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Potapenko A, Davidson JM, Lee A, Laird AS. The deubiquitinase function of ataxin-3 and its role in the pathogenesis of Machado-Joseph disease and other diseases. Biochem J 2024; 481:461-480. [PMID: 38497605 PMCID: PMC11088879 DOI: 10.1042/bcj20240017] [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: 01/18/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
Machado-Joseph disease (MJD) is a devastating and incurable neurodegenerative disease characterised by progressive ataxia, difficulty speaking and swallowing. Consequently, affected individuals ultimately become wheelchair dependent, require constant care, and face a shortened life expectancy. The monogenic cause of MJD is expansion of a trinucleotide (CAG) repeat region within the ATXN3 gene, which results in polyglutamine (polyQ) expansion within the resultant ataxin-3 protein. While it is well established that the ataxin-3 protein functions as a deubiquitinating (DUB) enzyme and is therefore critically involved in proteostasis, several unanswered questions remain regarding the impact of polyQ expansion in ataxin-3 on its DUB function. Here we review the current literature surrounding ataxin-3's DUB function, its DUB targets, and what is known regarding the impact of polyQ expansion on ataxin-3's DUB function. We also consider the potential neuroprotective effects of ataxin-3's DUB function, and the intersection of ataxin-3's role as a DUB enzyme and regulator of gene transcription. Ataxin-3 is the principal pathogenic protein in MJD and also appears to be involved in cancer. As aberrant deubiquitination has been linked to both neurodegeneration and cancer, a comprehensive understanding of ataxin-3's DUB function is important for elucidating potential therapeutic targets in these complex conditions. In this review, we aim to consolidate knowledge of ataxin-3 as a DUB and unveil areas for future research to aid therapeutic targeting of ataxin-3's DUB function for the treatment of MJD and other diseases.
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Affiliation(s)
- Anastasiya Potapenko
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jennilee M. Davidson
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Albert Lee
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Angela S. Laird
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Mackay HL, Stone HR, Ellis K, Ronson GE, Walker AK, Starowicz K, Garvin AJ, van Eijk P, Vaitsiankova A, Vijayendran S, Beesley JF, Petermann E, Brown EJ, Densham RM, Reed SH, Dobbs F, Saponaro M, Morris JR. USP50 suppresses alternative RecQ helicase use and deleterious DNA2 activity during replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574674. [PMID: 38260523 PMCID: PMC10802463 DOI: 10.1101/2024.01.10.574674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Mammalian DNA replication employs several RecQ DNA helicases to orchestrate the faithful duplication of genetic information. Helicase function is often coupled to the activity of specific nucleases, but how helicase and nuclease activities are co-directed is unclear. Here we identify the inactive ubiquitin-specific protease, USP50, as a ubiquitin-binding and chromatin-associated protein required for ongoing replication, fork restart, telomere maintenance and cellular survival during replicative stress. USP50 supports WRN:FEN1 at stalled replication forks, suppresses MUS81-dependent fork collapse and restricts double-strand DNA breaks at GC-rich sequences. Surprisingly we find that cells depleted for USP50 and recovering from a replication block exhibit increased DNA2 and RECQL4 foci and that the defects in ongoing replication, poor fork restart and increased fork collapse seen in these cells are mediated by DNA2, RECQL4 and RECQL5. These data define a novel ubiquitin-dependent pathway that promotes the balance of helicase: nuclease use at ongoing and stalled replication forks.
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3
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Yuan T, Zeng C, Liu J, Zhao C, Ge F, Li Y, Qian M, Du J, Wang W, Li Y, Liu Y, Dai X, Zhou J, Chen X, Ma S, Zhu H, He Q, Yang B. Josephin domain containing 2 (JOSD2) promotes lung cancer by inhibiting LKB1 (Liver kinase B1) activity. Signal Transduct Target Ther 2024; 9:11. [PMID: 38177135 PMCID: PMC10766984 DOI: 10.1038/s41392-023-01706-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 10/17/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) ranks as one of the leading causes of cancer-related deaths worldwide. Despite the prominence and effectiveness of kinase-target therapies in NSCLC treatment, these drugs are suitable for and beneficial to a mere ~30% of NSCLC patients. Consequently, the need for novel strategies addressing NSCLC remains pressing. Deubiquitinases (DUBs), a group of diverse enzymes with well-defined catalytic sites that are frequently overactivated in cancers and associated with tumorigenesis and regarded as promising therapeutic targets. Nevertheless, the mechanisms by which DUBs promote NSCLC remain poorly understood. Through a global analysis of the 97 DUBs' contribution to NSCLC survival possibilities using The Cancer Genome Atlas (TCGA) database, we found that high expression of Josephin Domain-containing protein 2 (JOSD2) predicted the poor prognosis of patients. Depletion of JOSD2 significantly impeded NSCLC growth in both cell/patient-derived xenografts in vivo. Mechanically, we found that JOSD2 restricts the kinase activity of LKB1, an important tumor suppressor generally inactivated in NSCLC, by removing K6-linked polyubiquitination, an action vital for maintaining the integrity of the LKB1-STRAD-MO25 complex. Notably, we identified the first small-molecule inhibitor of JOSD2, and observed that its pharmacological inhibition significantly arrested NSCLC proliferation in vitro/in vivo. Our findings highlight the vital role of JOSD2 in hindering LKB1 activity, underscoring the therapeutic potential of targeting JOSD2 in NSCLC, especially in those with inactivated LKB1, and presenting its inhibitors as a promising strategy for NSCLC treatment.
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Affiliation(s)
- Tao Yuan
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chenming Zeng
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 311199, China
| | - Jiawei Liu
- Ministry of Education Key Laboratory of Chinese Medicinal Plants Resource from Lingnan, Research Center of Medicinal Plants Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Chenxi Zhao
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fujing Ge
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuekang Li
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meijia Qian
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiamin Du
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Weihua Wang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yonghao Li
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yue Liu
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoyang Dai
- Center for Drug Safety Evaluation and Research of Zhejiang University, Hangzhou, 310058, China
| | - Jianya Zhou
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Xueqin Chen
- Department of Oncology, Hangzhou Cancer Hospital, Hangzhou, 310002, China
| | - Shenglin Ma
- Department of Oncology, Hangzhou Cancer Hospital, Hangzhou, 310002, China
| | - Hong Zhu
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- Cancer Center of Zhejiang University, Hangzhou, China.
| | - Qiaojun He
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, China.
| | - Bo Yang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
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Ren J, Yu P, Liu S, Li R, Niu X, Chen Y, Zhang Z, Zhou F, Zhang L. Deubiquitylating Enzymes in Cancer and Immunity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303807. [PMID: 37888853 PMCID: PMC10754134 DOI: 10.1002/advs.202303807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/30/2023] [Indexed: 10/28/2023]
Abstract
Deubiquitylating enzymes (DUBs) maintain relative homeostasis of the cellular ubiquitome by removing the post-translational modification ubiquitin moiety from substrates. Numerous DUBs have been demonstrated specificity for cleaving a certain type of ubiquitin linkage or positions within ubiquitin chains. Moreover, several DUBs perform functions through specific protein-protein interactions in a catalytically independent manner, which further expands the versatility and complexity of DUBs' functions. Dysregulation of DUBs disrupts the dynamic equilibrium of ubiquitome and causes various diseases, especially cancer and immune disorders. This review summarizes the Janus-faced roles of DUBs in cancer including proteasomal degradation, DNA repair, apoptosis, and tumor metastasis, as well as in immunity involving innate immune receptor signaling and inflammatory and autoimmune disorders. The prospects and challenges for the clinical development of DUB inhibitors are further discussed. The review provides a comprehensive understanding of the multi-faced roles of DUBs in cancer and immunity.
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Affiliation(s)
- Jiang Ren
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
| | - Peng Yu
- Zhongshan Institute for Drug DiscoveryShanghai Institute of Materia MedicaChinese Academy of SciencesZhongshanGuangdongP. R. China
| | - Sijia Liu
- International Biomed‐X Research CenterSecond Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouP. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhou310058China
| | - Ran Li
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
| | - Xin Niu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
| | - Yan Chen
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
| | - Zhenyu Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan450003P. R. China
| | - Fangfang Zhou
- Institutes of Biology and Medical ScienceSoochow UniversitySuzhou215123P. R. China
| | - Long Zhang
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
- International Biomed‐X Research CenterSecond Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouP. R. China
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058P. R. China
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Felício D, du Mérac TR, Amorim A, Martins S. Functional implications of paralog genes in polyglutamine spinocerebellar ataxias. Hum Genet 2023; 142:1651-1676. [PMID: 37845370 PMCID: PMC10676324 DOI: 10.1007/s00439-023-02607-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023]
Abstract
Polyglutamine (polyQ) spinocerebellar ataxias (SCAs) comprise a group of autosomal dominant neurodegenerative disorders caused by (CAG/CAA)n expansions. The elongated stretches of adjacent glutamines alter the conformation of the native proteins inducing neurotoxicity, and subsequent motor and neurological symptoms. Although the etiology and neuropathology of most polyQ SCAs have been extensively studied, only a limited selection of therapies is available. Previous studies on SCA1 demonstrated that ATXN1L, a human duplicated gene of the disease-associated ATXN1, alleviated neuropathology in mice models. Other SCA-associated genes have paralogs (i.e., copies at different chromosomal locations derived from duplication of the parental gene), but their functional relevance and potential role in disease pathogenesis remain unexplored. Here, we review the protein homology, expression pattern, and molecular functions of paralogs in seven polyQ dominant ataxias-SCA1, SCA2, MJD/SCA3, SCA6, SCA7, SCA17, and DRPLA. Besides ATXN1L, we highlight ATXN2L, ATXN3L, CACNA1B, ATXN7L1, ATXN7L2, TBPL2, and RERE as promising functional candidates to play a role in the neuropathology of the respective SCA, along with the parental gene. Although most of these duplicates lack the (CAG/CAA)n region, if functionally redundant, they may compensate for a partial loss-of-function or dysfunction of the wild-type genes in SCAs. We aim to draw attention to the hypothesis that paralogs of disease-associated genes may underlie the complex neuropathology of dominant ataxias and potentiate new therapeutic strategies.
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Affiliation(s)
- Daniela Felício
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313, Porto, Portugal
| | - Tanguy Rubat du Mérac
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
| | - Sandra Martins
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal.
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Zhou L, Chen G, Liu T, Liu X, Yang C, Jiang J. MJDs family members: Potential prognostic targets and immune-associated biomarkers in hepatocellular carcinoma. Front Genet 2022; 13:965805. [PMID: 36159990 PMCID: PMC9500549 DOI: 10.3389/fgene.2022.965805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 11/21/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common gastrointestinal malignancies. It is not easy to be diagnosed in the early stage and is prone to relapse, with a very poor prognosis. And immune cell infiltration and tumor microenvironment play important roles in predicting therapeutic response and prognosis of HCC. Machado-Joseph domain-containing proteases (MJDs), as a gene family extensively involved in tumor progression, has pro-cancer and anti-cancer effects. However, the relationship between MJDs family members and immune cell infiltration and tumor microenvironment in HCC remains unclear. Therefore, cBio Cancer Genomics Portal (cBioPortal), The Cancer Genome Atlas (TCGA), UALCAN, Human Protein Atlas (HPA), MethSurv, and Tumor Immune Estimation Resource (TIMER) databases were performed to investigate the mRNA expression, DNA methylation, clinicopathologic features, immune cell infiltration and other related functions of MJDs family members in HCC. The results indicated that the expression of ATXN3, JOSD1, and JOSD2 was dramatically increased in HCC tissues and cell lines, and was correlated with histological grade, specimen type, TP53 mutation, lymph node metastatic, gender, and age of patients with HCC. Meanwhile, these genes also showed clinical value in improving the overall survival (OS), disease-specific survival (DSS), progression free survival (PFS), and relapse-free survival (RFS) in patients with HCC. The prognostic model indicated that the worse survival was associated with overall high expression of MJDs members. Next, the results suggested that promotor methylation levels of the MJDs family were closely related to these family mRNA expression levels, clinicopathologic features, and prognostic values in HCC. Moreover, the MJDs family were significantly correlated with CD4+ T cells, CD8+ T cells, B cells, neutrophils, macrophages, and DCs. And MJDs family members’ expression were substantially associated with the levels of several lymphocytes, immunomoinhibitors, immunomostimulators, chemokine ligands, and chemokine receptors. In addition, the expression levels of MJDs family were significantly correlated with cancer-related signaling pathways. Taken together, our results indicated that the aberrant expression of MJDs family in HCC played a critical role in clinical feature, prognosis, tumor microenvironment, immune-related molecules, mutation, gene copy number, and promoter methylation level. And MJDs family may be effective immunotherapeutic targets for patients with HCC and have the potential to be prognostic biomarkers.
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Affiliation(s)
- Lei Zhou
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Guojie Chen
- Hunan YoBon Biotechnology Limited Company, Changsha, China
| | - Tao Liu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Xinyuan Liu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Chengxiao Yang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Jianxin Jiang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Jianxin Jiang,
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Yu L, Fu J, Shen C. Ubiquitin specific peptidase 47 promotes proliferation of lung squamous cell carcinoma. Genes Genomics 2022; 44:721-731. [PMID: 35254655 DOI: 10.1007/s13258-022-01233-0] [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: 11/02/2021] [Accepted: 02/10/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Ubiquitin specific peptidase 47 (USP47) is a kind of deubiquitinase, which has been reported to play oncogenic roles in several malignancies including colorectal cancer and breast cancer. OBJECTIVE Here we aimed to investigate the clinical significance of USP47 in lung squamous cell carcinoma (LUSC). METHODS We retrospectively enrolled a cohort of LUSC patients who underwent surgical resection in our hospital (n = 280) and conducted immunohistochemistry staining for their tumor tissues targeting USP47. The correlations between USP47 expression and clinicopathological characteristics were evaluated by Chi-square test. Univariate and multivariate analyses were conducted to assess the prognostic predictive role of USP47 in LUSC. Cell lines and mice models were utilized to explore the tumor-related functions of USP47 in vitro and in vivo, respectively. RESULTS Among the 280 cases, there were 127 cases classified as high-USP47 expression and 153 cases with low-USP47 expression. Statistical analyses revealed that higher USP47 expression was independently correlated with larger tumor size, advanced T stage, and unfavorable prognosis. Knockdown of USP47 by shRNA resulted in impaired proliferation of LUSC cell lines and reduced nucleus beta-catenin level. Furthermore, xenograft assays demonstrated that silencing USP47 can inhibit LUSC tumor growth in vivo. CONCLUSION Our research established a novel tumor-promoting effect and prognostic predictive role of USP47 in LUSC, thereby providing evidence for further therapeutic development.
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Affiliation(s)
- Lin Yu
- Dalian Medical University, Dalian, 116044, China.,Department of Thoracic Surgery, Dalian University Affiliated Xinhua Hospital, Dalian, 116021, China
| | - Jiayu Fu
- Department of Cardiothoracic Surgery, Second Affiliated Hospital of Shenyang Medical College, 64 Qishan West Road, Shenyang, 110035, China
| | - Chunjian Shen
- Department of Cardiothoracic Surgery, Second Affiliated Hospital of Shenyang Medical College, 64 Qishan West Road, Shenyang, 110035, China.
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Wang F, Gao Y, Zhou L, Chen J, Xie Z, Ye Z, Wang Y. USP30: Structure, Emerging Physiological Role, and Target Inhibition. Front Pharmacol 2022; 13:851654. [PMID: 35308234 PMCID: PMC8927814 DOI: 10.3389/fphar.2022.851654] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/04/2022] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin-specific protease 30 (USP30) is a deubiquitinating enzyme (DUB) belonging to the USP subfamily, which was found localized in the mitochondrial outer membrane and peroxisomes owing to its unique transmembrane domain. Structural study revealed that USP30 employed a unique catalytic triad and molecular architecture to preferentially cleave the Lys6 linked ubiquitin chains. USP30 plays an essential role in several cellular events, such as the PINK1/Parkin-mediated mitophagy, pexophagy, BAX/BAK-dependent apoptosis, and IKKβ–USP30–ACLY-regulated lipogenesis/tumorigenesis, and is tightly regulated by post-translational modification including phosphorylation and mono-ubiquitination. Dysregulation of USP30 is associated with a range of physiological disorders, such as neurodegenerative disease, hepatocellular carcinoma, pulmonary disorders, and peroxisome biogenesis disorders. Nowadays, scientists and many biopharmaceutical companies are making much effort to explore USP30 inhibitors including natural compounds, phenylalanine derivatives, N-cyano pyrrolidines, benzosulphonamide, and other compounds. For the treatment of pulmonary disorders, the study in Mission Therapeutics of USP30 inhibitor is already in the pre-clinical stage. In this review, we will summarize the current knowledge of the structure, regulation, emerging physiological role, and target inhibition of USP30, hoping to prompt further investigation and understanding of it.
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Pan K, Fu J, Xu W. Role of Ubiquitin-Specific Peptidase 47 in Cancers and Other Diseases. Front Cell Dev Biol 2021; 9:726632. [PMID: 34604226 PMCID: PMC8484750 DOI: 10.3389/fcell.2021.726632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/24/2021] [Indexed: 12/24/2022] Open
Abstract
Deubiquitination is the reverse process of ubiquitination, which is catalyzed by deubiquitinase enzymes. More than 100 deubiquitinases have been identified. Ubiquitin-specific peptidase 47 (USP47), a member of the ubiquitin-specific protease family with high homology to USP7, is an active molecule with a wide range of functions and is closely associated with cancer and other diseases. However, no systematic summary exists regarding the functions of USP47. Here, we summarize the functions and expression regulation of USP47. USP47 is highly expressed in many tumors and is widely involved in tumor development, metastasis, drug resistance, epithelial-mesenchymal transition, and other processes. Targeted inhibition of USP47 can reverse malignant tumor behavior. USP47 also plays a role in inflammatory responses, myocardial infarction, and neuronal development. USP47 is involved in multiple levels of expression-regulating mechanisms, including transcriptional, post-transcriptional, and post-translational modifications. Development of targeted inhibitors against USP47 will provide a basis for studying the mechanisms of USP47 and developing therapeutic strategies for cancers and other diseases.
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Affiliation(s)
- Kailing Pan
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Junhao Fu
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Wenxia Xu
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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10
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Wang H, Liu Z, Sun Z, Zhou D, Mao H, Deng G. Ubiquitin specific peptidase 33 promotes cell proliferation and reduces apoptosis through regulation of the SP1/PI3K/AKT pathway in retinoblastoma. Cell Cycle 2021; 20:2066-2076. [PMID: 34470581 DOI: 10.1080/15384101.2021.1970305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Ubiquitin-specific protease 33 (USP33), a deubiquitinating enzyme (DUB), has been identified to serve as a tumor suppressor or an oncogene in different cancers. However, its role in retinoblastoma (RB) remains unknown. Here, we aimed to uncover USP33 expression profile and function in RB, and disclose the underlying mechanism. USP33 levels in RB tissues and cells were determined using RT-qPCR and western blotting assays. USP33 effects on cell growth, cycle, apoptosis and tumorigenesis were studied using MTT, Edu, cycle and western blotting and in vivo assays. The results showed that USP33 expression levels were elevated in RB tissues and cells as compared with normal retinal tissues and cells. Downregulation of USP33 in RB Y79 and WERI-RB1 cells leaded to significant increases in cell apoptosis, G1 phase arrest and tumorigenesis, and reductions in cell growth and G2 and S phase arrest, as well as inhibited the activation of the PI3K/AKT signaling. SP1 overexpression abolished the roles of USP33 downregulation in modulating the activation of PI3K/AKT signaling, cell growth, apoptosis, and cell cycle. This study uncovered that USP33 promoted the progression of RB through regulation of the SP1/PI3K/AKT pathway.
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Affiliation(s)
- Hao Wang
- Department of Ophthalmology, The Third People's Hospital of Changzhou, Changzhou City, Jiangsu Province, China
| | - Zhinan Liu
- Department of Ophthalmology, The Third People's Hospital of Changzhou, Changzhou City, Jiangsu Province, China
| | - Zhuo Sun
- Department of Ophthalmology, The Third People's Hospital of Changzhou, Changzhou City, Jiangsu Province, China
| | - Dong Zhou
- Department of Ophthalmology, The Third People's Hospital of Changzhou, Changzhou City, Jiangsu Province, China
| | - Hanyan Mao
- Department of Ophthalmology, The Third People's Hospital of Changzhou, Changzhou City, Jiangsu Province, China
| | - Guohua Deng
- Department of Ophthalmology, The Third People's Hospital of Changzhou, Changzhou City, Jiangsu Province, China
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11
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Gan Q, Shao J, Cao Y, Lei J, Xie P, Ge J, Hu G. USP33 regulates c-Met expression by deubiquitinating SP1 to facilitate metastasis in hepatocellular carcinoma. Life Sci 2020; 261:118316. [PMID: 32835698 DOI: 10.1016/j.lfs.2020.118316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/05/2020] [Accepted: 08/19/2020] [Indexed: 12/21/2022]
Abstract
AIMS Deubiquitinase ubiquitin-specific protease 33 (USP33) is abnormally expressed in various tumors and participates in tumor progression. However, the expression and biological role of USP33 in hepatocellular carcinoma (HCC) are still unclear. MAIN METHODS We performed immunohistochemistry, western blotting, and qRT-PCR analysis to determine the expression of USP33 in HCC. We then analyzed the effects of USP33 expression on the prognosis of HCC. The roles of USP33 in regulating HCC cell migration and invasion were further explored in vitro. Animal studies were performed to investigate the effects of USP33 on tumor metastasis. RNA sequencing and luciferase reporter and immunofluorescence assays were used to identify the activation of the specificity protein 1 (SP1)/c-Met axis. KEY FINDINGS Here, for the first time, we reported an abnormal increase in the expression of USP33 in HCC tissues and that USP33 may act as a prognostic biomarker for HCC patients. We found that USP33 knockdown inhibited the invasion and metastasis in HCC cells both in vitro and in vivo, which was partly dependent on c-Met. Further investigations revealed that USP33 regulated c-Met expression by enhancing the protein stability of the transcription factor SP1 in HCC cells. Mechanistically, USP33 directly bound SP1 and decreased its ubiquitination, thereby upregulating c-Met expression. SIGNIFICANCE Our results reveal that USP33 acts as the deubiquitinating enzyme of SP1 and contributes to HCC invasion and metastasis through activation of the SP1/c-Met axis. These data indicate a previously unknown function of USP33, which may provide potential targets for the treatment of HCC patients.
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Affiliation(s)
- Qin Gan
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Jiujiang Hospital of Nanchang University, Jiujiang 332000, China; Department of Hepatobiliary and Pancreatic Surgery, Jiujiang NO.1 People's Hospital, Jiujiang 332000, China
| | - Jia Shao
- Centre for Assisted Reproduction, The First Affiliated Hospital of Nanchang University, Jiangxi, Nanchang 330006, China
| | - Yan Cao
- Department of Gastroenterology, The Fourth Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Jun Lei
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Peiyi Xie
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Jin Ge
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, Nanchang 330006, China.
| | - Guohui Hu
- Department of General Practice, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China.
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12
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OTUD4 enhances TGFβ signalling through regulation of the TGFβ receptor complex. Sci Rep 2020; 10:15725. [PMID: 32973272 PMCID: PMC7519109 DOI: 10.1038/s41598-020-72791-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 09/02/2020] [Indexed: 11/18/2022] Open
Abstract
Systematic control of the transforming growth factor-β (TGFβ) pathway is essential to keep the amplitude and the intensity of downstream signalling at appropriate levels. Ubiquitination plays a crucial role in the general regulation of this pathway. Here we identify the deubiquitinating enzyme OTUD4 as a transcriptional target of the TGFβ pathway that functions through a positive feedback loop to enhance overall TGFβ activity. Interestingly we demonstrate that OTUD4 functions through both catalytically dependent and independent mechanisms to regulate TGFβ activity. Specifically, we find that OTUD4 enhances TGFβ signalling by promoting the membrane presence of TGFβ receptor I. Furthermore, we demonstrate that OTUD4 inactivates the TGFβ negative regulator SMURF2 suggesting that OTUD4 regulates multiple nodes of the TGFβ pathway to enhance TGFβ activity.
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13
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Zeng C, Zhao C, Ge F, Li Y, Cao J, Ying M, Lu J, He Q, Yang B, Dai X, Zhu H. Machado-Joseph Deubiquitinases: From Cellular Functions to Potential Therapy Targets. Front Pharmacol 2020; 11:1311. [PMID: 32982735 PMCID: PMC7479174 DOI: 10.3389/fphar.2020.01311] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/07/2020] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is known as important post-translational modification in cancer-related pathways. Human deubiquitinases (DUBs), with functions of modulating the ubiquitination process, are a family with about 100 proteins. They mainly function by cutting ubiquitin chains of the substrates. The Machado-Joseph domain-containing proteases (MJDs) is one of the sub-families of DUBs, consisting of four members, namely, Ataxin-3, Ataxin-3L, JOSD1, and JOSD2. Recent studies have provided new insights into biological functions of MJDs in the progression of Machado-Joseph disease or cancer diseases. In this review, we summarized the cellular functions and regulatory mechanisms of MJDs in Machado-Joseph disease and cancer pathways. Furthermore, we summarized MJDs genetic alterations in different human cancers by exploring the public databases (cBioportal). The aim of this review is to provide a comprehensive account based on our current knowledge about emerging insights into MJDs in physiology and disease, which might shed light on fundamental biological questions and promise to provide a potential target for therapeutic intervention.
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Affiliation(s)
- Chenming Zeng
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Chenxi Zhao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Fujing Ge
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yuekang Li
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jinjian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, Macau
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoyang Dai
- Center for Drug Safety Evaluation and Research, Zhejiang University, Hangzhou, China
| | - Hong Zhu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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14
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Mirzapoiazova T, Pozhitkov A, Nam A, Mambetsariev I, Nelson MS, Tan YHC, Zhang K, Raz D, Singhal S, Nasser MW, Kulkarni P, Batra SK, Sattler M, Salgia R. Effects of selected deubiquitinating enzyme inhibitors on the proliferation and motility of lung cancer and mesothelioma cell lines. Int J Oncol 2020; 57:80-86. [PMID: 32236606 PMCID: PMC7252467 DOI: 10.3892/ijo.2020.5034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/19/2020] [Indexed: 11/06/2022] Open
Abstract
The post‑translational modification of proteins by ubiquitinating enzymes plays a central role in a number of cellular functions, such as cell proteolysis, DNA repair, and cell signaling and communication. Deubiquitinating enzymes (DUBs) disassemble ubiquitin chains and remove ubiquitin moieties from proteins. Targeting DUBs in cancer models has revealed an important role for these enzymes in tumorigenesis, and they therefore have emerged as attractive therapeutic targets. In the present study, the effects of three DUB inhibitors, PR‑619, RA‑9 and LDN‑91946, on a non‑small cell lung cancer cell line (A549) and a mesothelioma cell line (H2373) were investigated. PR‑619 significantly inhibited cell adhesion and the proliferation of both cell lines. RA‑9 exerted an inhibitory effect on the adhesion and proliferation of H2373 cells, whereas it had no effect on A549 cells. Notably, however, while PR‑619 attenuated the proliferation of both cell lines, it exerted an opposite effect on cell motility; in the case of A549 cells, there was a significant increase in cell motility, while for the H2373 cells, there was a significant decrease. Furthermore, protein phosphorylation kinetic analyses revealed that the effects were cell line‑specific. In H2373 cells, the phosphorylation of only one peptide corresponding to the P85A protein was significantly affected, and while LDN‑91946 treatment increased phosphorylation, treatment with RA‑9 or PR‑619 decreased its phosphorylation compared to the DMSO control. By contrast, in the case of A549 cells, the phosphorylation of 21 peptides was significantly affected by the same compounds. In light of the potential for the negative side‑effects of DUB inhibition, such as increased cancer cell motility, the data presented herein underscore the dire need for the development of specific DUB inhibitors and to elucidate the individual role of DUB family members in cancer biology before they can be specifically pharmacologically targeted.
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Affiliation(s)
- Tamara Mirzapoiazova
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010‑3000, USA
| | - Alexander Pozhitkov
- Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010‑3000, USA
| | - Arin Nam
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010‑3000, USA
| | - Isa Mambetsariev
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010‑3000, USA
| | - Michael S Nelson
- The Light Microscopy and Digital Imaging Core, Beckman Research Institute, City of Hope, Duarte, CA 91010‑3000, USA
| | - Yi-Hung Carol Tan
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Keqiang Zhang
- Department of Surgery, City of Hope National Medical Center, Duarte, CA 91010‑3000, USA
| | - Dan Raz
- Department of Surgery, City of Hope National Medical Center, Duarte, CA 91010‑3000, USA
| | - Sharad Singhal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010‑3000, USA
| | - Mohd W Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010‑3000, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Martin Sattler
- Department of Medical Oncology, Dana‑Farber Cancer Institute, Boston, MA 02215, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010‑3000, USA
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15
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Targeting the ubiquitin-proteasome pathway to overcome anti-cancer drug resistance. Drug Resist Updat 2020; 48:100663. [DOI: 10.1016/j.drup.2019.100663] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 02/07/2023]
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16
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Chae YC, Jung H, Kim JY, Lee DH, Seo SB. Ubiquitin-specific peptidase 3 induces TPA-mediated leukemia cell differentiation via regulating H2AK119ub. Anim Cells Syst (Seoul) 2019; 23:311-317. [PMID: 31700696 PMCID: PMC6830191 DOI: 10.1080/19768354.2019.1661283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022] Open
Abstract
Acute myeloid leukemia (AML) is the most common type of leukemia in adults. Owing to the chemotherapy associated side effects and toxicity, it is necessary to find a new mechanism, which can identify new potential therapeutic targets at the molecular level. Here, we identified new target genes that are induced during the TPA-induced HL-60 cell differentiation by ChIP-seq and microarray data analysis. Using q-PCR and ChIP assay, we confirmed that the target genes including USP3, USP35, TCF4, and SGK1 are upregulated during TPA-mediated HL-60 cell differentiation. Levels of USP3, one of the deubiquitinating enzymes (DUBs), increased by TPA treatment, resulting in the reduction of H2AK119ub levels. In addition, we revealed that depletion of USP3 inhibits TPA-mediated leukemia cell differentiation q-PCR and FACS analysis. Taken together, our data indicate that USP3 promotes TPA-mediated leukemia cell differentiation via regulating H2AK119ub levels.
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Affiliation(s)
- Yun-Cheol Chae
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul, South Korea
| | - Hyeonsoo Jung
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul, South Korea
| | - Ji-Young Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul, South Korea
| | - Dong Ho Lee
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul, South Korea
| | - Sang-Beom Seo
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul, South Korea
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17
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Ubiquitin Specific Peptidase 15 (USP15) suppresses glioblastoma cell growth via stabilization of HECTD1 E3 ligase attenuating WNT pathway activity. Oncotarget 2017; 8:110490-110502. [PMID: 29299163 PMCID: PMC5746398 DOI: 10.18632/oncotarget.22798] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/13/2017] [Indexed: 01/12/2023] Open
Abstract
Expression based prediction of new genomic alterations in glioblastoma identified the de-ubiquitinase Ubiquitin Specific Peptidase 15 (USP15) as potential tumor suppressor gene associated with genomic deletions (11%). Ectopic expression of USP15 in glioblastoma cell-lines reduced colony formation and growth in soft agar, while overexpression of its functional mutant had the opposite effect. Evaluation of the protein binding network of USP15 by Mass Spectrometry in glioblastoma cells uncovered eight novel interacting proteins, including HECT Domain Containing E3 Ubiquitin Protein Ligase 1 (HECTD1), whose mouse homologue has been associated with an inhibitory effect on the WNT-pathway. USP15 de-ubiquitinated and thereby stabilized HECTD1 in glioblastoma cells, while depletion of USP15 led to decreased HECTD1 protein levels. Expression of USP15 in glioblastoma cells attenuated WNT-pathway activity, while expression of the functional mutant enhanced the activity. Modulation of HECTD1 expression pheno-copied the effects observed for USP15. In accordance, human glioblastoma display a weak but significant negative correlation between USP15 and AXIN2 expression. Taken together, the data provide evidence that USP15 attenuates the canonical WNT pathway mediated by stabilization of HECTD1, supporting a tumor suppressing role of USP15 in a subset of glioblastoma.
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18
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Su ZJ, Cao JS, Wu YF, Chen WN, Lin X, Wu YL, Lin X. Deubiquitylation of hepatitis B virus X protein (HBx) by ubiquitin-specific peptidase 15 (USP15) increases HBx stability and its transactivation activity. Sci Rep 2017; 7:40246. [PMID: 28074857 PMCID: PMC5225491 DOI: 10.1038/srep40246] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/05/2016] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus X protein (HBx) plays important roles in viral replication and the development of hepatocellular carcinoma. HBx is a rapid turnover protein and ubiquitin-proteasome pathway has been suggested to influence HBx stability as treatment with proteasome inhibitors increases the levels of HBx protein and causes accumulation of the polyubiquitinated forms of HBx. Deubiquitinases (DUBs) are known to act by removing ubiquitin moieties from proteins and thereby reverse their stability and/or activity. However, no information is available regarding the involvement of DUBs in regulation of ubiquitylation-dependent proteasomal degradation of HBx protein. This study identified the deubiquitylating enzyme USP15 as a critical regulator of HBx protein level. USP15 was found to directly interact with HBx via binding to the HBx region between amino acid residues 51 and 80. USP15 increased HBx protein levels in a dose-dependent manner and siRNA-mediated knockdown of endogenous USP15 reduced HBx protein levels. Increased HBx stability and steady-state level by USP15 were attributable to reduced HBx ubiquitination and proteasomal degradation. Importantly, the transcriptional transactivation function of HBx is enhanced by overexpression of USP15. These results suggest that USP15 plays an essential role in stabilizing HBx and subsequently affects the biological function of HBx.
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Affiliation(s)
- Zhi-Jun Su
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Department of Infectious Diseases, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, China
| | - Jia-Shou Cao
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Yan-Fang Wu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Wan-Nan Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Xinjian Lin
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Yun-Li Wu
- Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Xu Lin
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.,Department of Infectious Diseases, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, China
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19
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Greenall SA, Adams TE, Johns TG. Incomplete target neutralization by the anti-cancer antibody rilotumumab. MAbs 2016; 8:246-52. [PMID: 26750997 DOI: 10.1080/19420862.2015.1122149] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The antibody rilotumumab, which has been tested in multiple Phase 2 and Phase 3 trials, has been reported to neutralize hepatocyte growth factor (HGF), the ligand for the oncogene MET. However, we report that rilotumumab does not prevent HGF from directly binding to MET on conventional and primary patient-derived human gliomasphere lines, a trait driven by the HGF α-chain, which remains free to engage cell-surface glycosaminoglycans and the receptor MET. This binding induces MET phosphorylation, initiates robust AKT and ERK signaling and potentiates biological effects such as cell scattering. This partial antagonism was highly exacerbated in the presence of activated epidermal growth factor receptor, which is common in several cancers. Hence, we confirm that rilotumumab is only a partial antagonist of HGF activity, a finding that has considerable implications for the therapeutic use of rilotumumab.
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Affiliation(s)
- Sameer A Greenall
- a Oncogenic Signalling Laboratory and Brain Cancer Discovery Collaborative, Centre for Cancer Research, Hudson Institute of Medical Research , 27-31 Wright Street, Clayton , VIC 3168 , Australia.,b Monash University, Wellington Parade , Clayton , VIC 3800 , Australia.,c Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation , 343 Royal Parade, Parkville , VIC 3052 , Australia
| | - Timothy E Adams
- c Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation , 343 Royal Parade, Parkville , VIC 3052 , Australia
| | - Terrance G Johns
- a Oncogenic Signalling Laboratory and Brain Cancer Discovery Collaborative, Centre for Cancer Research, Hudson Institute of Medical Research , 27-31 Wright Street, Clayton , VIC 3168 , Australia.,b Monash University, Wellington Parade , Clayton , VIC 3800 , Australia
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20
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Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Couté Y, Chaoui K, Com E, Gateau A, Hesse AM, Marcellin M, Méar L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianferani S, Ferro M, Fréour T, Lindskog C, Garin J, Pineau C. Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update. J Proteome Res 2016; 15:3998-4019. [PMID: 27444420 DOI: 10.1021/acs.jproteome.6b00400] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The Chromosome-Centric Human Proteome Project (C-HPP) aims to identify "missing" proteins in the neXtProt knowledgebase. We present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using protein extraction procedures and LC-MS/MS analysis, we detected 235 proteins (PE2-PE4) for which no previous evidence of protein expression was annotated. Through LC-MS/MS and LC-PRM analysis, data mining, and immunohistochemistry, we confirmed the expression of 206 missing proteins (PE2-PE4) in line with current HPP guidelines (version 2.0). Parallel reaction monitoring acquisition and sythetic heavy labeled peptides targeted 36 ≪one-hit wonder≫ candidates selected based on prior peptide spectrum match assessment. 24 were validated with additional predicted and specifically targeted peptides. Evidence was found for 16 more missing proteins using immunohistochemistry on human testis sections. The expression pattern for some of these proteins was specific to the testis, and they could possibly be valuable markers with fertility assessment applications. Strong evidence was also found of four "uncertain" proteins (PE5); their status should be re-examined. We show how using a range of sample preparation techniques combined with MS-based analysis, expert knowledge, and complementary antibody-based techniques can produce data of interest to the community. All MS/MS data are available via ProteomeXchange under identifier PXD003947. In addition to contributing to the C-HPP, we hope these data will stimulate continued exploration of the sperm proteome.
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Affiliation(s)
- Yves Vandenbrouck
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Lydie Lane
- Department of Human Protein Sciences, Faculty of Medicine, University of Geneva , 1, rue Michel-Servet, 1211 Geneva 4, Switzerland.,CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU , rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Paula Duek
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU , rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Karine Rondel
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
| | - Christophe Bruley
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Charlotte Macron
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Anne Gonzalez de Peredo
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Yohann Couté
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Karima Chaoui
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Emmanuelle Com
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
| | - Alain Gateau
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU , rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Anne-Marie Hesse
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Marlene Marcellin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Loren Méar
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Thibault Robin
- Proteome Informatics Group, Centre Universitaire d'Informatique , Route de Drize 7, 1227 Carouge, CH, Switzerland
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Myriam Ferro
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Thomas Fréour
- Service de Médecine de la Reproduction, CHU de Nantes , 38 boulevard Jean Monnet, 44093 Nantes cedex, France.,INSERM UMR1064 , Nantes 44093, France
| | - Cecilia Lindskog
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France
| | - Jérôme Garin
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Charles Pineau
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
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21
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Anta B, Martín-Rodríguez C, Gomis-Perez C, Calvo L, López-Benito S, Calderón-García AA, Vicente-García C, Villarroel Á, Arévalo JC. Ubiquitin-specific Protease 36 (USP36) Controls Neuronal Precursor Cell-expressed Developmentally Down-regulated 4-2 (Nedd4-2) Actions over the Neurotrophin Receptor TrkA and Potassium Voltage-gated Channels 7.2/3 (Kv7.2/3). J Biol Chem 2016; 291:19132-45. [PMID: 27445338 DOI: 10.1074/jbc.m116.722637] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 11/06/2022] Open
Abstract
Ubiquitination of the TrkA neurotrophin receptor in response to NGF is critical in the regulation of TrkA activation and functions. TrkA is ubiquitinated, among other E3 ubiquitin ligases, by Nedd4-2. To understand mechanistically how TrkA ubiquitination is regulated, we performed a siRNA screening to identify deubiquitinating enzymes and found that USP36 acts as an important regulator of TrkA activation kinetics and ubiquitination. However, USP36 action on TrkA was indirect because it does not deubiquitinate TrkA. Instead, USP36 binds to Nedd4-2 and regulates the association of TrkA and Nedd4-2. In addition, depletion of USP36 increases TrkA·Nedd4-2 complex formation, whereas USP36 expression disrupts the complex, resulting in an enhancement or impairment of Nedd4-2-dependent TrkA ubiquitination, respectively. Moreover, USP36 depletion leads to enhanced total and surface TrkA expression that results in increased NGF-mediated TrkA activation and signaling that augments PC12 cell differentiation. USP36 actions extend beyond TrkA because the presence of USP36 interferes with Nedd4-2-dependent Kv7.2/3 channel regulation. Our results demonstrate that USP36 binds to and regulates the actions of Nedd4-2 over different substrates affecting their expression and functions.
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Affiliation(s)
- Begoña Anta
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Carlos Martín-Rodríguez
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Carolina Gomis-Perez
- the Unidad de Biofísica, Consejo Superior de Investigaciones Científicas, CSIC, UPV/EHU, Universidad del País Vasco, barrio Sarriena s/n, 48940 Leoia, Spain
| | - Laura Calvo
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Saray López-Benito
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Andrés A Calderón-García
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
| | - Cristina Vicente-García
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Álvaro Villarroel
- the Unidad de Biofísica, Consejo Superior de Investigaciones Científicas, CSIC, UPV/EHU, Universidad del País Vasco, barrio Sarriena s/n, 48940 Leoia, Spain
| | - Juan C Arévalo
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
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22
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Ge F, Chen W, Qin J, Zhou Z, Liu R, Liu L, Tan J, Zou T, Li H, Ren G, Chen C. Ataxin-3 like (ATXN3L), a member of the Josephin family of deubiquitinating enzymes, promotes breast cancer proliferation by deubiquitinating Krüppel-like factor 5 (KLF5). Oncotarget 2016; 6:21369-78. [PMID: 26079537 PMCID: PMC4673271 DOI: 10.18632/oncotarget.4128] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/02/2015] [Indexed: 11/25/2022] Open
Abstract
The Krüppel-like factor 5 (KLF5) has been suggested to promote breast cell proliferation, survival and tumorigenesis. KLF5 protein degradation is increased by several E3 ubiquitin ligases, including WWP1 and SCFFbw7, through the ubiquitin-proteasome pathway. However, the deubiquitinase (DUB) of KLF5 has not been demonstrated. In this study, we identified ATXN3L as a KLF5 DUB by genome-wide siRNA screening. ATXN3L directly binds to KLF5, decreasing its ubiquitination and thus degradation. Functionally, knockdown of ATXN3L inhibits breast cancer cell proliferation partially through KLF5. These findings reveal a previously unrecognized role of ATXN3L in the regulation of KLF5 stability in breast cancer. ATXN3L might be a therapeutic target for breast cancer.
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Affiliation(s)
- Fei Ge
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wenlin Chen
- Department of Breast Surgery, The 3rd Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Junying Qin
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhongmei Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Rong Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Linlin Liu
- Laboratory for Conservation and Utilization of Bioresource, Yunnan University, Kunming, China
| | - Jing Tan
- Department of Breast Surgery, The 3rd Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Tianning Zou
- Department of Breast Surgery, The 3rd Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Hongyuan Li
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guosheng Ren
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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23
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Savio MG, Wollscheid N, Cavallaro E, Algisi V, Di Fiore PP, Sigismund S, Maspero E, Polo S. USP9X Controls EGFR Fate by Deubiquitinating the Endocytic Adaptor Eps15. Curr Biol 2016; 26:173-183. [PMID: 26748853 DOI: 10.1016/j.cub.2015.11.050] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/16/2015] [Accepted: 11/20/2015] [Indexed: 01/16/2023]
Abstract
Following activation by its cognate ligand(s), the epidermal growth factor receptor (EGFR) is rapidly routed to the lysosome for degradation in a ubiquitination-dependent fashion. This pathway represents the major mechanism of long-term attenuation of EGFR signaling, and its deregulation is a significant feature in different types of cancers. Here we demonstrate, through a systematic RNAi-based approach, that several deubiquitinating (DUB) enzymes extend or decrease EGFR half-life upon EGF stimulation. We focus on USP9X, whose depletion severely affects EGFR turnover, interfering with its internalization and trafficking. We identify the endocytic protein Eps15 as one of the critical substrates of USP9X, and we map the Eps15 ubiquitination sites. We found that Eps15 monoubiquitination occurs already at minimal dose of EGF stimulation and is essential for EGFR internalization. Overall, our findings identify USP9X as a novel regulator of EGFR endocytosis and suggest a model whereby cycles of ubiquitination and deubiquitination events on endocytic accessory proteins may regulate the internalization and trafficking of the EGFR toward the lysosomes.
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Affiliation(s)
- Michol Giovanna Savio
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; DIPO, Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Via di Rudinì 8, 20122 Milan, Italy
| | - Nadine Wollscheid
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Elena Cavallaro
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Veronica Algisi
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Pier Paolo Di Fiore
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; DIPO, Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Via di Rudinì 8, 20122 Milan, Italy; IEO, Istituto Europeo di Oncologia, Via Ripamonti 435, 20141 Milan, Italy
| | - Sara Sigismund
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Elena Maspero
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Simona Polo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; DIPO, Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Via di Rudinì 8, 20122 Milan, Italy.
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24
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Harrigan J, Jacq X. Monitoring Target Engagement of Deubiquitylating Enzymes Using Activity Probes: Past, Present, and Future. Methods Mol Biol 2016; 1449:395-410. [PMID: 27613052 PMCID: PMC7120244 DOI: 10.1007/978-1-4939-3756-1_26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Deubiquitylating enzymes or DUBs are a class of enzymes that selectively remove the polypeptide posttranslational modification ubiquitin from a number of substrates. Approximately 100 DUBs exist in human cells and are involved in key regulatory cellular processes, which drive many disease states, making them attractive therapeutic targets. Several aspects of DUB biology have been studied through genetic knock-out or knock-down, genomic, or proteomic studies. However, investigation of enzyme activation and regulation requires additional tools to monitor cellular and physiological dynamics. A comparison between genetic ablation and dominant-negative target validation with pharmacological inhibition often leads to striking discrepancies. Activity probes have been used to profile classes of enzymes, including DUBs, and allow functional and dynamic properties to be assigned to individual proteins. The ability to directly monitor DUB activity within a native biological system is essential for understanding the physiological and pathological role of individual DUBs. We will discuss the evolution of DUB activity probes, from in vitro assay development to their use in monitoring DUB activity in cells and in animal tissues, as well as recent progress and prospects for assessing DUB inhibition in vivo.
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Affiliation(s)
- Jeanine Harrigan
- MISSION Therapeutics Limited, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Xavier Jacq
- MISSION Therapeutics Limited, Moneta, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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25
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Citterio E. Fine-tuning the ubiquitin code at DNA double-strand breaks: deubiquitinating enzymes at work. Front Genet 2015; 6:282. [PMID: 26442100 PMCID: PMC4561801 DOI: 10.3389/fgene.2015.00282] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/23/2015] [Indexed: 01/23/2023] Open
Abstract
Ubiquitination is a reversible protein modification broadly implicated in cellular functions. Signaling processes mediated by ubiquitin (ub) are crucial for the cellular response to DNA double-strand breaks (DSBs), one of the most dangerous types of DNA lesions. In particular, the DSB response critically relies on active ubiquitination by the RNF8 and RNF168 ub ligases at the chromatin, which is essential for proper DSB signaling and repair. How this pathway is fine-tuned and what the functional consequences are of its deregulation for genome integrity and tissue homeostasis are subject of intense investigation. One important regulatory mechanism is by reversal of substrate ubiquitination through the activity of specific deubiquitinating enzymes (DUBs), as supported by the implication of a growing number of DUBs in DNA damage response processes. Here, we discuss the current knowledge of how ub-mediated signaling at DSBs is controlled by DUBs, with main focus on DUBs targeting histone H2A and on their recent implication in stem cell biology and cancer.
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Affiliation(s)
- Elisabetta Citterio
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam Netherlands
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26
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Liang JR, Martinez A, Lane JD, Mayor U, Clague MJ, Urbé S. USP30 deubiquitylates mitochondrial Parkin substrates and restricts apoptotic cell death. EMBO Rep 2015; 16:618-27. [PMID: 25739811 PMCID: PMC4428036 DOI: 10.15252/embr.201439820] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/11/2015] [Indexed: 12/21/2022] Open
Abstract
Mitochondria play a pivotal role in the orchestration of cell death pathways. Here, we show that the control of ubiquitin dynamics at mitochondria contributes to the regulation of apoptotic cell death. The unique mitochondrial deubiquitylase, USP30, opposes Parkin-dependent ubiquitylation of TOM20, and its depletion enhances depolarization-induced cell death in Parkin-overexpressing cells. Importantly, USP30 also regulates BAX/BAK-dependent apoptosis, and its depletion sensitizes cancer cells to BH3-mimetics. These results provide the first evidence for a fundamental role of USP30 in determining the threshold for mitochondrial cell death and suggest USP30 as a potential target for combinatorial anti-cancer therapy.
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Affiliation(s)
- Jin-Rui Liang
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Aitor Martinez
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK CIC Biogune Bizkaia Teknologi Parkea, Derio, Spain IKERBASQUE Basque Foundation for Science, Bilbao, Spain
| | - Jon D Lane
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Ugo Mayor
- CIC Biogune Bizkaia Teknologi Parkea, Derio, Spain IKERBASQUE Basque Foundation for Science, Bilbao, Spain
| | - Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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27
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Deubiquitinase inhibition as a cancer therapeutic strategy. Pharmacol Ther 2015; 147:32-54. [DOI: 10.1016/j.pharmthera.2014.11.002] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 09/16/2014] [Indexed: 12/27/2022]
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28
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Sako-Kubota K, Tanaka N, Nagae S, Meng W, Takeichi M. Minus end-directed motor KIFC3 suppresses E-cadherin degradation by recruiting USP47 to adherens junctions. Mol Biol Cell 2014; 25:3851-60. [PMID: 25253721 PMCID: PMC4244195 DOI: 10.1091/mbc.e14-07-1245] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
KIFC3, a minus end–directed kinesin motor, recruits the ubiquitin-specific protease USP47, a protease that removes ubiquitin chains from substrates, to epithelial adherens junctions. This process suppresses the ubiquitination and resultant degradation of E-cadherin, thereby maintaining stable cell–cell adhesion in epithelial sheets. The adherens junction (AJ) plays a crucial role in maintaining cell–cell adhesion in epithelial tissues. Previous studies show that KIFC3, a minus end–directed kinesin motor, moves into AJs via microtubules that grow from clusters of CAMSAP3 (also known as Nezha), a protein that binds microtubule minus ends. The function of junction-associated KIFC3, however, remains to be elucidated. Here we find that KIFC3 binds the ubiquitin-specific protease USP47, a protease that removes ubiquitin chains from substrates and hence inhibits proteasome-mediated proteolysis, and recruits it to AJs. Depletion of KIFC3 or USP47 promotes cleavage of E-cadherin at a juxtamembrane region of the cytoplasmic domain, resulting in the production of a 90-kDa fragment and the internalization of E-cadherin. This cleavage depends on the E3 ubiquitin protein ligase Hakai and is inhibited by proteasome inhibitors. E-cadherin ubiquitination consistently increases after depletion of KIFC3 or USP47. These findings suggest that KIFC3 suppresses the ubiquitination and resultant degradation of E-cadherin by recruiting USP47 to AJs, a process that may be involved in maintaining stable cell–cell adhesion in epithelial sheets.
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Affiliation(s)
| | | | - Shigenori Nagae
- RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Wenxiang Meng
- RIKEN Center for Developmental Biology, Kobe 650-0047, Japan State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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29
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Wen P, Kong R, Liu J, Zhu L, Chen X, Li X, Nie Y, Wu K, Wu JY. USP33, a new player in lung cancer, mediates Slit-Robo signaling. Protein Cell 2014; 5:704-13. [PMID: 24981056 PMCID: PMC4145083 DOI: 10.1007/s13238-014-0070-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 04/09/2014] [Indexed: 10/25/2022] Open
Abstract
Ubiquitin specific protease 33 (USP33) is a multifunctional protein regulating diverse cellular processes. The expression and role of USP33 in lung cancer remain unexplored. In this study, we show that USP33 is down-regulated in multiple cohorts of lung cancer patients and that low expression of USP33 is associated with poor prognosis. USP33 mediates Slit-Robo signaling in lung cancer cell migration. Downregulation of USP33 reduces the protein stability of Robo1 in lung cancer cells, providing a previously unknown mechanism for USP33 function in mediating Slit activity in lung cancer cells. Taken together, USP33 is a new player in lung cancer that regulates Slit-Robo signaling. Our data suggest that USP33 may be a candidate tumor suppressor for lung cancer with potential as a prognostic marker.
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Affiliation(s)
- Pushuai Wen
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Department of Pathophysiology, Liaoning Medical University, Jinzhou, 121001 China
| | - Ruirui Kong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jianghong Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Li Zhu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiaoping Chen
- Department of Neurology, Center for Genetic Medicine, Lurie Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611 USA
| | - Xiaofei Li
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, 710038 China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, 710032 China
| | - Kaichun Wu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, 710032 China
| | - Jane Y. Wu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- Department of Neurology, Center for Genetic Medicine, Lurie Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611 USA
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30
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Bedi U, Mishra VK, Wasilewski D, Scheel C, Johnsen SA. Epigenetic plasticity: a central regulator of epithelial-to-mesenchymal transition in cancer. Oncotarget 2014; 5:2016-29. [PMID: 24840099 PMCID: PMC4039141 DOI: 10.18632/oncotarget.1875] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 03/27/2014] [Indexed: 12/20/2022] Open
Abstract
Tumor metastasis is the major cause of mortality and morbidity in most solid cancers. A growing body of evidence suggests that the epithelial-to-mesenchymal transition (EMT) plays a central role during tumor metastasis and frequently imparts a stem cell-like phenotype and therapeutic resistance to tumor cells. The induction of EMT is accompanied by a dynamic reprogramming of the epigenome involving changes in DNA methylation and several post-translational histone modifications. These changes in turn promote the expression of mesenchymal genes or repress those associated with an epithelial phenotype. Importantly, in order for metastatic colonization and the formation of macrometastases to occur, tumor cells frequently undergo a reversal of EMT referred to as the mesenchymal-to-epithelial transition (MET). Thus, a high degree of epigenetic plasticity is required in order to induce and reverse EMT during tumor progression. In this review, we describe various epigenetic regulatory mechanisms employed by tumor cells during EMT and elaborate on the importance of the histone code in controlling both the expression and activity of EMT-associated transcription factors. We propose that a more thorough understanding of the epigenetic mechanisms controlling EMT may provide new opportunities which may be harnessed for improved and individualized cancer therapy based on defined molecular mechanisms.
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Affiliation(s)
- Upasana Bedi
- Department of Molecular Oncology, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany
| | | | | | | | - Steven A Johnsen
- ²Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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31
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Jacq X, Kemp M, Martin NMB, Jackson SP. Deubiquitylating enzymes and DNA damage response pathways. Cell Biochem Biophys 2014; 67:25-43. [PMID: 23712866 PMCID: PMC3756857 DOI: 10.1007/s12013-013-9635-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Covalent post-translational modification of proteins by ubiquitin and ubiquitin-like factors has emerged as a general mechanism to regulate myriad intra-cellular processes. The addition and removal of ubiquitin or ubiquitin-like proteins from factors has recently been demonstrated as a key mechanism to modulate DNA damage response (DDR) pathways. It is thus, timely to evaluate the potential for ubiquitin pathway enzymes as DDR drug targets for therapeutic intervention. The synthetic lethal approach provides exciting opportunities for the development of targeted therapies to treat cancer: most tumours have lost critical DDR pathways, and thus rely more heavily on the remaining pathways, while normal tissues are still equipped with all DDR pathways. Here, we review key deubiquitylating enzymes (DUBs) involved in DDR pathways, and describe how targeting DUBs may lead to selective therapies to treat cancer patients.
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Affiliation(s)
- Xavier Jacq
- MISSION Therapeutics Ltd, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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32
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The deubiquitylase Ataxin-3 restricts PTEN transcription in lung cancer cells. Oncogene 2013; 33:4265-72. [PMID: 24292675 PMCID: PMC4351423 DOI: 10.1038/onc.2013.512] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/22/2013] [Accepted: 10/23/2013] [Indexed: 12/12/2022]
Abstract
The phosphatidylinositol-3-kinase (PI3K) pathway is commonly hyperactivated in cancer. One mechanism by which this occurs is by silencing of the phosphatase and tensin homolog (PTEN), a tumor suppressor and major antagonist of the pathway, through genetic, epigenetic or posttranscriptional mechanisms. Here, we used an unbiased siRNA screen in non-small-cell lung cancer cells to identify deubiquitylases (DUBs) that have an impact on PI3K signaling by regulating the abundance of PTEN. We found that PTEN expression was induced by depleting any of three members of the Josephin family DUBs: ataxin 3 (ATXN3), ataxin 3-like (ATXN3L) and Josephin domain containing 1 (JOSD1). However, this effect is not mediated through altered PTEN protein stability. Instead, depletion of each DUB increases expression of both the PTEN transcript and its competing endogenous RNA, PTENP1. In ATXN3-depleted cells, under conditions of transcriptional inhibition, PTEN and PTENP1 mRNAs rapidly decay, suggesting that ATXN3 acts primarily by repressing their transcription. Importantly, the PTEN induction observed in response to ATXN3 siRNA is sufficient to downregulate Akt phosphorylation and hence PI3K signaling. Histone deacetylase inhibitors (HDACi) have been suggested as potential mediators of PTEN transcriptional reactivation in non-small-cell lung cancer. Although PTEN exhibits a very limited response to the broad-spectrum HDACi Vorinostat (SAHA) in A549 cells, we find that combination with ATXN3 depletion enhances PTEN induction in an additive manner. Similarly, these interventions additively decrease cell viability. Thus, ATXN3 provides an autonomous, complementary therapeutic target in cancers with epigenetic downregulation of PTEN.
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33
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Knockdown of specific host factors protects against influenza virus-induced cell death. Cell Death Dis 2013; 4:e769. [PMID: 23949218 PMCID: PMC3763457 DOI: 10.1038/cddis.2013.296] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 07/12/2013] [Accepted: 07/15/2013] [Indexed: 12/15/2022]
Abstract
Cell death is a characteristic consequence of cellular infection by influenza virus. Mounting evidence indicates the critical involvement of host-mediated cellular death pathways in promoting efficient influenza virus replication. Furthermore, it appears that many signaling pathways, such as NF-κB, formerly suspected to solely promote cell survival, can also be manipulated to induce cell death. Current understanding of the cell death pathways involved in influenza virus-mediated cytopathology and in virus replication is limited. This study was designed to identify host genes that are required for influenza-induced cell death. The approach was to perform genome-wide lentiviral-mediated human gene silencing in A549 cells and determine which genes could be silenced to provide resistance to influenza-induced cell death. The assay proved to be highly reproducible with 138 genes being identified in independent screens. The results were independently validated using siRNA to each of these candidates. Graded protection was observed in this screen with the silencing of any of 19 genes, each providing >85% protection. Three gene products, TNFSF13 (APRIL), TNFSF12-TNFSF13 (TWE-PRIL) and USP47, were selected because of the high levels of protection conferred by their silencing. Protein and mRNA silencing and protection from influenza-induced cell death was confirmed using multiple shRNA clones and siRNA, indicating the specificity of the effects. USP47 knockdown prevented proper viral entry into the host cell, whereas TNFSF12-13/TNFSF13 knockdown blocked a late stage in viral replication. This screening approach offers the means to identify a large number of potential candidates for the analysis of viral-induced cell death. These results may also have much broader applicability in defining regulatory mechanisms involved in cell survival.
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34
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Bachet JB, Tabone-Eglinger S, Dessaux S, Besse A, Brahimi-Adouane S, Emile JF, Blay JY, Alberti L. Gene expression patterns of hemizygous and heterozygous KIT mutations suggest distinct oncogenic pathways: a study in NIH3T3 cell lines and GIST samples. PLoS One 2013; 8:e61103. [PMID: 23593401 PMCID: PMC3625162 DOI: 10.1371/journal.pone.0061103] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 03/05/2013] [Indexed: 12/18/2022] Open
Abstract
Objective Most gain of function mutations of tyrosine kinase receptors in human tumours are hemizygous. Gastrointestinal stromal tumours (GIST) with homozygous mutations have a worse prognosis. We aimed to identify genes differentially regulated by hemizygous and heterozygous KIT mutations. Materials and Methods Expression of 94 genes and 384 miRNA was analysed with low density arrays in five NIH3T3 cell lines expressing the full-length human KIT cDNA wild-type (WT), hemizygous KIT mutation with del557-558 (D6) or del564-581 (D54) and heterozygous WT/D6 or WT/D54. Expression of 5 of these genes and 384 miRNA was then analysed in GISTs samples. Results Unsupervised and supervised hierarchical clustering of the mRNA and miRNA profiles showed that heterozygous mutants clustered with KIT WT expressing cells while hemizygous mutants were distinct. Among hemizygous cells, D6 and D54 expressing cells clustered separately. Most deregulated genes have been reported as potentially implicated in cancer and severals, as ANXA8 and FBN1, are highlighted by both, mRNA and miRNA analyses. MiRNA and mRNA analyses in GISTs samples confirmed that their expressions varied according to the mutation of the alleles. Interestingly, RGS16, a membrane protein of the regulator of G protein family, correlate with the subcellular localization of KIT mutants and might be responsible for regulation of the PI3K/AKT signalling pathway. Conclusion Patterns of mRNA and miRNA expression in cells and tumours depend on heterozygous/hemizygous status of KIT mutations, and deletion/presence of TYR568 & TYR570 residues. Thus each mutation of KIT may drive specific oncogenic pathways.
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Affiliation(s)
- Jean-Baptiste Bachet
- EA4340 'Epidémiologie et Oncogénèse des tumeurs digestives', Faculté de médecine PIFO, UVSQ, Guyancourt, France
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35
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Abstract
Ubiquitylation is a reversible post-translational modification that has emerged as a key regulator of most complex cellular processes. It may rival phosphorylation in scope and exceed it in complexity. The dynamic nature of ubiquitylation events is important for governing protein stability, maintaining ubiquitin homeostasis and controlling ubiquitin-dependent signalling pathways. The human genome encodes ~80 active deubiquitylating enzymes (DUBs, also referred to as deubiquitinases), which exhibit distinct specificity profiles towards the various ubiquitin chain topologies. As a result of their ability to reverse ubiquitylation, these enzymes control a broad range of key cellular processes. In this Commentary we discuss the cellular functions of DUBs, such as their role in governing membrane traffic and protein quality control. We highlight two key signalling pathways--the Wnt and transforming growth factor β (TGF-β) pathways, for which dynamic ubiquitylation has emerged as a key regulator. We also discuss the roles of DUBs in the nucleus, where they govern transcriptional activity and DNA repair pathways.
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Affiliation(s)
- Michael J Clague
- Physiological Laboratory, Institute of Translational Medicine, University of Liverpool, Crown Street, L69 3BX Liverpool, UK.
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36
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Fang Z, Luna EJ. Supervillin-mediated suppression of p53 protein enhances cell survival. J Biol Chem 2013; 288:7918-7929. [PMID: 23382381 DOI: 10.1074/jbc.m112.416842] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Integrin-based adhesions promote cell survival as well as cell motility and invasion. We show here that the adhesion regulatory protein supervillin increases cell survival by decreasing levels of the tumor suppressor protein p53 and downstream target genes. RNAi-mediated knockdown of a new splice form of supervillin (isoform 4) or both isoforms 1 and 4 increases the amount of p53 and cell death, whereas p53 levels decrease after overexpression of either supervillin isoform. Cellular responses to DNA damage induced by etoposide or doxorubicin include down-regulation of endogenous supervillin coincident with increases in p53. In DNA-damaged supervillin knockdown cells, p53 knockdown or inhibition partially rescues the loss of cell metabolic activity, a measure of cell proliferation. Knockdown of the p53 deubiquitinating enzyme USP7/HAUSP also reverses the supervillin phenotype, blocking the increase in p53 levels seen after supervillin knockdown and accentuating the decrease in p53 levels triggered by supervillin overexpression. Conversely, supervillin overexpression decreases the association of USP7 and p53 and attenuates USP7-mediated p53 deubiquitination. USP7 binds directly to the supervillin N terminus and can deubiquitinate and stabilize supervillin. Supervillin also is stabilized by derivatization with the ubiquitin-like protein SUMO1. These results show that supervillin regulates cell survival through control of p53 levels and suggest that supervillin and its interaction partners at sites of cell-substrate adhesion constitute a locus for cross-talk between survival signaling and cell motility pathways.
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Affiliation(s)
- Zhiyou Fang
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.
| | - Elizabeth J Luna
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.
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37
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A targeted in vivo RNAi screen reveals deubiquitinases as new regulators of Notch signaling. G3-GENES GENOMES GENETICS 2012; 2:1563-75. [PMID: 23275879 PMCID: PMC3516478 DOI: 10.1534/g3.112.003780] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/27/2012] [Indexed: 01/11/2023]
Abstract
Notch signaling is highly conserved in all metazoan animals and plays critical roles in cell fate specification, cell proliferation, apoptosis, and stem cell maintenance. Although core components of the Notch signaling cascade have been identified, many gaps in the understanding of the Notch signaling pathway remain to be filled. One form of posttranslational regulation, which is controlled by the ubiquitin-proteasome system, is known to modulate Notch signaling. The ubiquitination pathway is a highly coordinated process in which the ubiquitin moiety is either conjugated to or removed from target proteins by opposing E3 ubiquitin ligases and deubiquitinases (DUBs). Several E3 ubiquitin ligases have been implicated in ubiquitin conjugation to the receptors and the ligands of the Notch signaling cascade. In contrast, little is known about a direct role of DUBs in Notch signaling in vivo. Here, we report an in vivo RNA interference screen in Drosophila melanogaster targeting all 45 DUBs that we annotated in the fly genome. We show that at least four DUBs function specifically in the formation of the fly wing margin and/or the specification of the scutellar sensory organ precursors, two processes that are strictly dependent on the balanced Notch signaling activity. Furthermore, we provide genetic evidence suggesting that these DUBs are necessary to positively modulate Notch signaling activity. Our study reveals a conserved molecular mechanism by which protein deubiquitination process contributes to the complex posttranslational regulation of Notch signaling in vivo.
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38
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Frisan T, Coppotelli G, Dryselius R, Masucci MG. Ubiquitin C-terminal hydrolase-L1 interacts with adhesion complexes and promotes cell migration, survival, and anchorage independent growth. FASEB J 2012; 26:5060-70. [PMID: 22932395 DOI: 10.1096/fj.12-211946] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Ubiquitin C-terminal hydrolase-L1 (UCH-L1) is a deubiquitinating enzyme of unknown function that is highly expressed in neurons and overexpressed in several human cancers. UCH-L1 has been implicated in the regulation of phenotypic properties associated with malignant cell growth but the underlying mechanisms have not been elucidated. By comparing cells expressing catalytically active or inactive versions of UCH-L1, we found that the active enzyme enhances cell adhesion, spreading, and migration; inhibits anoikis; and promotes anchorage independent growth. UCH-L1 accumulates at the motile edge of the cell membrane during the initial phases of adhesion, colocalizes with focal adhesion kinase (FAK), p120-catenin, and vinculin, and enhances the formation of focal adhesions, which correlates with enhanced FAK activation. The involvement of UCH-L1 in the regulation of focal adhesions and adherens junctions is supported by coimmunoprecipitation with key components of these complexes, including FAK, paxillin, p120-catenin, β-catenin, and vinculin. UCH-L1 stabilizes focal adhesion signaling in the absence of adhesion, as assessed by reduced caspase-dependent cleavage of FAK following cell detachment and sustained activity of the AKT signaling pathway. These findings offer new insights on the molecular interactions through which the deubiquitinating enzyme regulates the survival, proliferation, and metastatic potential of malignant cells.
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Affiliation(s)
- Teresa Frisan
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden, Box 285, S-171 77 Stockholm, Sweden
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39
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Abstract
Post-translational modifications are used by cells to link additional information to proteins. Most modifications are subtle and concern small moieties such as a phosphate group or a lipid. In contrast, protein ubiquitylation entails the covalent attachment of a full-length protein such as ubiquitin. The protein ubiquitylation machinery is remarkably complex, comprising more than 15 Ubls (ubiquitin-like proteins) and several hundreds of ubiquitin-conjugating enzymes. Ubiquitin is best known for its role as a tag that induces protein destruction either by the proteasome or through targeting to lysosomes. However, addition of one or more Ubls also affects vesicular traffic, protein-protein interactions and signal transduction. It is by now well established that ubiquitylation is a component of most, if not all, cellular signalling pathways. Owing to its abundance in controlling cellular functions, ubiquitylation is also of key relevance to human pathologies, including cancer and inflammation. In the present review, we focus on its role in the control of cell adhesion, polarity and directional migration. It will become clear that protein modification by Ubls occurs at every level from the receptors at the plasma membrane down to cytoskeletal components such as actin, with differential consequences for the pathway's final output. Since ubiquitylation is fast as well as reversible, it represents a bona fide signalling event, which is used to fine-tune a cell's responses to receptor agonists.
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40
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Grou CP, Francisco T, Rodrigues TA, Freitas MO, Pinto MP, Carvalho AF, Domingues P, Wood SA, Rodríguez-Borges JE, Sá-Miranda C, Fransen M, Azevedo JE. Identification of ubiquitin-specific protease 9X (USP9X) as a deubiquitinase acting on ubiquitin-peroxin 5 (PEX5) thioester conjugate. J Biol Chem 2012; 287:12815-27. [PMID: 22371489 DOI: 10.1074/jbc.m112.340158] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Peroxin 5 (PEX5), the peroxisomal protein shuttling receptor, binds newly synthesized peroxisomal matrix proteins in the cytosol and promotes their translocation across the organelle membrane. During the translocation step, PEX5 itself becomes inserted into the peroxisomal docking/translocation machinery. PEX5 is then monoubiquitinated at a conserved cysteine residue and extracted back into the cytosol in an ATP-dependent manner. We have previously shown that the ubiquitin-PEX5 thioester conjugate (Ub-PEX5) released into the cytosol can be efficiently disrupted by physiological concentrations of glutathione, raising the possibility that a fraction of Ub-PEX5 is nonenzymatically deubiquitinated in vivo. However, data suggesting that Ub-PEX5 is also a target of a deubiquitinase were also obtained in that work. Here, we used an unbiased biochemical approach to identify this enzyme. Our results suggest that ubiquitin-specific protease 9X (USP9X) is by far the most active deubiquitinase acting on Ub-PEX5, both in female rat liver and HeLa cells. We also show that USP9X is an elongated monomeric protein with the capacity to hydrolyze thioester, isopeptide, and peptide bonds. The strategy described here will be useful in identifying deubiquitinases acting on other ubiquitin conjugates.
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Affiliation(s)
- Cláudia P Grou
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal
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41
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Thorne C, Eccles RL, Coulson JM, Urbé S, Clague MJ. Isoform-specific localization of the deubiquitinase USP33 to the Golgi apparatus. Traffic 2011; 12:1563-74. [PMID: 21801292 DOI: 10.1111/j.1600-0854.2011.01261.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ubiquitin-specific protease 33 (USP33) is a deubiquitinase that has been associated with a variety of physiological events. Here, we show the existence of multiple USP33 splice variants and characterize the sub-cellular localization of endogenous USP33 as well as GFP-USP33 isoforms 1-3. The localization of USP33 is broadly confined to the secretory pathway, with all variants localizing to endoplasmic reticulum-associated structures. In addition, GFP-USP33 variant 3 shows a marked accumulation at the Golgi apparatus. Several deubiquitinases have large insertions within their otherwise highly conserved catalytic domains, the function of which is poorly characterized. Analysis of USP33 reveals a role for two distinct inserts within the catalytic domain. One is required for association with the endoplasmic reticulum, whilst the second is required for membrane association, but can be alternatively spliced (variant 3) to excise eight amino acids, which otherwise suppress Golgi localization. We propose that varying the expression of differentially localized isoforms provides a means to influence the spectrum of substrates encountered by USP33.
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Affiliation(s)
- Christopher Thorne
- Physiological Laboratory, Institute of Translational Medicine, Cellular and Molecular Physiology, University of Liverpool, Crown Street, L69 3BX Liverpool, United Kingdom
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42
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Sippl W, Collura V, Colland F. Ubiquitin-specific proteases as cancer drug targets. Future Oncol 2011; 7:619-32. [DOI: 10.2217/fon.11.39] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ubiquitin-specific proteases are deubiquitinating enzymes involved in the removal of ubiquitin from specific protein substrates resulting in protein salvage from proteasome degradation, regulation of protein localization or activation. DNA alteration and overexpression in different cancer types, as well as involvement in many cancer-associated pathways, make ubiquitin-specific proteases attractive for the cancer drug discovery purposes. Their proteolytic function associated to available structural biology data reinforce their potential for pharmacological interference. Here, we review this class of enzymes as cancer drug targets in terms of validation and druggability.
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Affiliation(s)
- Wolfgang Sippl
- Department of Pharmaceutical Chemistry, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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43
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Bassères E, Coppotelli G, Pfirrmann T, Andersen JB, Masucci M, Frisan T. The ubiquitin C-terminal hydrolase UCH-L1 promotes bacterial invasion by altering the dynamics of the actin cytoskeleton. Cell Microbiol 2011; 12:1622-33. [PMID: 20608941 DOI: 10.1111/j.1462-5822.2010.01495.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Invasion of eukaryotic target cells by pathogenic bacteria requires extensive remodelling of the membrane and actin cytoskeleton. Here we show that the remodelling process is regulated by the ubiquitin C-terminal hydrolase UCH-L1 that promotes the invasion of epithelial cells by Listeria monocytogenes and Salmonella enterica. Knockdown of UCH-L1 reduced the uptake of both bacteria, while expression of the catalytically active enzyme promoted efficient internalization in the UCH-L1-negative HeLa cell line. The entry of L. monocytogenes involves binding to the receptor tyrosine kinase Met, which leads to receptor phosphorylation and ubiquitination. UCH-L1 controls the early membrane-associated events of this triggering cascade since knockdown was associated with altered phosphorylation of the c-cbl docking site on Tyr1003, reduced ubiquitination of the receptor and altered activation of downstream ERK1/2- and AKT-dependent signalling in response to the natural ligand Hepatocyte Growth Factor (HGF). The regulation of cytoskeleton dynamics was further confirmed by the induction of actin stress fibres in HeLa expressing the active enzyme but not the catalytic mutant UCH-L1(C90S) . These findings highlight a previously unrecognized involvement of the ubiquitin cycle in bacterial entry. UCH-L1 is highly expressed in malignant cells that may therefore be particularly susceptible to invasion by bacteria-based drug delivery systems.
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Affiliation(s)
- Eugénie Bassères
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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44
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Abstract
Deubiquitination is a crucial mechanism in ubiquitin-mediated signalling networks. The importance of Dubs (deubiquitinating enzymes) as regulators of diverse cellular processes is becoming ever clearer as new roles are elucidated and new pathways are shown to be affected by this mechanism. Recent work, reviewed in the present paper, provides new perspective on the widening influence of Dubs and a new tool to focus studies of not only Dub interactions, but also potentially many more cellular systems.
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45
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Sacco JJ, Coulson JM, Clague MJ, Urbé S. Emerging roles of deubiquitinases in cancer-associated pathways. IUBMB Life 2010; 62:140-57. [PMID: 20073038 PMCID: PMC7165618 DOI: 10.1002/iub.300] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 12/05/2009] [Indexed: 01/11/2023]
Abstract
Deubiquitinases (DUBs) are emerging as important regulators of many pathways germane to cancer. They may regulate the stability of key oncogenes, exemplified by USP28 stabilisation of c-Myc. Alternatively they can negatively regulate ubiquitin-dependent signalling cascades such as the NF-kappaB activation pathway. We review the current literature that associates DUBs with cancer and discuss their suitability as drug targets of the future.
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Affiliation(s)
- Joseph J. Sacco
- Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Judy M. Coulson
- Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Michael J. Clague
- Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Sylvie Urbé
- Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Liverpool, L69 3BX, UK
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