1
|
Pandya MJ, Augustyniak W, Cliff MJ, Lindner I, Stinn A, Kahmann J, Temmerman K, Dannatt HRW, Waltho JP, Watson MJ. Backbone 1H, 13C and 15N resonance assignment of the ubiquitin specific protease 7 catalytic domain (residues 208-554) in complex with a small molecule ligand. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:33-44. [PMID: 38472728 DOI: 10.1007/s12104-024-10165-7] [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: 12/08/2023] [Accepted: 02/05/2024] [Indexed: 03/14/2024]
Abstract
The backbone 1H, 13C and 15N resonance assignment of Ubiquitin Specific Protease 7 catalytic domain (residues 208-554) was performed in its complex with a small molecule ligand and in its apo form as a reference. The amide 1H-15N signal intensities were boosted by an amide hydrogen exchange protocol, where expressed 2H, 13C, 15N-labeled protein was unfolded and re-folded to ensure exchange of amide deuterons to protons. The resonance assignments were used to determine chemical shift perturbations on ligand binding, which are consistent with the binding site observed by crystallography.
Collapse
Affiliation(s)
- Maya J Pandya
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, United Kingdom
| | - Wojciech Augustyniak
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, United Kingdom.
| | - Matthew J Cliff
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Ilka Lindner
- Biophysics Department, NMR and Protein Production, Evotec SE, Hamburg, Germany
| | - Anne Stinn
- Biophysics Department, NMR and Protein Production, Evotec SE, Hamburg, Germany
| | - Jan Kahmann
- Biophysics Department, NMR and Protein Production, Evotec SE, Hamburg, Germany
| | - Koen Temmerman
- Biophysics Department, NMR and Protein Production, Evotec SE, Hamburg, Germany
| | - Hugh R W Dannatt
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, United Kingdom
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Martin J Watson
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, United Kingdom
| |
Collapse
|
2
|
Keijzer N, Priyanka A, Stijf-Bultsma Y, Fish A, Gersch M, Sixma TK. Variety in the USP deubiquitinase catalytic mechanism. Life Sci Alliance 2024; 7:e202302533. [PMID: 38355287 PMCID: PMC10867860 DOI: 10.26508/lsa.202302533] [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: 12/14/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
The ubiquitin-specific protease (USP) family of deubiquitinases (DUBs) controls cellular ubiquitin-dependent signaling events. This generates therapeutic potential, with active-site inhibitors in preclinical and clinical studies. Understanding of the USP active site is primarily guided by USP7 data, where the catalytic triad consists of cysteine, histidine, and a third residue (third critical residue), which polarizes the histidine through a hydrogen bond. A conserved aspartate (fourth critical residue) is directly adjacent to this third critical residue. Although both critical residues accommodate catalysis in USP2, these residues have not been comprehensively investigated in other USPs. Here, we quantitatively investigate their roles in five USPs. Although USP7 relies on the third critical residue for catalysis, this residue is dispensable in USP1, USP15, USP40, and USP48, where the fourth critical residue is vital instead. Furthermore, these residues vary in importance for nucleophilic attack. The diverging catalytic mechanisms of USP1 and USP7 are independent of substrate and retained in cells for USP1. This unexpected variety of catalytic mechanisms in this well-conserved protein family may generate opportunities for selective targeting of individual USPs.
Collapse
Affiliation(s)
- Niels Keijzer
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anu Priyanka
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Yvette Stijf-Bultsma
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Alexander Fish
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Malte Gersch
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Dortmund, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Titia K Sixma
- https://ror.org/03xqtf034 Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| |
Collapse
|
3
|
Staniek J, Kalina T, Andrieux G, Boerries M, Janowska I, Fuentes M, Díez P, Bakardjieva M, Stancikova J, Raabe J, Neumann J, Schwenk S, Arpesella L, Stuchly J, Benes V, García Valiente R, Fernández García J, Carsetti R, Piano Mortari E, Catala A, de la Calle O, Sogkas G, Neven B, Rieux-Laucat F, Magerus A, Neth O, Olbrich P, Voll RE, Alsina L, Allende LM, Gonzalez-Granado LI, Böhler C, Thiel J, Venhoff N, Lorenzetti R, Warnatz K, Unger S, Seidl M, Mielenz D, Schneider P, Ehl S, Rensing-Ehl A, Smulski CR, Rizzi M. Non-apoptotic FAS signaling controls mTOR activation and extrafollicular maturation in human B cells. Sci Immunol 2024; 9:eadj5948. [PMID: 38215192 DOI: 10.1126/sciimmunol.adj5948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024]
Abstract
Defective FAS (CD95/Apo-1/TNFRSF6) signaling causes autoimmune lymphoproliferative syndrome (ALPS). Hypergammaglobulinemia is a common feature in ALPS with FAS mutations (ALPS-FAS), but paradoxically, fewer conventional memory cells differentiate from FAS-expressing germinal center (GC) B cells. Resistance to FAS-induced apoptosis does not explain this phenotype. We tested the hypothesis that defective non-apoptotic FAS signaling may contribute to impaired B cell differentiation in ALPS. We analyzed secondary lymphoid organs of patients with ALPS-FAS and found low numbers of memory B cells, fewer GC B cells, and an expanded extrafollicular (EF) B cell response. Enhanced mTOR activity has been shown to favor EF versus GC fate decision, and we found enhanced PI3K/mTOR and BCR signaling in ALPS-FAS splenic B cells. Modeling initial T-dependent B cell activation with CD40L in vitro, we showed that FAS competent cells with transient FAS ligation showed specifically decreased mTOR axis activation without apoptosis. Mechanistically, transient FAS engagement with involvement of caspase-8 induced nuclear exclusion of PTEN, leading to mTOR inhibition. In addition, FASL-dependent PTEN nuclear exclusion and mTOR modulation were defective in patients with ALPS-FAS. In the early phase of activation, FAS stimulation promoted expression of genes related to GC initiation at the expense of processes related to the EF response. Hence, our data suggest that non-apoptotic FAS signaling acts as molecular switch between EF versus GC fate decisions via regulation of the mTOR axis and transcription. The defect of this modulatory circuit may explain the observed hypergammaglobulinemia and low memory B cell numbers in ALPS.
Collapse
Affiliation(s)
- Julian Staniek
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Tomas Kalina
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Iga Janowska
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC CB16/12/00400, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC CB16/12/00400, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Salamanca, Spain
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Marina Bakardjieva
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jitka Stancikova
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Raabe
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julika Neumann
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sabine Schwenk
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Leonardo Arpesella
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jan Stuchly
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rodrigo García Valiente
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC CB16/12/00400, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - Jonatan Fernández García
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC CB16/12/00400, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - Rita Carsetti
- B Cell Unit, Immunology Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Eva Piano Mortari
- B Cell Unit, Immunology Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Albert Catala
- Department of Hematology, Institut de Recerca Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Oscar de la Calle
- Immunology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Georgios Sogkas
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Bénédicte Neven
- Pediatric Hematology-Immunology and Rheumatology Department, University Hospital Necker-Enfants Malades, Paris, France
| | - Frédéric Rieux-Laucat
- Université de Paris, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Aude Magerus
- Université de Paris, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Olaf Neth
- Department of Paediatric Infectious Diseases, Rheumatology and Immunology, Hospital Universitario Virgen del Rocio (HUVR), Instituto de Biomedicina de Sevilla (IBIS), Universidad de Sevilla/CSIC, Red de Investigación Traslacional en Infectología Pediátrica RITIP, Sevilla, Spain
| | - Peter Olbrich
- Department of Paediatric Infectious Diseases, Rheumatology and Immunology, Hospital Universitario Virgen del Rocio (HUVR), Instituto de Biomedicina de Sevilla (IBIS), Universidad de Sevilla/CSIC, Red de Investigación Traslacional en Infectología Pediátrica RITIP, Sevilla, Spain
| | - Reinhard E Voll
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laia Alsina
- Department of Hematology, Institut de Recerca Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
- Clinical Immunology and Primary Immunodeficiencies Unit, Department of Pediatric Allergy and Clinical Immunology, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Luis M Allende
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Luis I Gonzalez-Granado
- Primary Immunodeficiencies Unit, Department of Pediatrics, Research Institute Hospital 12 Octubre (i+12), Madrid, Spain
- School of Medicine, Complutense University, Madrid, Spain
| | - Chiara Böhler
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jens Thiel
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Division of Rheumatology and Clinical Immunology, Medical University Graz, Graz, Austria
| | - Nils Venhoff
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Raquel Lorenzetti
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Division of Rheumatology and Clinical Immunology, Medical University Graz, Graz, Austria
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Susanne Unger
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maximilian Seidl
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany
- Institute of Pathology, Heinrich-Heine University and University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus Fiebiger Zentrum, Friedrich Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Pascal Schneider
- Department of Immunobiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Stephan Ehl
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Anne Rensing-Ehl
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Cristian Roberto Smulski
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Medical Physics Department, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (CNEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Carlos de Bariloche, Argentina
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
4
|
Park HB, Baek KH. Current and future directions of USP7 interactome in cancer study. Biochim Biophys Acta Rev Cancer 2023; 1878:188992. [PMID: 37775071 DOI: 10.1016/j.bbcan.2023.188992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
The ubiquitin-proteasome system (UPS) is an essential protein quality controller for regulating protein homeostasis and autophagy. Ubiquitination is a protein modification process that involves the binding of one or more ubiquitins to substrates through a series of enzymatic processes. These include ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligases (E3). Conversely, deubiquitination is a reverse process that removes ubiquitin from substrates via deubiquitinating enzymes (DUBs). Dysregulation of ubiquitination-related enzymes can lead to various human diseases, including cancer, through the modulation of protein ubiquitination. The most structurally and functionally studied DUB is the ubiquitin-specific protease 7 (USP7). Both the TRAF and UBL domains of USP7 are known to bind to the [P/A/E]-X-X-S or K-X-X-X-K motif of substrates. USP7 has been shown to be involved in cancer pathogenesis by binding with numerous substrates. Recently, a novel substrate of USP7 was discovered through a systemic analysis of its binding motif. This review summarizes the currently discovered substrates and cellular functions of USP7 in cancer and suggests putative substrates of USP7 through a comprehensive systemic analysis.
Collapse
Affiliation(s)
- Hong-Beom Park
- Department of Convergence, CHA University, Gyeonggi-Do 13488, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Convergence, CHA University, Gyeonggi-Do 13488, Republic of Korea; International Ubiquitin Center(,) CHA University, Gyeonggi-Do 13488, Republic of Korea.
| |
Collapse
|
5
|
Gao H, Yin J, Ji C, Yu X, Xue J, Guan X, Zhang S, Liu X, Xing F. Targeting ubiquitin specific proteases (USPs) in cancer immunotherapy: from basic research to preclinical application. J Exp Clin Cancer Res 2023; 42:225. [PMID: 37658402 PMCID: PMC10472646 DOI: 10.1186/s13046-023-02805-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023] Open
Abstract
Tumors have evolved in various mechanisms to evade the immune system, hindering the antitumor immune response and facilitating tumor progression. Immunotherapy has become a potential treatment strategy specific to different cancer types by utilizing multifarious molecular mechanisms to enhance the immune response against tumors. Among these mechanisms, the ubiquitin-proteasome system (UPS) is a significant non-lysosomal pathway specific to protein degradation, regulated by deubiquitinating enzymes (DUBs) that counterbalance ubiquitin signaling. Ubiquitin-specific proteases (USPs), the largest DUB family with the strongest variety, play critical roles in modulating immune cell function, regulating immune response, and participating in antigen processing and presentation during tumor progression. According to recent studies, the expressions of some USP family members in tumor cells are involved in tumor immune escape and immune microenvironment. This review explores the potential of targeting USPs as a new approach for cancer immunotherapy, highlighting recent basic and preclinical studies investigating the applications of USP inhibitors. By providing insights into the structure and function of USPs in cancer immunity, this review aims at assisting in developing new therapeutic approaches for enhancing the immunotherapy efficacy.
Collapse
Affiliation(s)
- Hongli Gao
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Jianqiao Yin
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Ce Ji
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xiaopeng Yu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Jinqi Xue
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xin Guan
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Shuang Zhang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xun Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
| | - Fei Xing
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
| |
Collapse
|
6
|
Xu J, Wang Y, Zhang J, Abdelmoneim AA, Liang Z, Wang L, Jin J, Dai Q, Ye F. Elastic network models and molecular dynamic simulations reveal the molecular basis of allosteric regulation in ubiquitin-specific protease 7 (USP7). Comput Biol Med 2023; 162:107068. [PMID: 37290391 DOI: 10.1016/j.compbiomed.2023.107068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/14/2023] [Accepted: 05/27/2023] [Indexed: 06/10/2023]
Abstract
Ubiquitin-specific protease 7 (USP7) is one of the most abundant deubiquitinases and plays an important role in various malignant tumors. However, the molecular mechanisms underlying USP7's structures, dynamics, and biological significance are yet to be investigated. In this study, we constructed the full-length models of USP7 in both the extended and compact state, and applied elastic network models (ENM), molecular dynamics (MD) simulations, perturbation response scanning (PRS) analysis, residue interaction networks as well as allosteric pocket prediction to investigate allosteric dynamics in USP7. Our analysis of intrinsic and conformational dynamics revealed that the structural transition between the two states is characterized by global clamp motions, during which the catalytic domain (CD) and UBL4-5 domain exhibit strong negative correlations. The PRS analysis, combined with the analysis of disease mutations and post-translational modifications (PTMs) further highlighted the allosteric potential of the two domains. The residue interaction network based on MD simulations captured an allosteric communication path which starts at CD domain and ends at UBL4-5 domain. Moreover, we identified a pocket at the TRAF-CD interface as a high-potential allosteric site for USP7. Overall, our studies not only provide molecular insights into the conformational changes of USP7, but also aid in the design of allosteric modulators that target USP7.
Collapse
Affiliation(s)
- Jing Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yiran Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Jiali Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Amr Abbas Abdelmoneim
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Lei Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jia Jin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Qi Dai
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| |
Collapse
|
7
|
Park HB, Min Y, Hwang S, Baek KH. Suppression of USP7 negatively regulates the stability of ETS proto-oncogene 2 protein. Biomed Pharmacother 2023; 162:114700. [PMID: 37062218 DOI: 10.1016/j.biopha.2023.114700] [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: 02/20/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/18/2023] Open
Abstract
Ubiquitin-specific protease 7 (USP7) is one of the deubiquitinating enzymes (DUBs) that remove mono or polyubiquitin chains from target proteins. Depending on cancer types, USP7 has two opposing roles: oncogene or tumor suppressor. Moreover, it also known that USP7 functions in the cell cycle, apoptosis, DNA repair, chromatin remodeling, and epigenetic regulation through deubiquitination of several substrates including p53, mouse double minute 2 homolog (MDM2), Myc, and phosphatase and tensin homolog (PTEN). The [P/A/E]-X-X-S and K-X-X-X-K motifs of target proteins are necessary elements for the binding of USP7. In a previous study, we identified a novel substrate of USP7 through bioinformatics analysis using the binding motifs for USP7, and suggested that it can be an effective tool for finding new substrates for USP7. In the current study, gene ontology (GO) analysis revealed that putative target proteins having the [P/A/E]-X-X-S and K-X-X-K motifs are involved in transcriptional regulation. Moreover, through protein-protein interaction (PPI) analysis, we discovered that USP7 binds to the AVMS motif of ETS proto-oncogene 2 (ETS2) and deubiquitinates M1-, K11-, K27-, and K29-linked polyubiquitination of ETS2. Furthermore, we determined that suppression of USP7 decreases the protein stability of ETS2 and inhibits the transcriptional activity of ETS2 by disrupting the binding between the GGAA/T core motif and ETS2. Therefore, we propose that USP7 can be a novel target in cancers related to the dysregulation of ETS2.
Collapse
Affiliation(s)
- Hong-Beom Park
- Department of Biomedical Science, CHA University, Gyeonggi-Do 13488, Republic of Korea
| | - Yosuk Min
- Department of Biomedical Science, CHA University, Gyeonggi-Do 13488, Republic of Korea
| | - Sohyun Hwang
- Department of Biomedical Science, CHA University, Gyeonggi-Do 13488, Republic of Korea; Department of Pathology, CHA Bundang Medical Center, CHA University School of Medicine, Gyeonggi-Do 13496, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biomedical Science, CHA University, Gyeonggi-Do 13488, Republic of Korea.
| |
Collapse
|
8
|
Yang YC, Zhao CJ, Jin ZF, Zheng J, Ma LT. Targeted therapy based on ubiquitin-specific proteases, signalling pathways and E3 ligases in non-small-cell lung cancer. Front Oncol 2023; 13:1120828. [PMID: 36969062 PMCID: PMC10036052 DOI: 10.3389/fonc.2023.1120828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/01/2023] [Indexed: 03/11/2023] Open
Abstract
Lung cancer is one of the most common malignant tumours worldwide, with the highest mortality rate. Approximately 1.6 million deaths owing to lung cancer are reported annually; of which, 85% of deaths occur owing to non-small-cell lung cancer (NSCLC). At present, the conventional treatment methods for NSCLC include radiotherapy, chemotherapy, targeted therapy and surgery. However, drug resistance and tumour invasion or metastasis often lead to treatment failure. The ubiquitin–proteasome pathway (UPP) plays an important role in the occurrence and development of tumours. Upregulation or inhibition of proteins or enzymes involved in UPP can promote or inhibit the occurrence and development of tumours, respectively. As regulators of UPP, ubiquitin-specific proteases (USPs) primarily inhibit the degradation of target proteins by proteasomes through deubiquitination and hence play a carcinogenic or anticancer role. This review focuses on the role of USPs in the occurrence and development of NSCLC and the potential of corresponding targeted drugs, PROTACs and small-molecule inhibitors in the treatment of NSCLC.
Collapse
Affiliation(s)
- Yu-Chen Yang
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Can-Jun Zhao
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Zhao-Feng Jin
- School of Psychology, Weifang Medical University, Weifang, China
| | - Jin Zheng
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
- *Correspondence: Li-Tian Ma, ; Jin Zheng,
| | - Li-Tian Ma
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
- Department of Gastroenterology, Tangdu Hospital, Air Force Medical University, Xi’an, China
- *Correspondence: Li-Tian Ma, ; Jin Zheng,
| |
Collapse
|
9
|
Chi L, Wang H, Yu F, Gao C, Dai H, Si X, Liu L, Wang Z, Zheng J, Ke Y, Liu H, Zhang Q. Recent Progress of Ubiquitin-Specific-Processing Protease 7 Inhibitors. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2023. [DOI: 10.1134/s1068162023020073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
|
10
|
Activation Dynamics of Ubiquitin Specific Protease 7. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523550. [PMID: 36711877 PMCID: PMC9882073 DOI: 10.1101/2023.01.11.523550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme responsible for the regulation of key human oncoproteins and tumor suppressors including Mdm2 and p53, respectively. Unlike other members of the USP family of proteases, the isolated catalytic domain of USP7 adopts an enzymatically inactive conformation that has been well characterized using X-ray crystallography. The catalytic domain also samples an active conformation, which has only been captured upon USP7 substrate-binding. Here, we utilized CPMG NMR relaxation dispersion studies to observe the dynamic motions of USP7 in solution. Our results reveal that the catalytic domain of USP7 exchanges between two distinct conformations, the inactive conformation populated at 95% and the active conformation at 5%. The largest structural changes are localized within functionally important regions of the enzyme including the active site, the ubiquitin-binding fingers, and the allosteric helix of the enzyme, suggesting that USP7 can adopt its active conformation in the absence of a substrate. Furthermore, we show that the allosteric L299A activating mutation disturbs this equilibrium, slows down the exchange, and increases the residence time of USP7 in its active conformation, thus, explaining the elevated activity of the mutant. Overall, this work shows that the isolated USP7 catalytic domain pre-samples its "invisible" active conformation in solution, which may contribute to its activation mechanism.
Collapse
|
11
|
USP7 Inhibitors in Cancer Immunotherapy: Current Status and Perspective. Cancers (Basel) 2022; 14:cancers14225539. [PMID: 36428632 PMCID: PMC9688046 DOI: 10.3390/cancers14225539] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/03/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022] Open
Abstract
Ubiquitin-specific protease 7 (USP7) regulates the stability of a plethora of intracellular proteins involved in the suppression of anti-tumor immune responses and its overexpression is associated with poor survival in many cancers. USP7 impairs the balance of the p53/MDM2 axis resulting in the proteasomal degradation of the p53 tumor suppressor, a process that can be reversed by small-molecule inhibitors of USP7. USP7 was shown to regulate the anti-tumor immune responses in several cases. Its inhibition impedes the function of regulatory T cells, promotes polarization of tumor-associated macrophages, and reduces programmed death-ligand 1 (PD-L1) expression in tumor cells. The efficacy of small-molecule USP7 inhibitors was demonstrated in vivo. The synergistic effect of combining USP7 inhibition with cancer immunotherapy is a promising therapeutic approach, though its clinical efficacy is yet to be proven. In this review, we focus on the recent developments in understanding the intrinsic role of USP7, its interplay with other molecular pathways, and the therapeutic potential of targeting USP7 functions.
Collapse
|
12
|
Valles G, Pozhidaeva A, Korzhnev DM, Bezsonova I. Backbone and ILV side-chain NMR resonance assignments of the catalytic domain of human deubiquitinating enzyme USP7. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:197-203. [PMID: 35536398 PMCID: PMC9529858 DOI: 10.1007/s12104-022-10079-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Ubiquitin specific protease 7 (USP7) is a deubiquitinating enzyme, which removes ubiquitin tag from numerous protein substrates involved in diverse cellular processes such as cell cycle regulation, apoptosis and DNA damage response. USP7 affects stability, interaction network and cellular localization of its cellular and viral substrates by controlling their ubiquitination status. The large 41 kDa catalytic domain of USP7 harbors the active site of the enzyme. Here we present a nearly complete (93%) NMR resonance assignment of isoleucine, leucine and valine (ILV) side-chains of the USP7 catalytic domain along with a refined nearly complete (93%) assignment of its backbone resonances. The reported ILV methyl group assignment will facilitate further NMR investigations of structure, interactions and conformational dynamics of the USP7 enzyme.
Collapse
Affiliation(s)
- Gabrielle Valles
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT, 06032, USA
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Alexandra Pozhidaeva
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT, 06032, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT, 06032, USA.
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT, 06032, USA.
| |
Collapse
|
13
|
Kumar P, Kumar P, Mandal D, Velayutham R. The emerging role of Deubiquitinases (DUBs) in parasites: A foresight review. Front Cell Infect Microbiol 2022; 12:985178. [PMID: 36237424 PMCID: PMC9552668 DOI: 10.3389/fcimb.2022.985178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
Before the discovery of the proteasome complex, the lysosomes with acidic proteases and caspases in apoptotic pathways were thought to be the only pathways for the degradation of damaged, unfolded, and aged proteins. However, the discovery of 26S and 20S proteasome complexes in eukaryotes and microbes, respectively, established that the degradation of most proteins is a highly regulated ATP-dependent pathway that is significantly conserved across each domain of life. The proteasome is part of the ubiquitin-proteasome system (UPS), where the covalent tagging of a small molecule called ubiquitin (Ub) on the proteins marks its proteasomal degradation. The type and chain length of ubiquitination further determine whether a protein is designated for further roles in multi-cellular processes like DNA repair, trafficking, signal transduction, etc., or whether it will be degraded by the proteasome to recycle the peptides and amino acids. Deubiquitination, on the contrary, is the removal of ubiquitin from its substrate molecule or the conversion of polyubiquitin chains into monoubiquitin as a precursor to ubiquitin. Therefore, deubiquitylating enzymes (DUBs) can maintain the dynamic state of cellular ubiquitination by releasing conjugated ubiquitin from proteins and controlling many cellular pathways that are essential for their survival. Many DUBs are well characterized in the human system with potential drug targets in different cancers. Although, proteasome complex and UPS of parasites, like plasmodium and leishmania, were recently coined as multi-stage drug targets the role of DUBs is completely unexplored even though structural domains and functions of many of these parasite DUBs are conserved having high similarity even with its eukaryotic counterpart. This review summarizes the identification & characterization of different parasite DUBs based on in silico and a few functional studies among different phylogenetic classes of parasites including Metazoan (Schistosoma, Trichinella), Apicomplexan protozoans (Plasmodium, Toxoplasma, Eimeria, Cryptosporidium), Kinetoplastidie (Leishmania, Trypanosoma) and Microsporidia (Nosema). The identification of different homologs of parasite DUBs with structurally similar domains with eukaryotes, and the role of these DUBs alone or in combination with the 20S proteosome complex in regulating the parasite survival/death is further elaborated. We propose that small molecules/inhibitors of human DUBs can be potential antiparasitic agents due to their significant structural conservation.
Collapse
Affiliation(s)
- Prakash Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, India
| | - Pawan Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, India
| | - Debabrata Mandal
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, India
- *Correspondence: Ravichandiran Velayutham, ; Debabrata Mandal,
| | - Ravichandiran Velayutham
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, India
- National Institute of Pharmaceutical Education and Research, Kolkata, India
- *Correspondence: Ravichandiran Velayutham, ; Debabrata Mandal,
| |
Collapse
|
14
|
Park SH, Jeong JS, Zhou Y, Binte Mustafa NF, Chua NH. Deubiquitination of BES1 by UBP12/UBP13 promotes brassinosteroid signaling and plant growth. PLANT COMMUNICATIONS 2022; 3:100348. [PMID: 35706355 PMCID: PMC9483116 DOI: 10.1016/j.xplc.2022.100348] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 05/26/2023]
Abstract
As a key transcription factor in the brassinosteroid (BR) signaling pathway, the activity and expression of BES1 (BRI1-EMS-SUPPRESSOR 1) are stringently regulated. BES1 degradation is mediated by ubiquitin-related 26S proteasomal and autophagy pathways, which attenuate and terminate BR signaling; however, the opposing deubiquitinases (DUBs) are still unknown. Here, we showed that the ubp12-2w/13-3 double mutant phenocopies the BR-deficient dwarf mutant, suggesting that the two DUBs UBP12/UBP13 antagonize ubiquitin-mediated degradation to stabilize BES1. These two DUBs can trim tetraubiquitin with K46 and K63 linkages in vitro. UBP12/BES1 and UBP13/BES1 complexes are localized in both cytosol and nuclei. UBP12/13 can deubiquitinate polyubiquitinated BES1 in vitro and in planta, and UBP12 interacts with and deubiquitinates both inactive, phosphorylated BES1 and active, dephosphorylated BES1 in vivo. UBP12 overexpression in BES1OE plants significantly enhances cell elongation in hypocotyls and petioles and increases the ratio of leaf length to width compared with BES1OE or UBP12OE plants. Hypocotyl elongation and etiolation result from elevated BES1 levels because BES1 degradation is retarded by UBP12 in darkness or in light with BR. Protein degradation inhibitor experiments show that the majority of BES1 can be degraded by either the proteasomal or the autophagy pathway, but a minor BES1 fraction remains pathway specific. In conclusion, UBP12/UBP13 deubiquitinate BES1 to stabilize the latter as a positive regulator for BR responses.
Collapse
Affiliation(s)
- Su-Hyun Park
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Jin Seo Jeong
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Yu Zhou
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Nur Fatimah Binte Mustafa
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
| |
Collapse
|
15
|
Zhang XW, Feng N, Liu YC, Guo Q, Wang JK, Bai YZ, Ye XM, Yang Z, Yang H, Liu Y, Yang MM, Wang YH, Shi XM, Liu D, Tu PF, Zeng KW. Neuroinflammation inhibition by small-molecule targeting USP7 noncatalytic domain for neurodegenerative disease therapy. SCIENCE ADVANCES 2022; 8:eabo0789. [PMID: 35947662 PMCID: PMC9365288 DOI: 10.1126/sciadv.abo0789] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Neuroinflammation is a fundamental contributor to progressive neuronal damage, which arouses a heightened interest in neurodegenerative disease therapy. Ubiquitin-specific protease 7 (USP7) has a crucial role in regulating protein stability in multiple biological processes; however, the potential role of USP7 in neurodegenerative progression is poorly understood. Here, we discover the natural small molecule eupalinolide B (EB), which targets USP7 to inhibit microglia activation. Cocrystal structure reveals a previously undisclosed covalent allosteric site, Cys576, in a unique noncatalytic HUBL domain. By selectively modifying Cys576, EB allosterically inhibits USP7 to cause a ubiquitination-dependent degradation of Keap1. Keap1 function loss further results in an Nrf2-dependent transcription activation of anti-neuroinflammation genes in microglia. In vivo, pharmacological USP7 inhibition attenuates microglia activation and resultant neuron injury, thereby notably improving behavioral deficits in dementia and Parkinson's disease mouse models. Collectively, our findings provide an attractive future direction for neurodegenerative disease therapy by inhibiting microglia-mediated neuroinflammation by targeting USP7.
Collapse
Affiliation(s)
- Xiao-Wen Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Na Feng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yan-Chen Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qiang Guo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jing-Kang Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yi-Zhen Bai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiao-Ming Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhuo Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Heng Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yang Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Mi-Mi Yang
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, China
| | - Yan-Hang Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiao-Meng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Dan Liu
- Proteomics Laboratory, Medical and Healthy Analytical Center, Peking University Health Science Center, Beijing 100191, China
| | - Peng-Fei Tu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Corresponding author. (P.-F.T.); (K.-W.Z.)
| | - Ke-Wu Zeng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Corresponding author. (P.-F.T.); (K.-W.Z.)
| |
Collapse
|
16
|
Estavoyer B, Messmer C, Echbicheb M, Rudd CE, Milot E, Affar EB. Mechanisms orchestrating the enzymatic activity and cellular functions of deubiquitinases. J Biol Chem 2022; 298:102198. [PMID: 35764170 PMCID: PMC9356280 DOI: 10.1016/j.jbc.2022.102198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
Deubiquitinases (DUBs) are required for the reverse reaction of ubiquitination and act as major regulators of ubiquitin signaling processes. Emerging evidence suggests that these enzymes are regulated at multiple levels in order to ensure proper and timely substrate targeting and to prevent the adverse consequences of promiscuous deubiquitination. The importance of DUB regulation is highlighted by disease-associated mutations that inhibit or activate DUBs, deregulating their ability to coordinate cellular processes. Here, we describe the diverse mechanisms governing protein stability, enzymatic activity, and function of DUBs. In particular, we outline how DUBs are regulated by their protein domains and interacting partners. Intramolecular interactions can promote protein stability of DUBs, influence their subcellular localization, and/or modulate their enzymatic activity. Remarkably, these intramolecular interactions can induce self-deubiquitination to counteract DUB ubiquitination by cognate E3 ubiquitin ligases. In addition to intramolecular interactions, DUBs can also oligomerize and interact with a wide variety of cellular proteins, thereby forming obligate or facultative complexes that regulate their enzymatic activity and function. The importance of signaling and post-translational modifications in the integrated control of DUB function will also be discussed. While several DUBs are described with respect to the multiple layers of their regulation, the tumor suppressor BAP1 will be outlined as a model enzyme whose localization, stability, enzymatic activity, and substrate recognition are highly orchestrated by interacting partners and post-translational modifications.
Collapse
Affiliation(s)
- Benjamin Estavoyer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Clémence Messmer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Mohamed Echbicheb
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Christopher E Rudd
- Laboratory for Cell Signaling in Immunotherapy, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Eric Milot
- Laboratory for Malignant Hematopoiesis and Epigenetic Regulation of Gene Expression, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - El Bachir Affar
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada.
| |
Collapse
|
17
|
Veggiani G, Yates BP, Martyn GD, Manczyk N, Singer AU, Kurinov I, Sicheri F, Sidhu SS. Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs. ACS Chem Biol 2022; 17:941-956. [PMID: 35385646 PMCID: PMC9305627 DOI: 10.1021/acschembio.2c00089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ubiquitin (Ub)-binding domains embedded in intracellular proteins act as readers of the complex Ub code and contribute to regulation of numerous eukaryotic processes. Ub-interacting motifs (UIMs) are short α-helical modular recognition elements whose role in controlling proteostasis and signal transduction has been poorly investigated. Moreover, impaired or aberrant activity of UIM-containing proteins has been implicated in numerous diseases, but targeting modular recognition elements in proteins remains a major challenge. To overcome this limitation, we developed Ub variants (UbVs) that bind to 42 UIMs in the human proteome with high affinity and specificity. Structural analysis of a UbV:UIM complex revealed the molecular determinants of enhanced affinity and specificity. Furthermore, we showed that a UbV targeting a UIM in the cancer-associated Ub-specific protease 28 potently inhibited catalytic activity. Our work demonstrates the versatility of UbVs to target short α-helical Ub receptors with high affinity and specificity. Moreover, the UbVs provide a toolkit to investigate the role of UIMs in regulating and transducing Ub signals and establish a general strategy for the systematic development of probes for Ub-binding domains.
Collapse
Affiliation(s)
- Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Bradley P. Yates
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Gregory D. Martyn
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Noah Manczyk
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Alex U. Singer
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, NE-CAT, Cornell University, Argonne, Illinois 60439, United States
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
18
|
Perrakis A, Sixma TK. AI revolutions in biology: The joys and perils of AlphaFold. EMBO Rep 2021; 22:e54046. [PMID: 34668287 PMCID: PMC8567224 DOI: 10.15252/embr.202154046] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Anastassis Perrakis
- Oncode Institute and Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Titia K Sixma
- Oncode Institute and Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
19
|
Wilson P, Abdelmoti L, Norcross R, Jang ER, Palayam M, Galperin E. The role of USP7 in the Shoc2-ERK1/2 signaling axis and Noonan-like syndrome with loose anagen hair. J Cell Sci 2021; 134:272259. [PMID: 34553755 DOI: 10.1242/jcs.258922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023] Open
Abstract
The ERK1/2 (also known as MAPK3 and MAPK1, respectively) signaling pathway is critical in organismal development and tissue morphogenesis. Deregulation of this pathway leads to congenital abnormalities with severe developmental dysmorphisms. The core ERK1/2 cascade relies on scaffold proteins, such as Shoc2 to guide and fine-tune its signals. Mutations in SHOC2 lead to the development of the pathology termed Noonan-like Syndrome with Loose Anagen Hair (NSLAH). However, the mechanisms underlying the functions of Shoc2 and its contributions to disease progression remain unclear. Here, we show that ERK1/2 pathway activation triggers the interaction of Shoc2 with the ubiquitin-specific protease USP7. We reveal that, in the Shoc2 module, USP7 functions as a molecular 'switch' that controls the E3 ligase HUWE1 and the HUWE1-induced regulatory feedback loop. We also demonstrate that disruption of Shoc2-USP7 binding leads to aberrant activation of the Shoc2-ERK1/2 axis. Importantly, our studies reveal a possible role for USP7 in the pathogenic mechanisms underlying NSLAH, thereby extending our understanding of how ubiquitin-specific proteases regulate intracellular signaling.
Collapse
Affiliation(s)
- Patricia Wilson
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Lina Abdelmoti
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Rebecca Norcross
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Eun Ryoung Jang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Malathy Palayam
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Emilia Galperin
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| |
Collapse
|
20
|
Molecular Mechanisms of DUBs Regulation in Signaling and Disease. Int J Mol Sci 2021; 22:ijms22030986. [PMID: 33498168 PMCID: PMC7863924 DOI: 10.3390/ijms22030986] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
The large family of deubiquitinating enzymes (DUBs) are involved in the regulation of a plethora of processes carried out inside the cell by protein ubiquitination. Ubiquitination is a basic pathway responsible for the correct protein homeostasis in the cell, which could regulate the fate of proteins through the ubiquitin–proteasome system (UPS). In this review we will focus on recent advances on the molecular mechanisms and specificities found for some types of DUBs enzymes, highlighting illustrative examples in which the regulatory mechanism for DUBs has been understood in depth at the molecular level by structural biology. DUB proteases are responsible for cleavage and regulation of the multiple types of ubiquitin linkages that can be synthesized inside the cell, known as the ubiquitin-code, which are tightly connected to specific substrate functions. We will display some strategies carried out by members of different DUB families to provide specificity on the cleavage of particular ubiquitin linkages. Finally, we will also discuss recent progress made for the development of drug compounds targeting DUB proteases, which are usually correlated to the progress of many pathologies such as cancer and neurodegenerative diseases.
Collapse
|
21
|
The emerging nature of Ubiquitin-specific protease 7 (USP7): a new target in cancer therapy. Drug Discov Today 2020; 26:490-502. [PMID: 33157193 DOI: 10.1016/j.drudis.2020.10.028] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/05/2020] [Accepted: 10/28/2020] [Indexed: 11/24/2022]
Abstract
Human ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme that removes the ubiquitin (Ub) protein and spares substrates from degradation. Given its regulation of proteins involved in several cellular processes, abnormal expression and activity of USP7 are associated with several types of disease, including cancer. In this review, we summarize the developments in our understanding of USP7 over the past 5 years, focusing on its role in related cancers. Furthermore, we discuss clinical studies of USP7, including in vivo and pharmacological studies, as well as the development of USP7 inhibitors. A comprehensive understanding of USP7 will expand our knowledge of the structure and function of USP7-mediated signaling and shed light on drug discovery for different diseases in which USP7 is implicated.
Collapse
|
22
|
Valles GJ, Bezsonova I, Woodgate R, Ashton NW. USP7 Is a Master Regulator of Genome Stability. Front Cell Dev Biol 2020; 8:717. [PMID: 32850836 PMCID: PMC7419626 DOI: 10.3389/fcell.2020.00717] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/13/2020] [Indexed: 12/25/2022] Open
Abstract
Genetic alterations, including DNA mutations and chromosomal abnormalities, are primary drivers of tumor formation and cancer progression. These alterations can endow cells with a selective growth advantage, enabling cancers to evade cell death, proliferation limits, and immune checkpoints, to metastasize throughout the body. Genetic alterations occur due to failures of the genome stability pathways. In many cancers, the rate of alteration is further accelerated by the deregulation of these processes. The deubiquitinating enzyme ubiquitin specific protease 7 (USP7) has recently emerged as a key regulator of ubiquitination in the genome stability pathways. USP7 is also deregulated in many cancer types, where deviances in USP7 protein levels are correlated with cancer progression. In this work, we review the increasingly evident role of USP7 in maintaining genome stability, the links between USP7 deregulation and cancer progression, as well as the rationale of targeting USP7 in cancer therapy.
Collapse
Affiliation(s)
- Gabrielle J Valles
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Nicholas W Ashton
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
23
|
Qi SM, Cheng G, Cheng XD, Xu Z, Xu B, Zhang WD, Qin JJ. Targeting USP7-Mediated Deubiquitination of MDM2/MDMX-p53 Pathway for Cancer Therapy: Are We There Yet? Front Cell Dev Biol 2020; 8:233. [PMID: 32300595 PMCID: PMC7142254 DOI: 10.3389/fcell.2020.00233] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/19/2020] [Indexed: 01/13/2023] Open
Abstract
The p53 tumor suppressor protein and its major negative regulators MDM2 and MDMX oncoproteins form the MDM2/MDMX-p53 circuitry, which plays critical roles in regulating cancer cell growth, proliferation, cell cycle progression, apoptosis, senescence, angiogenesis, and immune response. Recent studies have shown that the stabilities of p53, MDM2, and MDMX are tightly controlled by the ubiquitin-proteasome system. Ubiquitin specific protease 7 (USP7), one of the most studied deubiquitinating enzymes plays a crucial role in protecting MDM2 and MDMX from ubiquitination-mediated proteasomal degradation. USP7 is overexpressed in human cancers and contributes to cancer initiation and progression. USP7 inhibition promotes the degradation of MDM2 and MDMX, activates the p53 signaling, and causes cell cycle arrest and apoptosis, making USP7 a potential target for cancer therapy. Several small-molecule inhibitors of USP7 have been developed and shown promising efficacy in preclinical settings. In the present review, we focus on recent advances in the understanding of the USP7-MDM2/MDMX-p53 network in human cancers as well as the discovery and development of USP7 inhibitors for cancer therapy.
Collapse
Affiliation(s)
- Si-Min Qi
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Gang Cheng
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiang-Dong Cheng
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Zhiyuan Xu
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Beihua Xu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Wei-Dong Zhang
- School of Pharmacy, Naval Medical University, Shanghai, China.,Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jiang-Jiang Qin
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China.,Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| |
Collapse
|
24
|
The Ubiquitin-Specific Protease Usp7, a Novel Merkel Cell Polyomavirus Large T-Antigen Interaction Partner, Modulates Viral DNA Replication. J Virol 2020; 94:JVI.01638-19. [PMID: 31801860 DOI: 10.1128/jvi.01638-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/01/2019] [Indexed: 02/06/2023] Open
Abstract
Merkel cell polyomavirus (MCPyV) is the major cause for Merkel cell carcinoma (MCC), a rare but highly aggressive skin cancer predominantly found in elderly and immunosuppressed patients. The early viral gene products large T-antigen (LT) and small T-antigen (sT) are important for efficient viral DNA replication, and both contribute to transformation processes. These functions are executed mainly through interactions with host factors. Here, we identify the cellular ubiquitin-specific processing protease 7 (Usp7) as a new interaction partner of the MCPyV LT. Using glutathione S-transferase pulldown experiments, we show that MCPyV LT directly binds to Usp7 and that N- as well as C-terminal regions of LT bind to the TRAF (tumor necrosis factor receptor-associated) domain of Usp7. We demonstrate that endogenous Usp7 coprecipitates with MCPyV T-antigens and relocalizes to viral DNA replication centers in cells actively replicating MCPyV genomes. We show that Usp7 does not alter ubiquitination levels of the T-antigens; however, Usp7 binding increases the binding affinity of LT to the origin of replication, thereby negatively regulating viral DNA replication. Together, these data identify Usp7 as a restriction factor of MCPyV replication. In contrast to other DNA viruses, Usp7 does not affect MCPyV gene expression via its ubiquitination activity but influences MCPyV DNA replication solely via a novel mechanism that modulates binding of LT to viral DNA.IMPORTANCE MCPyV is the only human polyomavirus that is associated with cancer; the majority of Merkel cell cancers have a viral etiology. While much emphasis was placed on investigations to understand the transformation process by MCPyV oncoproteins and cellular factors, we have only limited knowledge of cellular factors participating in the MCPyV life cycle. Here, we describe Usp7, a cellular deubiquitination enzyme, as a new factor involved in MCPyV replication. Usp7 is known in the context of large DNA tumor viruses, Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus, to restrict viral replication. Similar to EBV, where Usp7 binding to EBNA1 increases EBNA1 binding affinity to viral DNA, we find MCPyV LT binding to the origin of replication to be increased in the presence of Usp7, resulting in restriction of viral DNA replication. However, Usp7-induced restriction of MCPyV replication is independent of its enzymatic activity, thereby constituting a novel mechanism of Usp7-induced restriction of viral replication.
Collapse
|
25
|
Zhang W, Zhang J, Xu C, Zhang S, Bian S, Jiang F, Ni W, Qu L, Lu C, Ni R, Fan Y, Xiao M, Liu J. Ubiquitin-specific protease 7 is a drug-able target that promotes hepatocellular carcinoma and chemoresistance. Cancer Cell Int 2020; 20:28. [PMID: 32002017 PMCID: PMC6986148 DOI: 10.1186/s12935-020-1109-2] [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: 08/30/2019] [Accepted: 01/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background Ubiquitin-specific protease 7 (USP7) is a de-ubiquitin enzyme that plays an essential role in multiple cancers and becomes a target for treatment. However, the role of USP7 and its therapeutic value for HCC remains unclear. Methods USP7 expression was examined in HCC tissues by western blot and immunohistochemistry. The correlation of USP7 and HCC prognosis was analyzed by Kaplan–Meier survival method. Mass spectrometry was determined and cell proliferation and tumorigenicity assays were conducted in vitro and in vivo treated by P22077 and sgRNA-USP7. Results USP7 expression was significantly increased in HCC and associated with its progression. Interestingly, many HCC cells are sensitive to USP7 inhibition by using P22077. P22077 treatment not only induced cell death but also inhibited cell proliferation and migration in Huh7 and SK-Hep1 cells. In a xenograft model, P22077 efficiently inhibited tumor growth. In chemo-resistant HCC cells, P22077 decreased cell sensitivity to chemotherapy. In addition, mass spectrometry reveals 224 of significantly changed proteins upon P22077 treatment. Conclusions We demonstrate a critical role of USP7 in HCC devolvement and chemoresistance. Disruption of USP7 function results in dis-regulated several key biological processes and subsequently activates BAX. USP7 might be a novel and drug-able target in HCC.
Collapse
Affiliation(s)
- Wei Zhang
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China.,2Medical College, Nantong University, Nantong, 226001 China
| | - Jingxin Zhang
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China.,2Medical College, Nantong University, Nantong, 226001 China
| | - Chenzhou Xu
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China.,2Medical College, Nantong University, Nantong, 226001 China
| | - Shiqing Zhang
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China.,2Medical College, Nantong University, Nantong, 226001 China
| | - Saiyan Bian
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China.,2Medical College, Nantong University, Nantong, 226001 China
| | - Feng Jiang
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China
| | - Wenkai Ni
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China
| | - Lishuai Qu
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China
| | - Cuihua Lu
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China
| | - Runzhou Ni
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China
| | - Yihui Fan
- 3Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu, 226001 China
| | - Mingbing Xiao
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China.,4Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China
| | - Jinxia Liu
- 1Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, 226001 Jiangsu People's Republic of China
| |
Collapse
|
26
|
Dharadhar S, Kim RQ, Uckelmann M, Sixma TK. Quantitative analysis of USP activity in vitro. Methods Enzymol 2019; 618:281-319. [PMID: 30850056 DOI: 10.1016/bs.mie.2018.12.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Ubiquitin-specific proteases (USPs) are an important class of deubiquitinating enzymes (DUBs) that carry out critical roles in cellular physiology and are regulated at multiple levels. Quantitative characterization of USP activity is crucial for mechanistic understanding of USP function and regulation. This requires kinetic analysis using in vitro activity assays on minimal and natural substrates with purified proteins. In this chapter we give advice for efficient design of USP constructs and their optimal expression, followed by a series of purification strategies. We then present protocols for studying USP activity quantitatively on minimal and more natural substrates, and we discuss how to include possible regulatory elements such as internal USP domains or external interacting proteins. Lastly, we examine different binding assays for studying USP interactions and discuss how these can be included in full kinetic analyses.
Collapse
Affiliation(s)
- Shreya Dharadhar
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Robbert Q Kim
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michael Uckelmann
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| |
Collapse
|
27
|
USP7: Structure, substrate specificity, and inhibition. DNA Repair (Amst) 2019; 76:30-39. [PMID: 30807924 DOI: 10.1016/j.dnarep.2019.02.005] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/07/2019] [Indexed: 12/24/2022]
Abstract
Turnover of cellular proteins is regulated by Ubiquitin Proteasome System (UPS). Components of this pathway, including the proteasome, ubiquitinating enzymes and deubiquitinating enzymes, are highly specialized and tightly regulated. In this mini-review we focus on the de-ubiquitinating enzyme USP7, and summarize latest advances in understanding its structure, substrate specificity and relevance to human cancers. There is increasing interest in UPS components as targets for cancer therapy and here we also overview the recent progress in the development of small molecule inhibitors that target USP7.
Collapse
|
28
|
Kim RQ, Geurink PP, Mulder MPC, Fish A, Ekkebus R, El Oualid F, van Dijk WJ, van Dalen D, Ovaa H, van Ingen H, Sixma TK. Kinetic analysis of multistep USP7 mechanism shows critical role for target protein in activity. Nat Commun 2019; 10:231. [PMID: 30651545 PMCID: PMC6335408 DOI: 10.1038/s41467-018-08231-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
USP7 is a highly abundant deubiquitinating enzyme (DUB), involved in cellular processes including DNA damage response and apoptosis. USP7 has an unusual catalytic mechanism, where the low intrinsic activity of the catalytic domain (CD) increases when the C-terminal Ubl domains (Ubl45) fold onto the CD, allowing binding of the activating C-terminal tail near the catalytic site. Here we delineate how the target protein promotes the activation of USP7. Using NMR analysis and biochemistry we describe the order of activation steps, showing that ubiquitin binding is an instrumental step in USP7 activation. Using chemically synthesised p53-peptides we also demonstrate how the correct ubiquitinated substrate increases catalytic activity. We then used transient reaction kinetic modelling to define how the USP7 multistep mechanism is driven by target recognition. Our data show how this pleiotropic DUB can gain specificity for its cellular targets. Deubiquitinating enzymes (DUBs) are critical regulators of cellular processes by removing ubiquitin from specific targets. Here global kinetic modelling reveals the mechanism by which the low intrinsic activity of USP7 is substantially enhanced on a specific physiological target.
Collapse
Affiliation(s)
- Robbert Q Kim
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Paul P Geurink
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Monique P C Mulder
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexander Fish
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Reggy Ekkebus
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Farid El Oualid
- UbiQ Bio BV, Science Park 408, 1098 XH, Amsterdam, the Netherlands
| | - Willem J van Dijk
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Duco van Dalen
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Tumor Immunology department, Radboud Institute for Molecular Sciences, Nijmegen, the Netherlands
| | - Huib Ovaa
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands. .,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Hugo van Ingen
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands. .,Bijvoet center, Utrecht University, Utrecht, the Netherlands.
| | - Titia K Sixma
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.
| |
Collapse
|
29
|
Masuda Y, Kanao R, Kawai H, Kukimoto I, Masutani C. Preferential digestion of PCNA-ubiquitin and p53-ubiquitin linkages by USP7 to remove polyubiquitin chains from substrates. J Biol Chem 2019; 294:4177-4187. [PMID: 30647135 PMCID: PMC6422070 DOI: 10.1074/jbc.ra118.005167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/22/2018] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin-specific protease 7 (USP7) regulates various cellular pathways through its deubiquitination activity. Despite the identification of a growing number of substrates of USP7, the molecular mechanism by which USP7 removes ubiquitin chains from polyubiquitinated substrates remains unexplored. The present study investigated the mechanism underlying the deubiquitination of Lys63-linked polyubiquitinated proliferating cell nuclear antigen (PCNA). Biochemical analyses demonstrated that USP7 efficiently removes polyubiquitin chains from polyubiquitinated PCNA by preferential cleavage of the PCNA-ubiquitin linkage. This property was largely attributed to the poor activity toward Lys63-linked ubiquitin chains. The preferential cleavage of substrate-ubiquitin linkages was also observed for Lys48-linked polyubiquitinated p53 because of the inefficient cleavage of the Lys48-linked ubiquitin chains. The present findings suggest a mechanism underlying the removal of polyubiquitin signals by USP7.
Collapse
Affiliation(s)
- Yuji Masuda
- From the Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan, .,Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Rie Kanao
- From the Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Hidehiko Kawai
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan, and
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-murayama, Tokyo 208-0011, Japan
| | - Chikahide Masutani
- From the Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| |
Collapse
|
30
|
Srivastava M, Suri C, Singh M, Mathur R, Asthana S. Molecular dynamics simulation reveals the possible druggable hot-spots of USP7. Oncotarget 2018; 9:34289-34305. [PMID: 30344943 PMCID: PMC6188144 DOI: 10.18632/oncotarget.26136] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/03/2018] [Indexed: 12/20/2022] Open
Abstract
The plasticity in Ubiquitin Specific Proteases (USP7) inducing conformational changes at important areas has highlighted an intricate mechanism, by which USP7 is regulated. Given the importance of USP7 in oncogenic pathways and immune-oncology, identification of USP7 inhibitors has attracted considerable interest. Despite substantial efforts, the discovery of deubiquitinases (DUBs) inhibitors, knowledge of their binding site and understanding the possible mechanism of action has proven particularly challenging. We disclose the most likely binding site of P5091 (a potent USP7 inhibitor), which reveal a cryptic allosteric site through extensive computational studies in an inhibitor dependent and independent manner. Overall, these findings demonstrate the tractability and druggability of USP7. Through a series of molecular dynamics simulations and detailed quantitative analysis, a dynamically stable allosteric binding site near catalytic center of the inactive state of USP7 (site partially absent in active state), along with two newly identified sites have been revealed, which opens the avenue for rational structure-guided inhibitor designing in USP7 specific-manner.
Collapse
Affiliation(s)
- Mitul Srivastava
- Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Charu Suri
- Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Mrityunjay Singh
- Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Rajani Mathur
- Delhi Institute of Pharmaceutical Sciences and Research, Puspvihar, New Delhi, Delhi, India
| | - Shailendra Asthana
- Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| |
Collapse
|
31
|
What happens at the lesion does not stay at the lesion: Transcription-coupled nucleotide excision repair and the effects of DNA damage on transcription in cis and trans. DNA Repair (Amst) 2018; 71:56-68. [PMID: 30195642 DOI: 10.1016/j.dnarep.2018.08.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Unperturbed transcription of eukaryotic genes by RNA polymerase II (Pol II) is crucial for proper cell function and tissue homeostasis. However, the DNA template of Pol II is continuously challenged by damaging agents that can result in transcription impediment. Stalling of Pol II on transcription-blocking lesions triggers a highly orchestrated cellular response to cope with these cytotoxic lesions. One of the first lines of defense is the transcription-coupled nucleotide excision repair (TC-NER) pathway that specifically removes transcription-blocking lesions thereby safeguarding unperturbed gene expression. In this perspective, we outline recent data on how lesion-stalled Pol II initiates TC-NER and we discuss new mechanistic insights in the TC-NER reaction, which have resulted in a better understanding of the causative-linked Cockayne syndrome and UV-sensitive syndrome. In addition to these direct effects on lesion-stalled Pol II (effects in cis), accumulating evidence shows that transcription, and particularly Pol II, is also affected in a genome-wide manner (effects in trans). We will summarize the diverse consequences of DNA damage on transcription, including transcription inhibition, induction of specific transcriptional programs and regulation of alternative splicing. Finally, we will discuss the function of these diverse cellular responses to transcription-blocking lesions and their consequences on the process of transcription restart. This resumption of transcription, which takes place either directly at the lesion or is reinitiated from the transcription start site, is crucial to maintain proper gene expression following removal of the DNA damage.
Collapse
|
32
|
Kim RQ, Sixma TK. Regulation of USP7: A High Incidence of E3 Complexes. J Mol Biol 2017; 429:3395-3408. [DOI: 10.1016/j.jmb.2017.05.028] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/26/2017] [Accepted: 05/30/2017] [Indexed: 01/03/2023]
|
33
|
Turnbull AP, Ioannidis S, Krajewski WW, Pinto-Fernandez A, Heride C, Martin ACL, Tonkin LM, Townsend EC, Buker SM, Lancia DR, Caravella JA, Toms AV, Charlton TM, Lahdenranta J, Wilker E, Follows BC, Evans NJ, Stead L, Alli C, Zarayskiy VV, Talbot AC, Buckmelter AJ, Wang M, McKinnon CL, Saab F, McGouran JF, Century H, Gersch M, Pittman MS, Marshall CG, Raynham TM, Simcox M, Stewart LMD, McLoughlin SB, Escobedo JA, Bair KW, Dinsmore CJ, Hammonds TR, Kim S, Urbé S, Clague MJ, Kessler BM, Komander D. Molecular basis of USP7 inhibition by selective small-molecule inhibitors. Nature 2017; 550:481-486. [PMID: 29045389 DOI: 10.1038/nature24451] [Citation(s) in RCA: 291] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/25/2017] [Indexed: 12/16/2022]
Abstract
Ubiquitination controls the stability of most cellular proteins, and its deregulation contributes to human diseases including cancer. Deubiquitinases remove ubiquitin from proteins, and their inhibition can induce the degradation of selected proteins, potentially including otherwise 'undruggable' targets. For example, the inhibition of ubiquitin-specific protease 7 (USP7) results in the degradation of the oncogenic E3 ligase MDM2, and leads to re-activation of the tumour suppressor p53 in various cancers. Here we report that two compounds, FT671 and FT827, inhibit USP7 with high affinity and specificity in vitro and within human cells. Co-crystal structures reveal that both compounds target a dynamic pocket near the catalytic centre of the auto-inhibited apo form of USP7, which differs from other USP deubiquitinases. Consistent with USP7 target engagement in cells, FT671 destabilizes USP7 substrates including MDM2, increases levels of p53, and results in the transcription of p53 target genes, induction of the tumour suppressor p21, and inhibition of tumour growth in mice.
Collapse
Affiliation(s)
- Andrew P Turnbull
- CRUK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London NW1 0NH, UK
| | | | - Wojciech W Krajewski
- CRUK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London NW1 0NH, UK
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Claire Heride
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Agnes C L Martin
- CRUK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Louise M Tonkin
- CRUK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | | | - Shane M Buker
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | - David R Lancia
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | | | - Angela V Toms
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | - Thomas M Charlton
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | | | - Erik Wilker
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | - Bruce C Follows
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | - Nicola J Evans
- CRUK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London NW1 0NH, UK
| | - Lucy Stead
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Cristina Alli
- CRUK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | | | - Adam C Talbot
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | | | - Minghua Wang
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | | | - Fabienne Saab
- CRUK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London NW1 0NH, UK
| | - Joanna F McGouran
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Hannah Century
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Malte Gersch
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Marc S Pittman
- CRUK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London NW1 0NH, UK
| | - C Gary Marshall
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | - Tony M Raynham
- CRUK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London NW1 0NH, UK
| | - Mary Simcox
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | - Lorna M D Stewart
- CRUK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London NW1 0NH, UK
| | - Sheila B McLoughlin
- CRUK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Jaime A Escobedo
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | - Kenneth W Bair
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | | | - Tim R Hammonds
- CRUK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London NW1 0NH, UK
| | - Sunkyu Kim
- FORMA Therapeutics, Arsenal Street, Watertown, Massachusetts 02472, USA
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| |
Collapse
|
34
|
Tavana O, Gu W. Modulation of the p53/MDM2 interplay by HAUSP inhibitors. J Mol Cell Biol 2017; 9:45-52. [PMID: 27927749 DOI: 10.1093/jmcb/mjw049] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/24/2016] [Indexed: 11/13/2022] Open
Abstract
It is well established that both p53 and MDM2 are short-lived proteins whose stabilities are tightly controlled through ubiquitination-mediated degradation. Although numerous studies indicate that the MDM2 E3 ligase activity, as well as the protein-protein interaction between p53 and MDM2, is the major focus for this regulation, emerging evidence suggests that the deubiquitinase herpesvirus-associated ubiquitin-specific protease (HAUSP, also known as USP7) plays a critical role. Furthermore, HAUSP inhibition elevates p53 stability and might be beneficial for therapeutic purposes. In this review, we discuss the advances of this dynamic pathway and the contributions of positive and negative regulators affecting HAUSP activity. We also highlight the roles of HAUSP in cancer justifying the production of the first generation of HAUSP inhibitors.
Collapse
Affiliation(s)
- Omid Tavana
- College of Physicians and Surgeons, Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Wei Gu
- College of Physicians and Surgeons, Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.,Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| |
Collapse
|
35
|
Affiliation(s)
- Tycho E.T. Mevissen
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - David Komander
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| |
Collapse
|
36
|
Abstract
Loading of p53-binding protein 1 (53BP1) and receptor-associated protein 80 (RAP80) at DNA double-strand breaks (DSBs) drives cell cycle checkpoint activation but is counterproductive to high-fidelity DNA repair. ring finger protein 169 (RNF169) maintains the balance by limiting the deposition of DNA damage mediator proteins at the damaged chromatin. We report here that this attribute is accomplished, in part, by a predicted nuclear localization signal (NLS) that not only shuttles RNF169 into the nucleus but also promotes its stability by mediating a direct interaction with the ubiquitin-specific protease USP7. Guided by the crystal structure of USP7 in complex with the RNF169 NLS, we uncoupled USP7 binding from its nuclear import function and showed that perturbing the USP7-RNF169 complex destabilized RNF169, compromised high-fidelity DSB repair, and hypersensitized cells to poly (ADP-ribose) polymerase inhibition. Finally, expression of USP7 and RNF169 positively correlated in breast cancer specimens. Collectively, our findings uncover an NLS-mediated bipartite mechanism that supports the nuclear function of a DSB response protein.
Collapse
|