51
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Lim KH, Park JJ, Gu BH, Kim JO, Park SG, Baek KH. HAUSP-nucleolin interaction is regulated by p53-Mdm2 complex in response to DNA damage response. Sci Rep 2015; 5:12793. [PMID: 26238070 PMCID: PMC4523935 DOI: 10.1038/srep12793] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 07/09/2015] [Indexed: 11/08/2022] Open
Abstract
HAUSP (herpes virus-associated ubiquitin specific protease, known as ubiquitin specific protease 7), one of DUBs, regulates the dynamics of the p53 and Mdm2 network in response to DNA damage by deubiquitinating both p53 and its E3 ubiquitin ligase, Mdm2. Its concerted action increases the level of functional p53 by preventing proteasome-dependent degradation of p53. However, the protein substrates that are targeted by HAUSP to mediate DNA damage responses in the context of the HAUSP-p53-Mdm2 complex are not fully identified. Here, we identified nucleolin as a new substrate for HAUSP by proteomic analysis. Nucleolin has two HAUSP binding sites in its N- and C-terminal regions, and the mutation of HAUSP interacting peptides on nucleolin disrupts their interaction and it leads to the increased level of nucleolin ubiquitination. In addition, HAUSP regulates the stability of nucleolin by removing ubiquitin from nucleolin. Nucleolin exists as a component of the HAUSP-p53-Mdm2 complex, and both Mdm2 and p53 are required for the interaction between HAUSP and nucleolin. Importantly, the irradiation increases the HAUSP-nucleolin interaction, leading to nucleolin stabilization significantly. Taken together, this study reveals a new component of the HAUSP-p53-Mdm2 complex that governs dynamic cellular responses to DNA damage.
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Affiliation(s)
- Key-Hwan Lim
- Department of Biomedical Science, CHA University, Bundang CHA General Hospital, Gyeonggi-Do 463-400, Republic of Korea
| | - Jang-Joon Park
- Department of Biomedical Science, CHA University, Bundang CHA General Hospital, Gyeonggi-Do 463-400, Republic of Korea
| | - Bon-Hee Gu
- Department of Biomedical Science, CHA University, Bundang CHA General Hospital, Gyeonggi-Do 463-400, Republic of Korea
| | - Jin-Ock Kim
- Department of Biomedical Science, CHA University, Bundang CHA General Hospital, Gyeonggi-Do 463-400, Republic of Korea
| | - Sang Gyu Park
- College of Pharmacy, Ajou University, Suwon, Gyeonggi-Do 443-749, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biomedical Science, CHA University, Bundang CHA General Hospital, Gyeonggi-Do 463-400, Republic of Korea
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52
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USP7 is essential for maintaining Rad18 stability and DNA damage tolerance. Oncogene 2015; 35:965-76. [PMID: 25961918 DOI: 10.1038/onc.2015.149] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 01/08/2023]
Abstract
Rad18 functions at the cross-roads of three different DNA damage response (DDR) pathways involved in protecting stressed replication forks: homologous recombination repair, DNA inter-strand cross-link repair and DNA damage tolerance. Although Rad18 serves to facilitate replication of damaged genomes by promoting translesion synthesis (TLS), this comes at a cost of potentially error-prone lesion bypass. In contrast, loss of Rad18-dependent TLS potentiates the collapse of stalled forks and leads to incomplete genome replication. Given the pivotal nature with which Rad18 governs the fine balance between replication fidelity and genome stability, Rad18 levels and activity have a major impact on genomic integrity. Here, we identify the de-ubiquitylating enzyme USP7 as a critical regulator of Rad18 protein levels. Loss of USP7 destabilizes Rad18 and compromises UV-induced PCNA mono-ubiquitylation and Pol η recruitment to stalled replication forks. USP7-depleted cells also fail to elongate nascent daughter strand DNA following UV irradiation and show reduced DNA damage tolerance. We demonstrate that USP7 associates with Rad18 directly via a consensus USP7-binding motif and can disassemble Rad18-dependent poly-ubiquitin chains both in vitro and in vivo. Taken together, these observations identify USP7 as a novel component of the cellular DDR involved in preserving the genome stability.
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53
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Abstract
The post-translational modification of proteins with ubiquitin represents a complex signalling system that co-ordinates essential cellular functions, including proteolysis, DNA repair, receptor signalling and cell communication. DUBs (deubiquitinases), the enzymes that disassemble ubiquitin chains and remove ubiquitin from proteins, are central to this system. Reflecting the complexity and versatility of ubiquitin signalling, DUB activity is controlled in multiple ways. Although several lines of evidence indicate that aberrant DUB function may promote human disease, the underlying molecular mechanisms are often unclear. Notwithstanding, considerable interest in DUBs as potential drug targets has emerged over the past years. The future success of DUB-based therapy development will require connecting the basic science of DUB function and enzymology with drug discovery. In the present review, we discuss new insights into DUB activity regulation and their links to disease, focusing on the role of DUBs as regulators of cell identity and differentiation, and discuss their potential as emerging drug targets.
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54
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Brown JS, Jackson SP. Ubiquitylation, neddylation and the DNA damage response. Open Biol 2015; 5:150018. [PMID: 25833379 PMCID: PMC4422126 DOI: 10.1098/rsob.150018] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/09/2015] [Indexed: 12/19/2022] Open
Abstract
Failure of accurate DNA damage sensing and repair mechanisms manifests as a variety of human diseases, including neurodegenerative disorders, immunodeficiency, infertility and cancer. The accuracy and efficiency of DNA damage detection and repair, collectively termed the DNA damage response (DDR), requires the recruitment and subsequent post-translational modification (PTM) of a complex network of proteins. Ubiquitin and the ubiquitin-like protein (UBL) SUMO have established roles in regulating the cellular response to DNA double-strand breaks (DSBs). A role for other UBLs, such as NEDD8, is also now emerging. This article provides an overview of the DDR, discusses our current understanding of the process and function of PTM by ubiquitin and NEDD8, and reviews the literature surrounding the role of ubiquitylation and neddylation in DNA repair processes, focusing particularly on DNA DSB repair.
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Affiliation(s)
- Jessica S Brown
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
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55
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Papp SJ, Huber AL, Jordan SD, Kriebs A, Nguyen M, Moresco JJ, Yates JR, Lamia KA. DNA damage shifts circadian clock time via Hausp-dependent Cry1 stabilization. eLife 2015; 4. [PMID: 25756610 PMCID: PMC4352707 DOI: 10.7554/elife.04883] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/10/2015] [Indexed: 11/13/2022] Open
Abstract
The circadian transcriptional repressors cryptochrome 1 (Cry1) and 2 (Cry2) evolved from photolyases, bacterial light-activated DNA repair enzymes. In this study, we report that while they have lost DNA repair activity, Cry1/2 adapted to protect genomic integrity by responding to DNA damage through posttranslational modification and coordinating the downstream transcriptional response. We demonstrate that genotoxic stress stimulates Cry1 phosphorylation and its deubiquitination by Herpes virus associated ubiquitin-specific protease (Hausp, a.k.a Usp7), stabilizing Cry1 and shifting circadian clock time. DNA damage also increases Cry2 interaction with Fbxl3, destabilizing Cry2. Thus, genotoxic stress increases the Cry1/Cry2 ratio, suggesting distinct functions for Cry1 and Cry2 following DNA damage. Indeed, the transcriptional response to genotoxic stress is enhanced in Cry1-/- and blunted in Cry2-/- cells. Furthermore, Cry2-/- cells accumulate damaged DNA. These results suggest that Cry1 and Cry2, which evolved from DNA repair enzymes, protect genomic integrity via coordinated transcriptional regulation.
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Affiliation(s)
- Stephanie J Papp
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Anne-Laure Huber
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Sabine D Jordan
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Anna Kriebs
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Madelena Nguyen
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - James J Moresco
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
| | - Katja A Lamia
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States
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56
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BRUCE regulates DNA double-strand break response by promoting USP8 deubiquitination of BRIT1. Proc Natl Acad Sci U S A 2015; 112:E1210-9. [PMID: 25733871 DOI: 10.1073/pnas.1418335112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The DNA damage response (DDR) is crucial for genomic integrity. BRIT1 (breast cancer susceptibility gene C terminus-repeat inhibitor of human telomerase repeat transcriptase expression), a tumor suppressor and early DDR factor, is recruited to DNA double-strand breaks (DSBs) by phosphorylated H2A histone family, member X (γ-H2AX), where it promotes chromatin relaxation by recruiting the switch/sucrose nonfermentable (SWI-SNF) chromatin remodeler to facilitate DDR. However, regulation of BRIT1 recruitment is not fully understood. The baculovirus IAP repeat (BIR)-containing ubiquitin-conjugating enzyme (BRUCE) is an inhibitor of apoptosis protein (IAP). Here, we report a non-IAP function of BRUCE in the regulation of the BRIT1-SWI-SNF DSB-response pathway and genomic stability. We demonstrate that BRIT1 is K63 ubiquitinated in unstimulated cells and that deubiquitination of BRIT1 is a prerequisite for its recruitment to DSB sites by γ-H2AX. We show mechanistically that BRUCE acts as a scaffold, bridging the ubiquitin-specific peptidase 8 (USP8) and BRIT1 in a complex to coordinate USP8-catalyzed deubiquitination of BRIT1. Loss of BRUCE or USP8 impairs BRIT1 deubiquitination, BRIT1 binding with γ-H2AX, the formation of BRIT1 DNA damage foci, and chromatin relaxation. Moreover, BRUCE-depleted cells display reduced homologous recombination repair, and BRUCE-mutant mice exhibit repair defects and genomic instability. These findings identify BRUCE and USP8 as two hitherto uncharacterized critical DDR regulators and uncover a deubiquitination regulation of BRIT1 assembly at damaged chromatin for efficient DDR and genomic stability.
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57
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Pearl LH, Schierz AC, Ward SE, Al-Lazikani B, Pearl FMG. Therapeutic opportunities within the DNA damage response. Nat Rev Cancer 2015; 15:166-80. [PMID: 25709118 DOI: 10.1038/nrc3891] [Citation(s) in RCA: 388] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The DNA damage response (DDR) is essential for maintaining the genomic integrity of the cell, and its disruption is one of the hallmarks of cancer. Classically, defects in the DDR have been exploited therapeutically in the treatment of cancer with radiation therapies or genotoxic chemotherapies. More recently, protein components of the DDR systems have been identified as promising avenues for targeted cancer therapeutics. Here, we present an in-depth analysis of the function, role in cancer and therapeutic potential of 450 expert-curated human DDR genes. We discuss the DDR drugs that have been approved by the US Food and Drug Administration (FDA) or that are under clinical investigation. We examine large-scale genomic and expression data for 15 cancers to identify deregulated components of the DDR, and we apply systematic computational analysis to identify DDR proteins that are amenable to modulation by small molecules, highlighting potential novel therapeutic targets.
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Affiliation(s)
- Laurence H Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Amanda C Schierz
- 1] Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK. [2] Bluefool Innovations, 4 May Close, Sandhurst, Berkshire GU47 0UG, UK
| | - Simon E Ward
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Bissan Al-Lazikani
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK
| | - Frances M G Pearl
- 1] Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK. [2] Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
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58
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Zhang L, Gong F. Involvement of USP24 in the DNA damage response. Mol Cell Oncol 2015; 3:e1011888. [PMID: 27308530 DOI: 10.1080/23723556.2015.1011888] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 01/21/2015] [Accepted: 01/22/2015] [Indexed: 10/23/2022]
Abstract
Deubiquitination has emerged as an important mechanism of regulating DNA repair pathways. We recently reported that USP24 is a novel p53 deubiquitinase that stabilizes p53 upon DNA damage. USP24 is upregulated by DNA damaging agents and plays an important role in maintaining genome stability.
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Affiliation(s)
- Ling Zhang
- Department of Biochemistry and Molecular Biology; University of Miami Miller School of Medicine ; Miami, FL USA
| | - Feng Gong
- Department of Biochemistry and Molecular Biology; University of Miami Miller School of Medicine ; Miami, FL USA
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59
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Marsh DJ. Networks regulating ubiquitin and ubiquitin-like proteins promise new therapeutic targets. Endocr Relat Cancer 2015; 22:E1-3. [PMID: 25549994 DOI: 10.1530/erc-14-0585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Deborah J Marsh
- Hormones and Cancer GroupKolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, St Leonards, Sydney, New South Wales 2065, Australia
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60
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Abstract
Ubiquitination has traditionally been viewed in the context of polyubiquitination that is essential for marking proteins for degradation via the proteasome. Recent discoveries have shed light on key cellular roles for monoubiquitination, including as a post-translational modification (PTM) of histones such as histone H2B. Monoubiquitination plays a significant role as one of the largest histone PTMs, alongside smaller, better-studied modifications such as methylation, acetylation and phosphorylation. Monoubiquitination of histone H2B at lysine 120 (H2Bub1) has been shown to have key roles in transcription, the DNA damage response and stem cell differentiation. The H2Bub1 enzymatic cascade involves E3 RING finger ubiquitin ligases, with the main E3 generally accepted to be the RNF20-RNF40 complex, and deubiquitinases including ubiquitin-specific protease 7 (USP7), USP22 and USP44. H2Bub1 has been shown to physically disrupt chromatin strands, fostering a more open chromatin structure accessible to transcription factors and DNA repair proteins. It also acts as a recruiting signal, actively attracting proteins with roles in transcription and DNA damage. H2Bub1 also appears to play central roles in histone cross-talk, influencing methylation events on histone H3, including H3K4 and H3K79. Most significantly, global levels of H2Bub1 are low to absent in advanced cancers including breast, colorectal, lung and parathyroid, marking H2Bub1 and the enzymes that regulate it as key molecules of interest as possible new therapeutic targets for the treatment of cancer. This review offers an overview of current knowledge regarding H2Bub1 and highlights links between dysregulation of H2Bub1-associated enzymes, stem cells and malignancy.
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Affiliation(s)
- Alexander J Cole
- Hormones and Cancer GroupKolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, New South Wales 2065, Australia
| | - Roderick Clifton-Bligh
- Hormones and Cancer GroupKolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, New South Wales 2065, Australia
| | - Deborah J Marsh
- Hormones and Cancer GroupKolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, New South Wales 2065, Australia
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61
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Davis MI, Simeonov A. Ubiquitin-Specific Proteases as Druggable Targets. DRUG TARGET REVIEW 2015; 2:60-64. [PMID: 26835158 PMCID: PMC4729384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Mindy I Davis
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
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62
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Yuan J, Luo K, Deng M, Li Y, Yin P, Gao B, Fang Y, Wu P, Liu T, Lou Z. HERC2-USP20 axis regulates DNA damage checkpoint through Claspin. Nucleic Acids Res 2014; 42:13110-21. [PMID: 25355518 PMCID: PMC4245938 DOI: 10.1093/nar/gku1034] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/23/2014] [Accepted: 10/12/2014] [Indexed: 12/26/2022] Open
Abstract
The DNA damage response triggers cell-cycle checkpoints, DNA repair and apoptosis using multiple post-translational modifications as molecular switches. However, how ubiquitination regulates ATR signaling in response to replication stress and single-strand break is still unclear. Here, we identified the deubiquitination enzyme (DUB) USP20 as a pivotal regulator of ATR-related DDR pathway. Through screening a panel of DUBs, we identified USP20 as critical for replication stress response. USP20 is phosphorylated by ATR, resulting in disassociation of the E3 ubiquitin ligase HERC2 from USP20 and USP20 stabilization. USP20 in turn deubiquitinates and stabilizes Claspin and enhances the activation of ATR-Chk1 signaling. These findings reveal USP20 to be a novel regulator of ATR-dependent DNA damage signaling.
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Affiliation(s)
- Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China
| | - Kuntian Luo
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China
| | - Min Deng
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Yunhui Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China
| | - Ping Yin
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Bowen Gao
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Yuan Fang
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Puqiang Wu
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Tongzheng Liu
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Zhenkun Lou
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
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63
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van Cuijk L, Vermeulen W, Marteijn JA. Ubiquitin at work: The ubiquitous regulation of the damage recognition step of NER. Exp Cell Res 2014; 329:101-9. [DOI: 10.1016/j.yexcr.2014.07.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/14/2014] [Indexed: 12/28/2022]
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64
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Zhen Y, Knobel PA, Stracker TH, Reverter D. Regulation of USP28 deubiquitinating activity by SUMO conjugation. J Biol Chem 2014; 289:34838-50. [PMID: 25359778 DOI: 10.1074/jbc.m114.601849] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
USP28 (ubiquitin-specific protease 28) is a deubiquitinating enzyme that has been implicated in the DNA damage response, the regulation of Myc signaling, and cancer progression. The half-life stability of major regulators of critical cellular pathways depends on the activities of specific ubiquitin E3 ligases that target them for proteosomal degradation and deubiquitinating enzymes that promote their stabilization. One function of the post-translational small ubiquitin modifier (SUMO) is the regulation of enzymatic activity of protein targets. In this work, we demonstrate that the SUMO modification of the N-terminal domain of USP28 negatively regulates its deubiquitinating activity, revealing a role for the N-terminal region as a regulatory module in the control of USP28 activity. Despite the presence of ubiquitin-binding domains in the N-terminal domain, its truncation does not impair deubiquitinating activity on diubiquitin or polyubiquitin chain substrates. In contrast to other characterized USP deubiquitinases, our results indicate that USP28 has a chain preference activity for Lys(11), Lys(48), and Lys(63) diubiquitin linkages.
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Affiliation(s)
- Yang Zhen
- From the Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain and
| | - Philip A Knobel
- the Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | | | - David Reverter
- From the Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain and
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65
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Pal A, Young MA, Donato NJ. Emerging potential of therapeutic targeting of ubiquitin-specific proteases in the treatment of cancer. Cancer Res 2014; 74:4955-66. [PMID: 25172841 DOI: 10.1158/0008-5472.can-14-1211] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The ubiquitin-proteasome system (UPS) has emerged as a therapeutic focus and target for the treatment of cancer. The most clinically successful UPS-active agents (bortezomib and lenalidomide) are limited in application to hematologic malignancies, with only marginal efficacy in solid tumors. Inhibition of specific ubiquitin E3 ligases has also emerged as a valid therapeutic strategy, and many targets are currently being investigated. Another emerging and promising approach in regulation of the UPS involves targeting deubiquitinases (DUB). The DUBs comprise a relatively small group of proteins, most with cysteine protease activity that target several key proteins involved in regulation of tumorigenesis, apoptosis, senescence, and autophagy. Through their multiple contacts with ubiquitinated protein substrates involved in these pathways, DUBs provide an untapped means of modulating many important regulatory proteins that support oncogenic transformation and progression. Ubiquitin-specific proteases (USP) are one class of DUBs that have drawn special attention as cancer targets, as many are differentially expressed or activated in tumors or their microenvironment, making them ideal candidates for drug development. This review attempts to summarize the USPs implicated in different cancers, the current status of USP inhibitor-mediated pharmacologic intervention, and future prospects for USP inhibitors to treat diverse cancers.
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Affiliation(s)
- Anupama Pal
- Department of Microbiology and Immunology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Matthew A Young
- Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Nicholas J Donato
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan School of Medicine and Comprehensive Cancer Center, Ann Arbor, Michigan.
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66
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Understanding nucleotide excision repair and its roles in cancer and ageing. Nat Rev Mol Cell Biol 2014; 15:465-81. [PMID: 24954209 DOI: 10.1038/nrm3822] [Citation(s) in RCA: 775] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nucleotide excision repair (NER) eliminates various structurally unrelated DNA lesions by a multiwise 'cut and patch'-type reaction. The global genome NER (GG-NER) subpathway prevents mutagenesis by probing the genome for helix-distorting lesions, whereas transcription-coupled NER (TC-NER) removes transcription-blocking lesions to permit unperturbed gene expression, thereby preventing cell death. Consequently, defects in GG-NER result in cancer predisposition, whereas defects in TC-NER cause a variety of diseases ranging from ultraviolet radiation-sensitive syndrome to severe premature ageing conditions such as Cockayne syndrome. Recent studies have uncovered new aspects of DNA-damage detection by NER, how NER is regulated by extensive post-translational modifications, and the dynamic chromatin interactions that control its efficiency. Based on these findings, a mechanistic model is proposed that explains the complex genotype-phenotype correlations of transcription-coupled repair disorders.
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67
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Baymaz HI, Fournier A, Laget S, Ji Z, Jansen PWTC, Smits AH, Ferry L, Mensinga A, Poser I, Sharrocks A, Defossez PA, Vermeulen M. MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain. Proteomics 2014; 14:2179-89. [DOI: 10.1002/pmic.201400013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/07/2014] [Indexed: 11/06/2022]
Affiliation(s)
- H. Irem Baymaz
- Molecular Cancer Research; Cancer Genomics; University Medical Center Utrecht; Utrecht The Netherlands
| | - Alexandra Fournier
- Epigenetics and Cell Fate; Sorbonne Paris Cité; Université Paris Diderot; Paris France
| | - Sophie Laget
- Epigenetics and Cell Fate; Sorbonne Paris Cité; Université Paris Diderot; Paris France
| | - Zongling Ji
- Faculty of Life Sciences, University of Manchester; Manchester UK
| | - Pascal W. T. C. Jansen
- Molecular Cancer Research; Cancer Genomics; University Medical Center Utrecht; Utrecht The Netherlands
| | - Arne H. Smits
- Molecular Cancer Research; Cancer Genomics; University Medical Center Utrecht; Utrecht The Netherlands
| | - Laure Ferry
- Epigenetics and Cell Fate; Sorbonne Paris Cité; Université Paris Diderot; Paris France
| | - Anneloes Mensinga
- Molecular Cancer Research; Cancer Genomics; University Medical Center Utrecht; Utrecht The Netherlands
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics; Dresden Germany
| | - Andrew Sharrocks
- Faculty of Life Sciences, University of Manchester; Manchester UK
| | | | - Michiel Vermeulen
- Molecular Cancer Research; Cancer Genomics; University Medical Center Utrecht; Utrecht The Netherlands
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68
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USP28 is recruited to sites of DNA damage by the tandem BRCT domains of 53BP1 but plays a minor role in double-strand break metabolism. Mol Cell Biol 2014; 34:2062-74. [PMID: 24687851 DOI: 10.1128/mcb.00197-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The DNA damage response (DDR) is critical for genome stability and the suppression of a wide variety of human malignancies, including neurodevelopmental disorders, immunodeficiency, and cancer. In addition, the efficacy of many chemotherapeutic strategies is dictated by the status of the DDR. Ubiquitin-specific protease 28 (USP28) was reported to govern the stability of multiple factors that are critical for diverse aspects of the DDR. Here, we examined the effects of USP28 depletion on the DDR in cells and in vivo. We found that USP28 is recruited to double-strand breaks in a manner that requires the tandem BRCT domains of the DDR protein 53BP1. However, we observed only minor DDR defects in USP28-depleted cells, and mice lacking USP28 showed normal longevity, immunological development, and radiation responses. Our results thus indicate that USP28 is not a critical factor in double-strand break metabolism and is unlikely to be an attractive target for therapeutic intervention aimed at chemotherapy sensitization.
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69
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USP29 controls the stability of checkpoint adaptor Claspin by deubiquitination. Oncogene 2014; 34:1058-63. [PMID: 24632611 DOI: 10.1038/onc.2014.38] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 01/18/2014] [Accepted: 02/07/2014] [Indexed: 01/02/2023]
Abstract
The DNA damage checkpoint is essential for the maintenance of genome integrity after genotoxic stress, and also for cell survival in eukaryotes. Claspin has a key role in the ATR (ATM and Rad3-related)-Chk1 branch of the DNA damage checkpoint and is also required for correct DNA replication. To achieve properly these functions, Claspin is tightly regulated by ubiquitinin-dependent proteasomal degradation, which controls Claspin levels in a DNA-damage- and cell-cycle-dependent manner. Here, we identified a new regulator of Claspin, the ubiquitin-specific peptidase 29, USP29. Downregulation of USP29 destabilizes Claspin, whereas its overexpression promotes an increase in Claspin levels. USP29 interacts with Claspin and is able to deubiquitinate it both in vivo and in vitro. Most importantly, USP29 knockdown results in an impaired phosphorylation of Chk1 after DNA damage and USP29-depleted cells show a major defect in the S-phase progression. With these results, we identified USP29 as a new player in the ATR-Chk1 pathway and the control of DNA replication.
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70
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Belle JI, Nijnik A. H2A-DUBbing the mammalian epigenome: expanding frontiers for histone H2A deubiquitinating enzymes in cell biology and physiology. Int J Biochem Cell Biol 2014; 50:161-74. [PMID: 24647359 DOI: 10.1016/j.biocel.2014.03.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/05/2014] [Accepted: 03/07/2014] [Indexed: 12/16/2022]
Abstract
Posttranslational modifications of histone H2A through the attachment of ubiquitin or poly-ubiquitin conjugates are common in mammalian genomes and play an important role in the regulation of chromatin structure, gene expression, and DNA repair. Histone H2A deubiquitinases (H2A-DUBs) are a group of structurally diverse enzymes that catalyze the removal ubiquitin from histone H2A. In this review we provide a concise summary of the mechanisms that mediate histone H2A ubiquitination in mammalian cells, and review our current knowledge of mammalian H2A-DUBs, their biochemical activities, and recent developments in our understanding of their functions in mammalian physiology.
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Affiliation(s)
- Jad I Belle
- Department of Physiology, McGill University, Canada; Complex Traits Group, McGill University, Canada
| | - Anastasia Nijnik
- Department of Physiology, McGill University, Canada; Complex Traits Group, McGill University, Canada.
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71
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Wolberger C. Mechanisms for regulating deubiquitinating enzymes. Protein Sci 2014; 23:344-53. [PMID: 24403057 DOI: 10.1002/pro.2415] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 12/23/2013] [Accepted: 12/23/2013] [Indexed: 12/26/2022]
Abstract
Ubiquitination is a reversible post-translational modification that plays a dynamic role in regulating most eukaryotic processes. Deubiquitinating enzymes (DUBs), which hydrolyze the isopeptide or peptide linkages joining ubiquitin to substrate lysines or N-termini, therefore play a key role in ubiquitin signaling. Cells employ multiple mechanisms to regulate DUB activity and thus ensure the appropriate biological response. Recent structural studies have shed light on several different mechanisms by which DUB activity and specificity is regulated.
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Affiliation(s)
- Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry and the Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
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72
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Kessler BM. Selective and reversible inhibitors of ubiquitin-specific protease 7: a patent evaluation (WO2013030218). Expert Opin Ther Pat 2014; 24:597-602. [PMID: 24456106 DOI: 10.1517/13543776.2014.882320] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The invention described in this review (WO2013030218) relates to compounds based on the quinazolin-4-one scaffold, their process of preparation and applications to inhibit the ubiquitin-specific protease 7 (USP7), a deubiquitinating enzyme (DUB), which is considered a potentially important new drug target for treating cancer and immunological disorders. Data are presented indicating that these small-molecule compounds are useful as selective and reversible inhibitors of USP7 in vitro and also in a cellular context, although the panel of other enzymes tested was limited. The synthesis strategy allows for the generation of a considerable variety of compounds, although similar properties of selective USP7 inhibition were reported for other related compound classes, thereby increasing the complexity of the patenting process. However, structural patterns that contribute to the selectivity of USP7 and other DUB enzyme inhibition are starting to emerge. Practical implications involve the treatment of cancer, neurodegenerative diseases, immunological disorders, diabetes, bone and joint diseases, cardiovascular diseases and viral and bacterial infections. The quality of these findings and a comparison to other compound classes with similar properties, as well as the potential for further development toward clinical exploitation are discussed.
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Affiliation(s)
- Benedikt M Kessler
- University of Oxford, Target Discovery Institute, Nuffield Department of Medicine , Roosevelt Drive, Oxford OX3, 7BN , UK +01 865 631 921 ;
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73
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Zhang W, Sidhu SS. Development of inhibitors in the ubiquitination cascade. FEBS Lett 2013; 588:356-67. [PMID: 24239534 PMCID: PMC7094371 DOI: 10.1016/j.febslet.2013.11.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/04/2013] [Accepted: 11/04/2013] [Indexed: 12/16/2022]
Abstract
The ubiquitin proteasome system (UPS) is essential in regulating myriad aspects of protein functions. It is therefore a fundamentally important regulatory mechanism that impacts most if not all aspects of cellular processes. Indeed, malfunction of UPS components is implicated in human diseases such as neurodegenerative and immunological disorders and many cancers. The success of proteasome inhibitors in cancer therapy suggests that modulating enzymes in the ubiquitination cascade would be clinically important for therapeutic benefits. In this review, we summarize advances in developing inhibitors of a variety of UPS components. In particular, we highlight recent work done on the protein engineering of ubiquitin as modulators of the UPS, a novel approach that may shed light on innovative drug discovery in the future.
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Affiliation(s)
- Wei Zhang
- 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, 160 College Street, Toronto, Ontario M5S3E1, 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, 160 College Street, Toronto, Ontario M5S3E1, Canada.
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