ability of RNF169 to displace 53BP1 from sites of DNA damage. Indeed, DYRK1A depletion increases cell sensitivity to ionizing irradiation. Therefore, our unbiased proteomic screen has revealed a novel activity of DYRK1A, expanding the complex role of this kinase in controlling cell homeostasis.
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Affiliation(s)
- Julia Roewenstrunk
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Chiara Di Vona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Jie Chen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, S.A.R., Hong Kong, China
| | - Eva Borras
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Chao Dong
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, S.A.R., Hong Kong, China
| | - Krisztina Arató
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Michael S Y Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, S.A.R., Hong Kong, China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, S.A.R., Hong Kong, China
| | - Susana de la Luna
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain.
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36
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R. Menon V, Ananthapadmanabhan V, Swanson S, Saini S, Sesay F, Yakovlev V, Florens L, DeCaprio JA, P. Washburn M, Dozmorov M, Litovchick L. DYRK1A regulates the recruitment of 53BP1 to the sites of DNA damage in part through interaction with RNF169. Cell Cycle 2019; 18:531-551. [PMID: 30773093 PMCID: PMC6464593 DOI: 10.1080/15384101.2019.1577525] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Human Dual-specificity tyrosine (Y) Regulated Kinase 1A (DYRK1A) is encoded by a dosage dependent gene whereby either trisomy or haploinsufficiency result in developmental abnormalities. However, the function and regulation of this important protein kinase are not fully understood. Here, we report proteomic analysis of DYRK1A in human cells that revealed a novel role of DYRK1A in DNA double-strand breaks (DSBs) repair, mediated in part by its interaction with the ubiquitin-binding protein RNF169 that accumulates at the DSB sites and promotes homologous recombination repair (HRR) by displacing 53BP1, a key mediator of non-homologous end joining (NHEJ). We found that overexpression of active, but not the kinase inactive DYRK1A in U-2 OS cells inhibits accumulation of 53BP1 at the DSB sites in the RNF169-dependent manner. DYRK1A phosphorylates RNF169 at two sites that influence its ability to displace 53BP1 from the DSBs. Although DYRK1A is not required for the recruitment of RNF169 to the DSB sites and 53BP1 displacement, inhibition of DYRK1A or mutation of the DYRK1A phosphorylation sites in RNF169 decreases its ability to block accumulation of 53BP1 at the DSB sites. Interestingly, CRISPR-Cas9 knockout of DYRK1A in human and mouse cells also diminished the 53BP1 DSB recruitment in a manner that did not require RNF169, suggesting that dosage of DYRK1A can influence the DNA repair processes through both RNF169-dependent and independent mechanisms. Human U-2 OS cells devoid of DYRK1A display an increased HRR efficiency and resistance to DNA damage, therefore our findings implicate DYRK1A in the DNA repair processes.
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Affiliation(s)
- Vijay R. Menon
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Varsha Ananthapadmanabhan
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Selene Swanson
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Siddharth Saini
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Fatmata Sesay
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Vasily Yakovlev
- Department of Radiation Oncology, Virginia Commonwealth University, Richmond, VA, USA
| | | | - James A. DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael P. Washburn
- Stowers and Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, USA
| | - Mikhail Dozmorov
- Department of Biostatistics and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Larisa Litovchick
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
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37
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Role of deubiquitinases in DNA damage response. DNA Repair (Amst) 2019; 76:89-98. [PMID: 30831436 DOI: 10.1016/j.dnarep.2019.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 12/13/2022]
Abstract
DNA damage response (DDR) serves as an integrated cellular network to detect cellular stress and react by activating pathways responsible for halting cell cycle progression, stimulating DNA damage repair, and initiating apoptosis. Efficient DDR protects cells from genomic instability while defective DDR can allow DNA lesions to go unrepaired, causing permanent mutations that will affect future generations of cells and possibly cause disease conditions such as cancer. Therefore, DDR mechanisms must be tightly regulated in order to ensure organismal health and viability. One major way of DDR regulation is ubiquitination, which has been long known to control DDR protein localization, activity, and stability. The reversal of this process, deubiquitination, has more recently come to the forefront of DDR research as an important new angle in ubiquitin-mediated regulation of DDR. As such, deubiquitinases have emerged as key factors in DDR. Importantly, deubiquitinases are attractive small-molecule drug targets due to their well-defined catalytic residues that provide a promising avenue for developing new cancer therapeutics. This review focuses on the emerging roles of deubiquitinases in various DNA repair pathways.
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38
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USP7: Structure, substrate specificity, and inhibition. DNA Repair (Amst) 2019; 76:30-39. [PMID: 30807924 DOI: 10.1016/j.dnarep.2019.02.005] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/07/2019] [Indexed: 12/24/2022]
Abstract
Turnover of cellular proteins is regulated by Ubiquitin Proteasome System (UPS). Components of this pathway, including the proteasome, ubiquitinating enzymes and deubiquitinating enzymes, are highly specialized and tightly regulated. In this mini-review we focus on the de-ubiquitinating enzyme USP7, and summarize latest advances in understanding its structure, substrate specificity and relevance to human cancers. There is increasing interest in UPS components as targets for cancer therapy and here we also overview the recent progress in the development of small molecule inhibitors that target USP7.
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39
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Reilly NM, Yard BD, Pittman DL. Homologous Recombination-Mediated DNA Repair and Implications for Clinical Treatment of Repair Defective Cancers. Methods Mol Biol 2019; 1999:3-29. [PMID: 31127567 DOI: 10.1007/978-1-4939-9500-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Double-strand DNA breaks (DSBs) are generated by ionizing radiation and as intermediates during the processing of DNA, such as repair of interstrand cross-links and collapsed replication forks. These potentially deleterious DSBs are repaired primarily by the homologous recombination (HR) and nonhomologous end joining (NHEJ) DNA repair pathways. HR utilizes a homologous template to accurately restore damaged DNA, whereas NHEJ utilizes microhomology to join breaks in close proximity. The pathway available for DSB repair is dependent upon the cell cycle stage; for example, HR primarily functions during the S/G2 stages while NHEJ can repair DSBs at any cell cycle stage. Posttranslational modifications (PTMs) promote activity of specific pathways and subpathways through enzyme activation and precisely timed protein recruitment and degradation. This chapter provides an overview of PTMs occurring during DSB repair. In addition, clinical phenotypes associated with HR-defective cancers, such as mutational signatures used to predict response to poly(ADP-ribose) polymerase inhibitors, are discussed. Understanding these processes will provide insight into mechanisms of genome maintenance and likely identify targets and new avenues for therapeutic interventions.
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Affiliation(s)
- Nicole M Reilly
- Fondazione Piemontese per la Ricerca sul Cancro ONLUS, Candiolo, Italy
| | - Brian D Yard
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Douglas L Pittman
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA.
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40
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Georges A, Marcon E, Greenblatt J, Frappier L. Identification and Characterization of USP7 Targets in Cancer Cells. Sci Rep 2018; 8:15833. [PMID: 30367141 PMCID: PMC6203733 DOI: 10.1038/s41598-018-34197-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin specific protease, USP7, regulates multiple cellular pathways relevant for cancer through its ability to bind and sometimes stabilize specific target proteins through deubiquitylation. To gain a more complete profile of USP7 interactions in cancer cells, we performed affinity purification coupled to mass spectrometry to identify USP7 binding targets in gastric carcinoma cells. This confirmed reported associations of USP7 with USP11, PPM1G phosphatase and TRIP12 E3 ubiquitin ligase as well as identifying novel interactions with two DEAD/DEAH-box RNA helicases, DDX24 and DHX40. Using USP7 binding pocket mutants, we show that USP11, PPM1G, TRIP12 and DDX24 bind USP7 through its TRAF domain binding pocket, while DHX40 interacts with USP7 through a distinct binding pocket in the Ubl2 domain. P/A/ExxS motifs in USP11 and DDX24 that are critical for USP7 binding were also identified. Modulation of USP7 expression levels and inhibition of USP7 catalytic activity in multiple cells lines showed that USP7 consistently stabilizes DDX24, DHX40 and TRIP12 dependent on its catalytic activity, while USP11 and PPM1G levels were not consistently affected. Our study better defines the mechanisms of USP7 interaction with known targets and identifies DDX24 and DHX40 as new targets that are specifically bound and regulated by USP7.
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Affiliation(s)
- Anna Georges
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre, University of Toronto, Toronto, Canada
| | - Lori Frappier
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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41
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Ubiquitination at the interface of tumor viruses and DNA damage responses. Curr Opin Virol 2018; 32:40-47. [PMID: 30261451 DOI: 10.1016/j.coviro.2018.08.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 08/31/2018] [Indexed: 01/09/2023]
Abstract
Viruses exploit cellular ubiquitination machinery to shape the host proteome and promote productive infection. Among the cellular processes influenced by viral manipulation of ubiquitination is the DNA damage response (DDR), a network of cellular signaling pathways that sense and respond to genomic damage. This host-pathogen interaction is particularly important during virus replication and transformation by DNA tumor viruses. Manipulating DDR pathways can promote virus replication but also impacts host genomic instability, potentially leading to cellular transformation and tumor formation. We review ways in which viruses are known to hijack the cellular ubiquitin system to reshape host DDR pathways.
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42
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Su D, Ma S, Shan L, Wang Y, Wang Y, Cao C, Liu B, Yang C, Wang L, Tian S, Ding X, Liu X, Yu N, Song N, Liu L, Yang S, Zhang Q, Yang F, Zhang K, Shi L. Ubiquitin-specific protease 7 sustains DNA damage response and promotes cervical carcinogenesis. J Clin Invest 2018; 128:4280-4296. [PMID: 30179224 DOI: 10.1172/jci120518] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/24/2018] [Indexed: 12/24/2022] Open
Abstract
Central to the recognition, signaling, and repair of DNA double-strand breaks (DSBs) are the MRE11-RAD50-NBS1 (MRN) complex and mediator of DNA damage checkpoint protein 1 (MDC1), the interplay of which is essential for initiation and amplification of the DNA damage response (DDR). The intrinsic rule governing the regulation of the function of this molecular machinery remains to be investigated. We report here that the ubiquitin-specific protease USP7 was physically associated with the MRN-MDC1 complex and that the MRN-MDC1 complex acted as a platform for USP7 to efficiently deubiquitinate and stabilize MDC1, thereby sustaining the DDR. Accordingly, depletion of USP7 impaired the engagement of the MRN-MDC1 complex and the consequent recruitment of the downstream factors p53-binding protein 1 (53BP1) and breast cancer protein 1 (BRCA1) at DNA lesions. Significantly, USP7 was overexpressed in cervical cancer, and the level of its expression positively correlated with that of MDC1 and worse survival rates for patients with cervical cancer. We demonstrate that USP7-mediated MDC1 stabilization promoted cervical cancer cell survival and conferred cellular resistance to genotoxic insults. Together, our study reveals a role for USP7 in regulating the function of the MRN-MDC1 complex and activity of the DDR, supporting the pursuit of USP7 as a potential therapeutic target for MDC1-proficient cancers.
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Affiliation(s)
- Dongxue Su
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Shuai Ma
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yuejiao Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Cheng Cao
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Beibei Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Chao Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Liyong Wang
- Core Facilities for Molecular Biology, Capital Medical University, Beijing, China
| | - Shanshan Tian
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiang Ding
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xinhua Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Na Yu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Nan Song
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ling Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Shangda Yang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Qi Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Fuquan Yang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Lei Shi
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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Abstract
53BP1 restrains DNA end resection, and its dosage imbalance upsets DNA double-strand break (DSB) repair pathway choice. Here, by monitoring 53BP1 distribution on DSB-flanking chromatin, we have established a dose-dependent role of the RING finger protein RNF169 in limiting 53BP1 DSB deposition. Moreover, we found that forced expression of RNF169 overcomes 53BP1 activity and stimulates mutagenic DSB repair via the single-strand annealing pathway. Our findings suggest that aberrant expression of RNF169 may represent a deleterious factor in DSB repair control and in maintenance of genome stability. Unrestrained 53BP1 activity at DNA double-strand breaks (DSBs) hampers DNA end resection and upsets DSB repair pathway choice. RNF169 acts as a molecular rheostat to limit 53BP1 deposition at DSBs, but how this fine balance translates to DSB repair control remains undefined. In striking contrast to 53BP1, ChIP analyses of AsiSI-induced DSBs unveiled that RNF169 exhibits robust accumulation at DNA end-proximal regions and preferentially targets resected, RPA-bound DSBs. Accordingly, we found that RNF169 promotes CtIP-dependent DSB resection and favors homology-mediated DSB repair, and further showed that RNF169 dose-dependently stimulates single-strand annealing repair, in part, by alleviating the 53BP1-imposed barrier to DSB end resection. Our results highlight the interplay of RNF169 with 53BP1 in fine-tuning choice of DSB repair pathways.
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Kim RQ, Sixma TK. Regulation of USP7: A High Incidence of E3 Complexes. J Mol Biol 2017; 429:3395-3408. [DOI: 10.1016/j.jmb.2017.05.028] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/26/2017] [Accepted: 05/30/2017] [Indexed: 01/03/2023]
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Lin YH, Lin YH, Lu YC, Liu TC, Chen CY, Hsu CJ, Chen PL, Wu CC. A novel missense variant in the nuclear localization signal of POU4F3 causes autosomal dominant non-syndromic hearing loss. Sci Rep 2017; 7:7551. [PMID: 28790396 PMCID: PMC5548901 DOI: 10.1038/s41598-017-08236-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/10/2017] [Indexed: 02/01/2023] Open
Abstract
Autosomal dominant non-syndromic hearing loss (ADNSHL) is genetically heterogeneous with more than 35 genes identified to date. Using a massively parallel sequencing panel targeting 159 deafness genes, we identified a novel missense variant of POU4F3 (c.982A>G, p.Lys328Glu) which co-segregated with the deafness phenotype in a three-generation Taiwanese family with ADNSHL. This variant could be classified as a "pathogenic variant" according to the American College of Medical Genetics and Genomics guidelines. We then performed subcellular localization experiments and confirmed that p.Lys328Glu compromised transportation of POU4F3 from the cytoplasm to the nucleus. POU3F4 p.Lys328Glu was located within a bipartite nuclear localization signal (NLS), and was the first missense variant in bipartite NLS of POU4F3 validated in functional studies. These findings expanded the mutation spectrum of POU4F3 and provided insight into the pathogenesis associated with aberrant POU4F3 localization.
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Affiliation(s)
- Yin-Hung Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yi-Hsin Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ying-Chang Lu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Tien-Chen Liu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Yu Chen
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, Taiwan
| | - Chuan-Jen Hsu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan. .,Department of Otolaryngology, Taichung Tzu-Chi Hospital, Taichung, Taiwan.
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan. .,Graduate Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan. .,Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan. .,Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan. .,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan. .,Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
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Mushegian AA. NLS protects DNA damage protein. Sci Signal 2017; 10:10/474/eaan4046. [PMID: 28400536 DOI: 10.1126/scisignal.aan4046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A single motif targets a protein to the nucleus and directs its deubiquitylation, promoting high-fidelity DNA damage repair.
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