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Gál Z, Boukoura S, Oxe KC, Badawi S, Nieto B, Korsholm LM, Geisler SB, Dulina E, Rasmussen AV, Dahl C, Lv W, Xu H, Pan X, Arampatzis S, Stratou DE, Galanos P, Lin L, Guldberg P, Bartek J, Luo Y, Larsen DH. Hyper-recombination in ribosomal DNA is driven by long-range resection-independent RAD51 accumulation. Nat Commun 2024; 15:7797. [PMID: 39242676 PMCID: PMC11379943 DOI: 10.1038/s41467-024-52189-6] [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: 09/29/2023] [Accepted: 08/28/2024] [Indexed: 09/09/2024] Open
Abstract
Ribosomal DNA (rDNA) encodes the ribosomal RNA genes and represents an intrinsically unstable genomic region. However, the underlying mechanisms and implications for genome integrity remain elusive. Here, we use Bloom syndrome (BS), a rare genetic disease characterized by DNA repair defects and hyper-unstable rDNA, as a model to investigate the mechanisms leading to rDNA instability. We find that in Bloom helicase (BLM) proficient cells, the homologous recombination (HR) pathway in rDNA resembles that in nuclear chromatin; it is initiated by resection, replication protein A (RPA) loading and BRCA2-dependent RAD51 filament formation. However, BLM deficiency compromises RPA-loading and BRCA1/2 recruitment to rDNA, but not RAD51 accumulation. RAD51 accumulates at rDNA despite depletion of long-range resection nucleases and rDNA damage results in micronuclei when BLM is absent. In summary, our findings indicate that rDNA is permissive to RAD51 accumulation in the absence of BLM, leading to micronucleation and potentially global genomic instability.
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Affiliation(s)
- Zita Gál
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark
| | - Stavroula Boukoura
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Kezia Catharina Oxe
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Sara Badawi
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Blanca Nieto
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Lea Milling Korsholm
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Ekaterina Dulina
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | | | - Christina Dahl
- Molecular Diagnostics, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Wei Lv
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
| | - Huixin Xu
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
| | - Xiaoguang Pan
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | | | | | - Panagiotis Galanos
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, 8200, Denmark
| | - Per Guldberg
- Molecular Diagnostics, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, 5000, Denmark
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Stockholm, Sweden
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, 8200, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark.
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Martinez S, Sentis S, Poulard C, Trédan O, Le Romancer M. Role of PRMT1 and PRMT5 in Breast Cancer. Int J Mol Sci 2024; 25:8854. [PMID: 39201539 PMCID: PMC11354362 DOI: 10.3390/ijms25168854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
Breast cancer is the most common cancer diagnosed in women worldwide. Early-stage breast cancer is curable in ~70-80% of patients, while advanced metastatic breast cancer is considered incurable with current therapies. Breast cancer is a highly heterogeneous disease categorized into three main subtypes based on key markers orientating specific treatment strategies for each subtype. The complexity of breast carcinogenesis is often associated with epigenetic modification regulating different signaling pathways, involved in breast tumor initiation and progression, particularly by the methylation of arginine residues. Protein arginine methyltransferases (PRMT1-9) have emerged, through their ability to methylate histones and non-histone substrates, as essential regulators of cancers. Here, we present an updated overview of the mechanisms by which PRMT1 and PRMT5, two major members of the PRMT family, control important signaling pathways impacting breast tumorigenesis, highlighting them as putative therapeutic targets.
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Affiliation(s)
- Sébastien Martinez
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
| | - Stéphanie Sentis
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
| | - Coralie Poulard
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
| | - Olivier Trédan
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- Oncology Department, Centre Leon Bérard, F-69008 Lyon, France
| | - Muriel Le Romancer
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, F-69000 Lyon, France
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3
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Foster BM, Wang Z, Schmidt CK. DoUBLing up: ubiquitin and ubiquitin-like proteases in genome stability. Biochem J 2024; 481:515-545. [PMID: 38572758 PMCID: PMC11088880 DOI: 10.1042/bcj20230284] [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: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.
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Affiliation(s)
- Benjamin M. Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Zijuan Wang
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Christine K. Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
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4
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Alfano L, Iannuzzi CA, Barone D, Forte IM, Ragosta MC, Cuomo M, Mazzarotti G, Dell'Aquila M, Altieri A, Caporaso A, Roma C, Marra L, Boffo S, Indovina P, De Laurentiis M, Giordano A. CDK9-55 guides the anaphase-promoting complex/cyclosome (APC/C) in choosing the DNA repair pathway choice. Oncogene 2024; 43:1263-1273. [PMID: 38433256 DOI: 10.1038/s41388-024-02982-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Abstract
DNA double-strand breaks (DSBs) contribute to genome instability, a key feature of cancer. DSBs are mainly repaired by homologous recombination (HR) and non-homologous end-joining (NHEJ). We investigated the role of an isoform of the multifunctional cyclin-dependent kinase 9, CDK9-55, in DNA repair, by generating CDK9-55-knockout HeLa clones (through CRISPR-Cas9), which showed potential HR dysfunction. A phosphoproteomic screening in these clones treated with camptothecin revealed that CDC23 (cell division cycle 23), a component of the E3-ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome), is a new substrate of CDK9-55, with S588 being its putative phosphorylation site. Mutated non-phosphorylatable CDC23(S588A) affected the repair pathway choice by impairing HR and favouring error-prone NHEJ. This CDK9 role should be considered when designing CDK-inhibitor-based cancer therapies.
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Affiliation(s)
- Luigi Alfano
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy.
| | - Carmelina Antonella Iannuzzi
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Daniela Barone
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Iris Maria Forte
- Breast Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | | | - Maria Cuomo
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Giulio Mazzarotti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Milena Dell'Aquila
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Angela Altieri
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Antonella Caporaso
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Laura Marra
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Silvia Boffo
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Paola Indovina
- Sbarro Research Health Organization, Candiolo, Torino, Italy
| | - Michelino De Laurentiis
- Breast Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA.
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5
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Mathias B, O'Leary D, Saucier N, Ahmad F, White LS, Russell L, Shinawi M, Smith MJ, Abraham RS, Cooper MA, Kitcharoensakkul M, Green AM, Bednarski JJ. MYSM1 attenuates DNA damage signals triggered by physiologic and genotoxic DNA breaks. J Allergy Clin Immunol 2024; 153:1113-1124.e7. [PMID: 38065233 PMCID: PMC11417613 DOI: 10.1016/j.jaci.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/31/2023]
Abstract
BACKGROUND Patients with deleterious variants in MYSM1 have an immune deficiency characterized by B-cell lymphopenia, hypogammaglobulinemia, and increased radiosensitivity. MYSM1 is a histone deubiquitinase with established activity in regulating gene expression. MYSM1 also localizes to sites of DNA injury but its function in cellular responses to DNA breaks has not been elucidated. OBJECTIVES This study sought to determine the activity of MYSM1 in regulating DNA damage responses (DDRs) to DNA double-stranded breaks (DSBs) generated during immunoglobulin receptor gene (Ig) recombination and by ionizing radiation. METHODS MYSM1-deficient pre- and non-B cells were used to determine the role of MYSM1 in DSB generation, DSB repair, and termination of DDRs. RESULTS Genetic testing in a newborn with abnormal screen for severe combined immune deficiency, T-cell lymphopenia, and near absence of B cells identified a novel splice variant in MYSM1 that results in nearly absent protein expression. Radiosensitivity testing in patient's peripheral blood lymphocytes showed constitutive γH2AX, a marker of DNA damage, in B cells in the absence of irradiation, suggesting a role for MYSM1 in response to DSBs generated during Ig recombination. Suppression of MYSM1 in pre-B cells did not alter generation or repair of Ig DSBs. Rather, loss of MYSM1 resulted in persistent DNA damage foci and prolonged DDR signaling. Loss of MYSM1 also led to protracted DDRs in U2OS cells with irradiation induced DSBs. CONCLUSIONS MYSM1 regulates termination of DNA damage responses but does not function in DNA break generation and repair.
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Affiliation(s)
- Brendan Mathias
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - David O'Leary
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Nermina Saucier
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Faiz Ahmad
- Department of Medicine, Washington University School of Medicine, St Louis, Mo
| | - Lynn S White
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Le'Mark Russell
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Marwan Shinawi
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Matthew J Smith
- Division of Hematology Research, Mayo Clinic, Rochester, Minn
| | - Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Megan A Cooper
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | | | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Jeffrey J Bednarski
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo.
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6
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Luan R, He M, Li H, Bai Y, Wang A, Sun G, Zhou B, Wang M, Wang C, Wang S, Zeng K, Feng J, Lin L, Wei Y, Kato S, Zhang Q, Zhao Y. MYSM1 acts as a novel co-activator of ERα to confer antiestrogen resistance in breast cancer. EMBO Mol Med 2024; 16:10-39. [PMID: 38177530 PMCID: PMC10883278 DOI: 10.1038/s44321-023-00003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 01/06/2024] Open
Abstract
Endocrine resistance is a crucial challenge in estrogen receptor alpha (ERα)-positive breast cancer (BCa). Aberrant alteration in modulation of E2/ERα signaling pathway has emerged as the putative contributor for endocrine resistance in BCa. Herein, we demonstrate that MYSM1 as a deubiquitinase participates in modulating ERα action via histone and non-histone deubiquitination. MYSM1 is involved in maintenance of ERα stability via ERα deubiquitination. MYSM1 regulates relevant histone modifications on cis regulatory elements of ERα-regulated genes, facilitating chromatin decondensation. MYSM1 is highly expressed in clinical BCa samples. MYSM1 depletion attenuates BCa-derived cell growth in xenograft models and increases the sensitivity of antiestrogen agents in BCa cells. A virtual screen shows that the small molecule Imatinib could potentially interact with catalytic MPN domain of MYSM1 to inhibit BCa cell growth via MYSM1-ERα axis. These findings clarify the molecular mechanism of MYSM1 as an epigenetic modifier in regulation of ERα action and provide a potential therapeutic target for endocrine resistance in BCa.
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Affiliation(s)
- Ruina Luan
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Mingcong He
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Hao Li
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Yu Bai
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Anqi Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
- First Clinical Medical College, China Medical University, 110001, Shenyang City, Liaoning Province, China
| | - Ge Sun
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Baosheng Zhou
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Manlin Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Chunyu Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Shengli Wang
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Kai Zeng
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Jianwei Feng
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Lin Lin
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China
| | - Yuntao Wei
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, 110042, Shenyang City, Liaoning Province, China
| | - Shigeaki Kato
- Graduate School of Life Science and Engineering, Iryo Sosei University, Iino, Chuo-dai, Iwaki, Fukushima, 9708551, Japan
- Research Institute of Innovative Medicine, Tokiwa Foundation, Iwaki, Fukushima, Japan
| | - Qiang Zhang
- Department of Breast Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, 110042, Shenyang City, Liaoning Province, China.
| | - Yue Zhao
- Department of Cell Biology, Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, 110122, Shenyang City, Liaoning Province, China.
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7
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Dagar G, Kumar R, Yadav KK, Singh M, Pandita TK. Ubiquitination and deubiquitination: Implications on cancer therapy. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194979. [PMID: 37633647 DOI: 10.1016/j.bbagrm.2023.194979] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023]
Abstract
The ubiquitin proteasomal system (UPS) represents a highly regulated protein degradation pathway essential for maintaining cellular homeostasis. This system plays a critical role in several cellular processes, which include DNA damage repair, cell cycle checkpoint control, and immune response regulation. Recently, the UPS has emerged as a promising target for cancer therapeutics due to its involvement in oncogenesis and tumor progression. Here we aim to summarize the key aspects of the UPS and its significance in cancer therapeutics. We begin by elucidating the fundamental components of the UPS, highlighting the role of ubiquitin, E1-E3 ligases, and the proteasome in protein degradation. Furthermore, we discuss the intricate process of ubiquitination and proteasomal degradation, emphasizing the specificity and selectivity achieved through various signaling pathways. The dysregulation of the UPS has been implicated in cancer development and progression. Aberrant ubiquitin-mediated degradation of key regulatory proteins, such as tumor suppressors and oncoproteins, can lead to uncontrolled cell proliferation, evasion of apoptosis, and metastasis. We outline the pivotal role of the UPS in modulating crucial oncogenic pathways, including the regulation of cyclins, transcription factors, Replication stress components and DNA damage response. The increasing recognition of the UPS as a target for cancer therapeutics has spurred the development of small molecules, peptides, and proteasome inhibitors with the potential to restore cellular balance and disrupt tumor growth. We provide an overview of current therapeutic strategies aimed at exploiting the UPS, including the use of proteasome inhibitors, deubiquitinating enzyme inhibitors, and novel E3 ligase modulators. We further discuss novel emerging strategies for the development of next-generation drugs that target proteasome inhibitors. Exploiting the UPS for cancer therapeutics offers promising avenues for developing innovative and effective treatment strategies, providing hope for improved patient outcomes in the fight against cancer.
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Affiliation(s)
- Gunjan Dagar
- Department of Medical Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir 182320, India.
| | - Kamlesh K Yadav
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA; School of Engineering Medicine, Texas A&M University, School of Medicine, Houston, TX 77030, USA.
| | - Mayank Singh
- Department of Medical Oncology, Dr BRAIRCH, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Tej K Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA.
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8
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Song J, Liu Y, Yin Y, Wang H, Zhang X, Li Y, Zhao X, Zhang G, Meng X, Jin Y, Lu D, Yin Y. PTIR1 acts as an isoform of DDX58 and promotes tumor immune resistance through activation of UCHL5. Cell Rep 2023; 42:113388. [PMID: 37934668 DOI: 10.1016/j.celrep.2023.113388] [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: 03/09/2023] [Revised: 09/22/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
Cancer evades host immune surveillance by virtue of poor immunogenicity. Here, we report an immune suppressor, designated as PTIR1, that acts as a promotor of tumor immune resistance. PTIR1 is selectively induced in human cancers via alternative splicing of DDX58 (RIG-I), and its induction is closely related to poor outcome in patients with cancer. Through blocking the recruitment of leukocytes, PTIR1 facilitates cancer immune escape and tumor-intrinsic resistance to immunotherapeutic treatments. Unlike RIG-I, PTIR1 is capable of binding to the C terminus of UCHL5 and activates its ubiquitinating function, which in turn inhibits immunoproteasome activity and limits neoantigen processing and presentation, consequently blocking T cell recognition and attack against cancer. Moreover, we find that the adenosine deaminase ADAR1 induces A-to-I RNA editing on DDX58 transcript, thus triggering PTIR1 production. Collectively, our data uncover the immunosuppressive role of PTIR1 in tumorigenesis and propose that ADAR1-PTIR1-UCHL5 signaling is a potential cancer immunotherapeutic target.
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Affiliation(s)
- Jia Song
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yang Liu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yue Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Hui Wang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Xin Zhang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yang Li
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Xuyang Zhao
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Guangze Zhang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Xiangyan Meng
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yan Jin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Dan Lu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China.
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China; Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, P.R. China.
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9
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Klonisch T, Logue SE, Hombach-Klonisch S, Vriend J. DUBing Primary Tumors of the Central Nervous System: Regulatory Roles of Deubiquitinases. Biomolecules 2023; 13:1503. [PMID: 37892185 PMCID: PMC10605193 DOI: 10.3390/biom13101503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
The ubiquitin proteasome system (UPS) utilizes an orchestrated enzymatic cascade of E1, E2, and E3 ligases to add single or multiple ubiquitin-like molecules as post-translational modification (PTM) to proteins. Ubiquitination can alter protein functions and/or mark ubiquitinated proteins for proteasomal degradation but deubiquitinases (DUBs) can reverse protein ubiquitination. While the importance of DUBs as regulatory factors in the UPS is undisputed, many questions remain on DUB selectivity for protein targeting, their mechanism of action, and the impact of DUBs on the regulation of diverse biological processes. Furthermore, little is known about the expression and role of DUBs in tumors of the human central nervous system (CNS). In this comprehensive review, we have used publicly available transcriptional datasets to determine the gene expression profiles of 99 deubiquitinases (DUBs) from five major DUB families in seven primary pediatric and adult CNS tumor entities. Our analysis identified selected DUBs as potential new functional players and biomarkers with prognostic value in specific subtypes of primary CNS tumors. Collectively, our analysis highlights an emerging role for DUBs in regulating CNS tumor cell biology and offers a rationale for future therapeutic targeting of DUBs in CNS tumors.
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Affiliation(s)
- Thomas Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pathology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Susan E. Logue
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pathology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Jerry Vriend
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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10
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Matsui M, Kajita S, Tsuchiya Y, Torii W, Tamekuni S, Nishi R. USP49 is a novel deubiquitylating enzyme for γ H2AX in DNA double-strand break repair. Gene 2022; 833:146599. [PMID: 35598681 DOI: 10.1016/j.gene.2022.146599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/16/2022] [Indexed: 12/29/2022]
Abstract
DNA double-strand break (DSB) that is one of the most serious DNA lesions is mainly repaired by two mutually exclusive pathways, homologous recombination and non-homologous end-joining. Proper choice of DSB repair pathway, in which recruitment of 53BP1 to chromatin around DSB sites plays a pivotal role, is crucial for maintaining genome integrity. Ubiquitylations of histone H2A and H2AX on Lys15 are prerequisite for 53BP1 loading onto chromatin. Although ubiquitylation mechanism of H2A and H2AX had been extensively studied, mechanism regulating deubiquitylation of γH2AX that is a phosphorylated form of H2AX remains elusive. Here, we identified USP49 as a novel deubiquitylating enzyme targeting DSB-induced γH2AX ubiquitylation. Over-expressed USP49 suppressed ubiquitylation of γH2AX in an enzymatic activity-dependent manner. Catalytic dead mutant of USP49 interacted and colocalized with γH2AX. Consequently, over-expression of USP49 inhibited the DSB-induced foci formation of 53BP1 and resulted in higher cell sensitivity to DSB-inducing drug treatment. Furthermore, endogenous USP49 protein was degraded via the proteasome upon DSB induction, indicating the importance of modulating USP49 protein level for γH2AX deubiquitylation. Consistent with our cell-based data, kidney renal clear cell carcinoma patients with higher expression of USP49 showed poor survival rate in comparison to the patients with unaltered USP49 expression. In conclusion, these data suggest that fine tuning of protein level of USP49 and USP49-mediated deubiquitylation of γH2AX are important for genome integrity.
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Affiliation(s)
- Misaki Matsui
- Graduate School of Bionics, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan
| | - Shoki Kajita
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yuina Tsuchiya
- School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan
| | - Wakana Torii
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Shiori Tamekuni
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Ryotaro Nishi
- Graduate School of Bionics, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan; Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan.
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11
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Yin X, Liu Q, Liu F, Tian X, Yan T, Han J, Jiang S. Emerging Roles of Non-proteolytic Ubiquitination in Tumorigenesis. Front Cell Dev Biol 2022; 10:944460. [PMID: 35874839 PMCID: PMC9298949 DOI: 10.3389/fcell.2022.944460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/15/2022] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a critical type of protein post-translational modification playing an essential role in many cellular processes. To date, more than eight types of ubiquitination exist, all of which are involved in distinct cellular processes based on their structural differences. Studies have indicated that activation of the ubiquitination pathway is tightly connected with inflammation-related diseases as well as cancer, especially in the non-proteolytic canonical pathway, highlighting the vital roles of ubiquitination in metabolic programming. Studies relating degradable ubiquitination through lys48 or lys11-linked pathways to cellular signaling have been well-characterized. However, emerging evidence shows that non-degradable ubiquitination (linked to lys6, lys27, lys29, lys33, lys63, and Met1) remains to be defined. In this review, we summarize the non-proteolytic ubiquitination involved in tumorigenesis and related signaling pathways, with the aim of providing a reference for future exploration of ubiquitination and the potential targets for cancer therapies.
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Affiliation(s)
- Xiu Yin
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Qingbin Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tinghao Yan
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Han
- Department of Thyroid and Breast Surgery, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
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12
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Peng Q, Wan D, Zhou R, Luo H, Wang J, Ren L, Zeng Y, Yu C, Zhang S, Huang X, Peng Y. The biological function of metazoan-specific subunit nuclear factor related to kappaB binding protein of INO80 complex. Int J Biol Macromol 2022; 203:176-183. [PMID: 35093437 DOI: 10.1016/j.ijbiomac.2022.01.155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 12/24/2022]
Abstract
The INO80 chromatin remodeling complex plays an essential role in the regulation of gene transcription, which participate in a variety of important biological processes in cells including DNA repair and DNA replication. Difference from the yeast INO80 complex, metazoan INO80 complex have the specific subunit G, which is known as nuclear factor related to kappaB binding protein (NFRKB). Recently, NFRKB has been received much attention in many aspects, such as DNA repair, cell pluripotency, telomere protection, and protein activity regulation. To dig the new function of metazoan INO80 complex, a better understanding of the role of NFRKB is required. In this review, we provide an overview of the structure and function of NFRKB and discuss its potential role in cancer treatment and telomere regulation. Overall, this review provides an important reference for further research of the INO80 complex and NFRKB.
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Affiliation(s)
- Qiyao Peng
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Dan Wan
- Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Rongrong Zhou
- Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Hongyu Luo
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 410016, China
| | - Junyi Wang
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Lingyan Ren
- School of Safety Engineering, Chongqing University of Science & Technology, Chongqing 401331, China
| | - Yajun Zeng
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; Department of Pharmacy, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Chao Yu
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Shuihan Zhang
- Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China
| | - Xuekuan Huang
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 410016, China.
| | - Yongbo Peng
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, College of Pharmacy, Chongqing Medical University, Chongqing 400016, China; Institute of Chinese Medicine, Hunan Academy of Traditional Chinese Medicine&Hunan University of Chinese Medicine, Changsha 410208, China.
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13
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A Proximity Ligation Method to Detect Proteins Bound to Single-Stranded DNA after DNA End Resection at DNA Double-Strand Breaks. Methods Protoc 2021; 5:mps5010003. [PMID: 35076555 PMCID: PMC8788478 DOI: 10.3390/mps5010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
After a DNA double-strand break, cells utilize either non-homologous end joining or homologous recombination to repair the broken DNA ends. Homologous recombination requires extensive nucleolytic processing of one of the DNA strands, resulting in long stretches of 3′ single-strand DNA overhangs. Typically, single-stranded DNA is measured using immunofluorescence microscopy to image the foci of replication protein A, a single-stranded DNA-binding protein. Microscopy analysis of bromodeoxyuridine foci under nondenaturing conditions has also been used to measure single-stranded DNA. Here, we describe a proximity ligation assay which uses genome-wide bromodeoxyuridine incorporation to label single-stranded DNA in order to measure the association of a protein of interest with single-stranded DNA. This method is advantageous over traditional foci analysis because it is more direct and specific than traditional foci co-localization microscopy methods, uses only one color channel, and can reveal protein-single-stranded DNA interactions that are rare and potentially undetectable using traditional microscopy methods. We show here the association of replication protein A and bromodeoxyuridine as proof-of-concept.
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14
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Foster B, Attwood M, Gibbs-Seymour I. Tools for Decoding Ubiquitin Signaling in DNA Repair. Front Cell Dev Biol 2021; 9:760226. [PMID: 34950659 PMCID: PMC8690248 DOI: 10.3389/fcell.2021.760226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/09/2021] [Indexed: 12/21/2022] Open
Abstract
The maintenance of genome stability requires dedicated DNA repair processes and pathways that are essential for the faithful duplication and propagation of chromosomes. These DNA repair mechanisms counteract the potentially deleterious impact of the frequent genotoxic challenges faced by cells from both exogenous and endogenous agents. Intrinsic to these mechanisms, cells have an arsenal of protein factors that can be utilised to promote repair processes in response to DNA lesions. Orchestration of the protein factors within the various cellular DNA repair pathways is performed, in part, by post-translational modifications, such as phosphorylation, ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs). In this review, we firstly explore recent advances in the tools for identifying factors involved in both DNA repair and ubiquitin signaling pathways. We then expand on this by evaluating the growing repertoire of proteomic, biochemical and structural techniques available to further understand the mechanistic basis by which these complex modifications regulate DNA repair. Together, we provide a snapshot of the range of methods now available to investigate and decode how ubiquitin signaling can promote DNA repair and maintain genome stability in mammalian cells.
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Affiliation(s)
| | | | - Ian Gibbs-Seymour
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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15
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Song A, Hazlett Z, Abeykoon D, Dortch J, Dillon A, Curtiss J, Martinez SB, Hill CP, Yu C, Huang L, Fushman D, Cohen RE, Yao T. Branched ubiquitin chain binding and deubiquitination by UCH37 facilitate proteasome clearance of stress-induced inclusions. eLife 2021; 10:72798. [PMID: 34761751 PMCID: PMC8635973 DOI: 10.7554/elife.72798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022] Open
Abstract
UCH37, also known as UCHL5, is a highly conserved deubiquitinating enzyme (DUB) that associates with the 26S proteasome. Recently, it was reported that UCH37 activity is stimulated by branched ubiquitin (Ub) chain architectures. To understand how UCH37 achieves its unique debranching specificity, we performed biochemical and Nuclear Magnetic Resonance (NMR) structural analyses and found that UCH37 is activated by contacts with the hydrophobic patches of both distal Ubs that emanate from a branched Ub. In addition, RPN13, which recruits UCH37 to the proteasome, further enhances branched-chain specificity by restricting linear Ub chains from having access to the UCH37 active site. In cultured human cells under conditions of proteolytic stress, we show that substrate clearance by the proteasome is promoted by both binding and deubiquitination of branched polyubiquitin by UCH37. Proteasomes containing UCH37(C88A), which is catalytically inactive, aberrantly retain polyubiquitinated species as well as the RAD23B substrate shuttle factor, suggesting a defect in recycling of the proteasome for the next round of substrate processing. These findings provide a foundation to understand how proteasome degradation of substrates modified by a unique Ub chain architecture is aided by a DUB.
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Affiliation(s)
- Aixin Song
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Zachary Hazlett
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Dulith Abeykoon
- Department of Chemistry and Biochemistry, University of Maryland, College Park, United States
| | - Jeremy Dortch
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Andrew Dillon
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Justin Curtiss
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Sarah Bollinger Martinez
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, United States
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, United States
| | - Robert E Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
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16
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Kim JJ, Lee SY, Hwang Y, Kim S, Chung JM, Park S, Yoon J, Yun H, Ji JH, Chae S, Cho H, Kim CG, Dawson TM, Kim H, Dawson VL, Kang HC. USP39 promotes non-homologous end-joining repair by poly(ADP-ribose)-induced liquid demixing. Nucleic Acids Res 2021; 49:11083-11102. [PMID: 34614178 PMCID: PMC8565343 DOI: 10.1093/nar/gkab892] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/18/2022] Open
Abstract
Mutual crosstalk among poly(ADP-ribose) (PAR), activated PAR polymerase 1 (PARP1) metabolites, and DNA repair machinery has emerged as a key regulatory mechanism of the DNA damage response (DDR). However, there is no conclusive evidence of how PAR precisely controls DDR. Herein, six deubiquitinating enzymes (DUBs) associated with PAR-coupled DDR were identified, and the role of USP39, an inactive DUB involved in spliceosome assembly, was characterized. USP39 rapidly localizes to DNA lesions in a PAR-dependent manner, where it regulates non-homologous end-joining (NHEJ) via a tripartite RG motif located in the N-terminus comprising 46 amino acids (N46). Furthermore, USP39 acts as a molecular trigger for liquid demixing in a PAR-coupled N46-dependent manner, thereby directly interacting with the XRCC4/LIG4 complex during NHEJ. In parallel, the USP39-associated spliceosome complex controls homologous recombination repair in a PAR-independent manner. These findings provide mechanistic insights into how PAR chains precisely control DNA repair processes in the DDR.
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Affiliation(s)
- Jae Jin Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Life Science, Hallym University, Chuncheon 24252, Republic of Korea
| | - Seo Yun Lee
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Yiseul Hwang
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Soyeon Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Jee Min Chung
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Sangwook Park
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Junghyun Yoon
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Hansol Yun
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Hyeseong Cho
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Chan Gil Kim
- Department of Biotechnology, Konkuk University, Chungju 380-701, Republic of Korea
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongtae Kim
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.,School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ho Chul Kang
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
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17
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Sanchez-Bailon MP, Choi SY, Dufficy ER, Sharma K, McNee GS, Gunnell E, Chiang K, Sahay D, Maslen S, Stewart GS, Skehel JM, Dreveny I, Davies CC. Arginine methylation and ubiquitylation crosstalk controls DNA end-resection and homologous recombination repair. Nat Commun 2021; 12:6313. [PMID: 34728620 PMCID: PMC8564520 DOI: 10.1038/s41467-021-26413-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/04/2021] [Indexed: 11/26/2022] Open
Abstract
Cross-talk between distinct protein post-translational modifications is critical for an effective DNA damage response. Arginine methylation plays an important role in maintaining genome stability, but how this modification integrates with other enzymatic activities is largely unknown. Here, we identify the deubiquitylating enzyme USP11 as a previously uncharacterised PRMT1 substrate, and demonstrate that the methylation of USP11 promotes DNA end-resection and the repair of DNA double strand breaks (DSB) by homologous recombination (HR), an event that is independent from another USP11-HR activity, the deubiquitylation of PALB2. We also show that PRMT1 is a ubiquitylated protein that it is targeted for deubiquitylation by USP11, which regulates the ability of PRMT1 to bind to and methylate MRE11. Taken together, our findings reveal a specific role for USP11 during the early stages of DSB repair, which is mediated through its ability to regulate the activity of the PRMT1-MRE11 pathway.
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Affiliation(s)
- Maria Pilar Sanchez-Bailon
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Soo-Youn Choi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Elizabeth R Dufficy
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Karan Sharma
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Gavin S McNee
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Emma Gunnell
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Kelly Chiang
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Debashish Sahay
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
- The Francis Crick Institute, London, UK
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Clare C Davies
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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18
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Snyder NA, Silva GM. Deubiquitinating enzymes (DUBs): Regulation, homeostasis, and oxidative stress response. J Biol Chem 2021; 297:101077. [PMID: 34391779 PMCID: PMC8424594 DOI: 10.1016/j.jbc.2021.101077] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Ubiquitin signaling is a conserved, widespread, and dynamic process in which protein substrates are rapidly modified by ubiquitin to impact protein activity, localization, or stability. To regulate this process, deubiquitinating enzymes (DUBs) counter the signal induced by ubiquitin conjugases and ligases by removing ubiquitin from these substrates. Many DUBs selectively regulate physiological pathways employing conserved mechanisms of ubiquitin bond cleavage. DUB activity is highly regulated in dynamic environments through protein-protein interaction, posttranslational modification, and relocalization. The largest family of DUBs, cysteine proteases, are also sensitive to regulation by oxidative stress, as reactive oxygen species (ROS) directly modify the catalytic cysteine required for their enzymatic activity. Current research has implicated DUB activity in human diseases, including various cancers and neurodegenerative disorders. Due to their selectivity and functional roles, DUBs have become important targets for therapeutic development to treat these conditions. This review will discuss the main classes of DUBs and their regulatory mechanisms with a particular focus on DUB redox regulation and its physiological impact during oxidative stress.
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Affiliation(s)
- Nathan A Snyder
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, North Carolina, USA.
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19
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Barabino SML, Citterio E, Ronchi AE. Transcription Factors, R-Loops and Deubiquitinating Enzymes: Emerging Targets in Myelodysplastic Syndromes and Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13153753. [PMID: 34359655 PMCID: PMC8345071 DOI: 10.3390/cancers13153753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The advent of DNA massive sequencing technologies has allowed for the first time an extensive look into the heterogeneous spectrum of genes and mutations underpinning myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). In this review, we wish to explore the most recent advances and the rationale for the potential therapeutic interest of three main actors in myelo-leukemic transformation: transcription factors that govern myeloid differentiation; RNA splicing factors, which ensure proper mRNA maturation and whose mutations increase R-loops formation; and deubiquitinating enzymes, which contribute to genome stability in hematopoietic stem cells (HSCs). Abstract Myeloid neoplasms encompass a very heterogeneous family of diseases characterized by the failure of the molecular mechanisms that ensure a balanced equilibrium between hematopoietic stem cells (HSCs) self-renewal and the proper production of differentiated cells. The origin of the driver mutations leading to preleukemia can be traced back to HSC/progenitor cells. Many properties typical to normal HSCs are exploited by leukemic stem cells (LSCs) to their advantage, leading to the emergence of a clonal population that can eventually progress to leukemia with variable latency and evolution. In fact, different subclones might in turn develop from the original malignant clone through accumulation of additional mutations, increasing their competitive fitness. This process ultimately leads to a complex cancer architecture where a mosaic of cellular clones—each carrying a unique set of mutations—coexists. The repertoire of genes whose mutations contribute to the progression toward leukemogenesis is broad. It encompasses genes involved in different cellular processes, including transcriptional regulation, epigenetics (DNA and histones modifications), DNA damage signaling and repair, chromosome segregation and replication (cohesin complex), RNA splicing, and signal transduction. Among these many players, transcription factors, RNA splicing proteins, and deubiquitinating enzymes are emerging as potential targets for therapeutic intervention.
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20
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Zheng W, Du L. The DUB family in Populus: identification, characterization, evolution and expression patterns. BMC Genomics 2021; 22:541. [PMID: 34266381 PMCID: PMC8281628 DOI: 10.1186/s12864-021-07844-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/24/2021] [Indexed: 11/20/2022] Open
Abstract
Background The deubiquitinase (DUB) family constitutes a group of proteases that regulate the stability or reverse the ubiquitination of many proteins in the cell. These enzymes participate in cell-cycle regulation, cell division and differentiation, diverse physiological activities such as DNA damage repair, growth and development, and response to stress. However, limited information is available on this family of genes in woody plants. Results In the present study, 88 DUB family genes were identified in the woody model plant Populus trichocarpa, comprising 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM genes with similar domains. According to phylogenetic analysis, the PtrUBP genes were classified into 16 groups, the PtrUCH genes into two, the PtrOTU genes into eight, the PtrMJD genes into two, and the PtrJAMM genes into seven. Members of same subfamily had similar gene structure and motif distribution characteristics. Synteny analysis of the DUB family genes from P. thrchocarpa and four other plant species provided insight into the evolutionary traits of DUB genes. Expression profiles derived from previously published transcriptome data revealed distinct expression patterns of DUB genes in various tissues. On the basis of the results of analysis of promoter cis-regulatory elements, we selected 16 representative PtrUBP genes to treatment with abscisic acid, methyl jasmonate, or salicylic acid applied as a foliar spray. The majority of PtrUBP genes were upregulated in response to the phytohormone treatments, which implied that the genes play potential roles in abiotic stress response in Populus. Conclusions The results of this study broaden our understanding of the DUB family in plants. Analysis of the gene structure, conserved elements, and expression patterns of the DUB family provides a solid foundation for exploration of their specific functions in Populus and to elucidate the potential role of PtrUBP gene in abiotic stress response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07844-3.
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Affiliation(s)
- Wenqing Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 10083, China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Liang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 10083, China. .,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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21
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Behrens KA, Girasek QL, Sickler A, Hyde J, Buonaccorsi VP. Regions of genetic divergence in depth-separated Sebastes rockfish species pairs: Depth as a potential driver of speciation. Mol Ecol 2021; 30:4259-4275. [PMID: 34181798 DOI: 10.1111/mec.16046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/20/2022]
Abstract
Depth separation is a proposed driver of speciation in marine fishes, with marine rockfish (genus Sebastes) providing a potentially informative study system. Sebastes rockfishes are commercially and ecologically important. This genus encompasses more than one hundred species and the ecological and morphological variance between these species provides opportunity for identifying speciation-driving adaptations, particularly along a depth gradient. A reduced-representation sequencing method (ddRADseq) was used to compare 95 individuals encompassing six Sebastes species. In this study, we sought to identify regions of divergence between species that were indicative of divergent adaptation and reproductive barriers leading to speciation. A pairwise comparison of S. chrysomelas (black-and-yellow rockfish) and S. carnatus (gopher rockfish) FST values revealed three major regions of elevated genomic divergence, two of which were also present in the S. miniatus (vermilion rockfish) and S. crocotulus (sunset rockfish) comparison. These corresponded with regions of both elevated DXY values and reduced nucleotide diversity in two cases, suggesting a speciation-with-gene-flow evolutionary model followed by post-speciation selective sweeps within each species. Limited whole-genome resequencing was also performed to identify mutations with predicted effects between S. chrysomelas and S. carnatus. Within these islands, we identified important SNPs in genes involved in immune function and vision. This supports their potential role in speciation, as these are adaptive vectors noted in other organisms. Additionally, changes to genes involved in pigment expression and mate recognition shed light on how S. chrysomelas and S. carnatus may have become reproductively isolated.
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Affiliation(s)
- Kristen A Behrens
- Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA
| | - Quinn L Girasek
- Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA
| | - Alex Sickler
- Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - John Hyde
- Fisheries Resources Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, California, USA
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22
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Tang M, Li S, Chen J. Ubiquitylation in DNA double-strand break repair. DNA Repair (Amst) 2021; 103:103129. [PMID: 33990032 DOI: 10.1016/j.dnarep.2021.103129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/26/2021] [Accepted: 05/05/2021] [Indexed: 12/28/2022]
Abstract
Genome integrity is constantly challenged by various DNA lesions with DNA double-strand breaks (DSBs) as the most cytotoxic lesions. In order to faithfully repair DSBs, DNA damage response (DDR) signaling networks have evolved, which organize many multi-protein complexes to deal with the encountered DNA damage. Spatiotemporal dynamics of these protein complexes at DSBs are mainly modulated by post-translational modifications (PTMs). One of the most well-studied PTMs in DDR is ubiquitylation which can orchestrate cellular responses to DSBs, promote accurate DNA repair, and maintain genome integrity. Here, we summarize the recent advances of ubiquitin-dependent signaling in DDR and discuss how ubiquitylation crosstalks with other PTMs to control fundamental biological processes in DSB repair.
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Affiliation(s)
- Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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23
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Qi Y, Warmenhoven JW, Henthorn NT, Ingram SP, Xu XG, Kirkby KJ, Merchant MJ. Mechanistic Modelling of Slow and Fast NHEJ DNA Repair Pathways Following Radiation for G0/G1 Normal Tissue Cells. Cancers (Basel) 2021; 13:2202. [PMID: 34063683 PMCID: PMC8124137 DOI: 10.3390/cancers13092202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/23/2021] [Accepted: 04/29/2021] [Indexed: 01/12/2023] Open
Abstract
Mechanistic in silico models can provide insight into biological mechanisms and highlight uncertainties for experimental investigation. Radiation-induced double-strand breaks (DSBs) are known to be toxic lesions if not repaired correctly. Non-homologous end joining (NHEJ) is the major DSB-repair pathway available throughout the cell cycle and, recently, has been hypothesised to consist of a fast and slow component in G0/G1. The slow component has been shown to be resection-dependent, requiring the nuclease Artemis to function. However, the pathway is not yet fully understood. This study compares two hypothesised models, simulating the action of individual repair proteins on DSB ends in a step-by-step manner, enabling the modelling of both wild-type and protein-deficient cell systems. Performance is benchmarked against experimental data from 21 cell lines and 18 radiation qualities. A model where resection-dependent and independent pathways are entirely separated can only reproduce experimental repair kinetics with additional restraints on end motion and protein recruitment. However, a model where the pathways are entwined was found to effectively fit without needing additional mechanisms. It has been shown that DaMaRiS is a useful tool when analysing the connections between resection-dependent and independent NHEJ repair pathways and robustly matches with experimental results from several sources.
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Affiliation(s)
- Yaping Qi
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026, China;
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
| | - John William Warmenhoven
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Nicholas Thomas Henthorn
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Samuel Peter Ingram
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester M13 9PL, UK
| | - Xie George Xu
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230026, China;
| | - Karen Joy Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Michael John Merchant
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.P.I.); (K.J.K.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
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24
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Jiang B, Zhou L, Lu J, Wang Y, Liu C, Liang Z, Zhou W, You L, Guo J. Clinicopathological and prognostic significance of ubiquitin-specific peptidase 15 and its relationship with transforming growth factor-β receptors in patients with pancreatic ductal adenocarcinoma. J Gastroenterol Hepatol 2021; 36:507-515. [PMID: 32875609 DOI: 10.1111/jgh.15244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 08/10/2020] [Accepted: 08/26/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND AND AIM Ubiquitin-specific peptidase 15 (USP15) has been correlated to aggressive oncogenic behavior in several types of carcinomas, but its function in pancreatic ductal adenocarcinoma (PDAC) has not been clarified. This study aimed to evaluate the clinicopathological and prognostic value of USP15 and its relationship with transforming growth factor-β (TGF-β) receptors (TβRs) in PDAC. METHODS By immunohistochemical staining of tissue microarrays, the expression patterns of USP15 and TβRs were retrospectively analyzed in 287 PDAC patients who underwent radical surgical resection without neoadjuvant therapy. Cancer-specific survival was compared based on USP15 expression, and the correlations between USP15 and TβRs were analyzed. RESULTS Ubiquitin-specific peptidase 15 expression in tumor tissues was significantly higher than that in para-tumor tissues (P < 0.0001), and high USP15 expression was associated with the pathological N (pN) stage (P = 0.033). In addition, high USP15 expression was significantly associated with shorter cancer-specific survival (P = 0.019). Univariate analyses showed that high USP15 expression (P = 0.024), a poor histopathological grade (P = 0.003), and the pN1 stage (P = 0.009) were significantly correlated with shorter survival. Although the independent prognostic value of USP15 alone was not established, the combination of USP15 and the histological grade was identified as an independent prognostic factor in multivariate analyses (P = 0.015). USP15 expression was correlated with TβR-I, TβR-II, or TβR-III expression in PDAC. CONCLUSIONS High USP15 expression is a potential prognostic indicator in patients with PDAC, and it might affect the TGF-β signaling pathway in PDAC.
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Affiliation(s)
- Bolun Jiang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li Zhou
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jun Lu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yizhi Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Chengxi Liu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Weixun Zhou
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Lei You
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Junchao Guo
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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25
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Neve B, Jonckheere N, Vincent A, Van Seuningen I. Long non-coding RNAs: the tentacles of chromatin remodeler complexes. Cell Mol Life Sci 2021; 78:1139-1161. [PMID: 33001247 PMCID: PMC11072783 DOI: 10.1007/s00018-020-03646-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/12/2020] [Indexed: 02/07/2023]
Abstract
Chromatin remodeler complexes regulate gene transcription, DNA replication and DNA repair by changing both nucleosome position and post-translational modifications. The chromatin remodeler complexes are categorized into four families: the SWI/SNF, INO80/SWR1, ISWI and CHD family. In this review, we describe the subunits of these chromatin remodeler complexes, in particular, the recently identified members of the ISWI family and novelties of the CHD family. Long non-coding (lnc) RNAs regulate gene expression through different epigenetic mechanisms, including interaction with chromatin remodelers. For example, interaction of lncBRM with BRM inhibits the SWI/SNF complex associated with a differentiated phenotype and favors assembly of a stem cell-related SWI/SNF complex. Today, over 50 lncRNAs have been shown to affect chromatin remodeler complexes and we here discuss the mechanisms involved.
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Affiliation(s)
- Bernadette Neve
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France.
| | - Nicolas Jonckheere
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Audrey Vincent
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Isabelle Van Seuningen
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
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26
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Özenver N, Boulos JC, Efferth T. Activity of Cordycepin From Cordyceps sinensis Against Drug-Resistant Tumor Cells as Determined by Gene Expression and Drug Sensitivity Profiling. Nat Prod Commun 2021. [DOI: 10.1177/1934578x21993350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cordycepin is one of the substantial components of the parasitic fungus Cordyceps sinensis as well as other Cordyceps species. It exerts various effects such as antimetastatic, antiinflammatory, antioxidant, and neuroprotective activities. Assorted studies revealed in vitro and in vivo anticancer influence of cordycepin and put forward its potential for cancer therapy. However, the role of multidrug resistance-associated mechanisms for the antitumor effect of cordycepin has not been investigated in great detail thus far. Therefore, we searched cordycepin’s cytotoxicity with regard to well-known anticancer drug resistance mechanisms, including ABCB1, ABCB5, ABCC1, ABCG2, EGFR, and TP53, and identified putative molecular determinants related to the cellular responsiveness of cordycepin. Bioinformatic analyses of NCI microarray data and gene promoter transcription factor binding motif analyses were performed to specify the mechanisms of cordycepin towards cancer cells. COMPARE and hierarchical analyses led to the detection of the genes involved in cordycepin’s cytotoxicity and sensitivity and resistance of cell lines towards cordycepin. Tumor-type dependent response and cross-resistance profiles were further unravelled. We found transcription factors potentially involved in the common transcriptional regulation of the genes identified by COMPARE analyses. Cordycepin bypassed resistance mediated by the expression of ATP-binding cassete (ABC) transporters (P-gp, ABCB5, ABCC1 and BCRP) and mutant epidermal growth factor receptor (EGFR). The drug sensitivity profiles of several DNA Topo I and II inhibitors were significantly correlated with those of cordycepin’s activity. Among eight different tumor types, prostate cancer was the most sensitive, whereas renal carcinoma was the most resistant to cordycepin. NF-κB was discovered as a common transcription factor. The potential of cordycepin is set forth as a potential new drug lead by bioinformatic evaluations. Further experimental studies are warranted for better understanding of cordycepin’s activity against cancer.
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Affiliation(s)
- Nadire Özenver
- Department of Pharmacognosy, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Joelle C. Boulos
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
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Li Y, Yuan J. Role of deubiquitinating enzymes in DNA double-strand break repair. J Zhejiang Univ Sci B 2021; 22:63-72. [PMID: 33448188 DOI: 10.1631/jzus.b2000309] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA is the hereditary material in humans and almost all other organisms. It is essential for maintaining accurate transmission of genetic information. In the life cycle, DNA replication, cell division, or genome damage, including that caused by endogenous and exogenous agents, may cause DNA aberrations. Of all forms of DNA damage, DNA double-strand breaks (DSBs) are the most serious. If the repair function is defective, DNA damage may cause gene mutation, genome instability, and cell chromosome loss, which in turn can even lead to tumorigenesis. DNA damage can be repaired through multiple mechanisms. Homologous recombination (HR) and non-homologous end joining (NHEJ) are the two main repair mechanisms for DNA DSBs. Increasing amounts of evidence reveal that protein modifications play an essential role in DNA damage repair. Protein deubiquitination is a vital post-translational modification which removes ubiquitin molecules or polyubiquitinated chains from substrates in order to reverse the ubiquitination reaction. This review discusses the role of deubiquitinating enzymes (DUBs) in repairing DNA DSBs. Exploring the molecular mechanisms of DUB regulation in DSB repair will provide new insights to combat human diseases and develop novel therapeutic approaches.
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Affiliation(s)
- Yunhui Li
- The Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jian Yuan
- The Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China. .,Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200092, China.
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28
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Tu Y, Li X, Zhu X, Liu X, Guo C, Jia D, Tang TS. Determining the Fate of Neurons in SCA3: ATX3, a Rising Decision Maker in Response to DNA Stresses and Beyond. Front Cell Dev Biol 2021; 8:619911. [PMID: 33425926 PMCID: PMC7793700 DOI: 10.3389/fcell.2020.619911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/01/2020] [Indexed: 12/14/2022] Open
Abstract
DNA damage response (DDR) and apoptosis are reported to be involved in the pathogenesis of many neurodegenerative diseases including polyglutamine (polyQ) disorders, such as Spinocerebellar ataxia type 3 (SCA3) and Huntington's disease (HD). Consistently, an increasing body of studies provide compelling evidence for the crucial roles of ATX3, whose polyQ expansion is defined as the cause of SCA3, in the maintenance of genome integrity and regulation of apoptosis. The polyQ expansion in ATX3 seems to affect its physiological functions in these distinct pathways. These advances have expanded our understanding of the relationship between ATX3's cellular functions and the underlying molecular mechanism of SCA3. Interestingly, dysregulated DDR pathways also contribute to the pathogenesis of other neurodegenerative disorder such as HD, which presents a common molecular mechanism yet distinct in detail among different diseases. In this review, we provide a comprehensive overview of the current studies about the physiological roles of ATX3 in DDR and related apoptosis, highlighting the crosslinks between these impaired pathways and the pathogenesis of SCA3. Moreover, whether these mechanisms are shared in other neurodegenerative diseases are analyzed. Finally, the preclinical studies targeting DDR and related apoptosis for treatment of polyQ disorders including SCA3 and HD are also summarized and discussed.
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Affiliation(s)
- Yingfeng Tu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Xiaoling Li
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, China
| | - Xuefei Zhu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University Health Science Center, Shenzhen, China
| | - Xiaokang Liu
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, China
| | - Caixia Guo
- Beijing Institute of Genomics (China National Center for Bioinformation), University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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29
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Deol KK, Crowe SO, Du J, Bisbee HA, Guenette RG, Strieter ER. Proteasome-Bound UCH37/UCHL5 Debranches Ubiquitin Chains to Promote Degradation. Mol Cell 2020; 80:796-809.e9. [PMID: 33156996 PMCID: PMC7718437 DOI: 10.1016/j.molcel.2020.10.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 09/13/2020] [Accepted: 10/13/2020] [Indexed: 01/10/2023]
Abstract
The linkage, length, and architecture of ubiquitin (Ub) chains are all important variables in providing tight control over many biological paradigms. There are clear roles for branched architectures in regulating proteasome-mediated degradation, but the proteins that selectively recognize and process these atypical chains are unknown. Here, using synthetic and enzyme-derived ubiquitin chains along with intact mass spectrometry, we report that UCH37/UCHL5, a proteasome-associated deubiquitinase, cleaves K48 branched chains. The activity and selectivity toward branched chains is markedly enhanced by the proteasomal Ub receptor RPN13/ADRM1. Using reconstituted proteasome complexes, we find that chain debranching promotes degradation of substrates modified with branched chains under multi-turnover conditions. These results are further supported by proteome-wide pulse-chase experiments, which show that the loss of UCH37 activity impairs global protein turnover. Our work therefore defines UCH37 as a debranching deubiquitinase important for promoting proteasomal degradation.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sean O Crowe
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jiale Du
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Heather A Bisbee
- Molecular & Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Robert G Guenette
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; Molecular & Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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van den Berk P, Lancini C, Company C, Serresi M, Sanchez-Bailon MP, Hulsman D, Pritchard C, Song JY, Schmitt MJ, Tanger E, Popp O, Mertins P, Huijbers IJ, Jacobs H, van Lohuizen M, Gargiulo G, Citterio E. USP15 Deubiquitinase Safeguards Hematopoiesis and Genome Integrity in Hematopoietic Stem Cells and Leukemia Cells. Cell Rep 2020; 33:108533. [PMID: 33378683 PMCID: PMC7788286 DOI: 10.1016/j.celrep.2020.108533] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 07/28/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
Altering ubiquitination by disruption of deubiquitinating enzymes (DUBs) affects hematopoietic stem cell (HSC) maintenance. However, comprehensive knowledge of DUB function during hematopoiesis in vivo is lacking. Here, we systematically inactivate DUBs in mouse hematopoietic progenitors using in vivo small hairpin RNA (shRNA) screens. We find that multiple DUBs may be individually required for hematopoiesis and identify ubiquitin-specific protease 15 (USP15) as essential for HSC maintenance in vitro and in transplantations and Usp15 knockout (KO) mice in vivo. USP15 is highly expressed in human hematopoietic tissues and leukemias. USP15 depletion in murine progenitors and leukemia cells impairs in vitro expansion and increases genotoxic stress. In leukemia cells, USP15 interacts with and stabilizes FUS (fused in sarcoma), a known DNA repair factor, directly linking USP15 to the DNA damage response (DDR). Our study underscores the importance of DUBs in preserving normal hematopoiesis and uncovers USP15 as a critical DUB in safeguarding genome integrity in HSCs and leukemia cells. In vivo shRNAs screens for deubiquitinases identify regulators of murine hematopoiesis Usp15 deletion compromises HSC maintenance and reconstitution potential in vivo USP15 loss affects genome integrity and growth of mHSPCs and human leukemia cells In human leukemia cells, USP15 stabilizes its interactor, FUS, a DNA repair factor
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Affiliation(s)
- Paul van den Berk
- Division of Tumor Biology and Immunology, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Cesare Lancini
- Division of Molecular Genetics, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Carlos Company
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Michela Serresi
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | | | - Danielle Hulsman
- Division of Molecular Genetics, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands; ONCODE Institute, Utrecht, the Netherlands
| | - Colin Pritchard
- Transgenic Core Facility, Mouse Clinic for Cancer and Aging (MCCA), the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Matthias Jürgen Schmitt
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Ellen Tanger
- Division of Molecular Genetics, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Oliver Popp
- Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Berlin Institute of Health, Robert Rössle Strasse 10, 13125 Berlin, Germany
| | - Philipp Mertins
- Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Berlin Institute of Health, Robert Rössle Strasse 10, 13125 Berlin, Germany
| | - Ivo J Huijbers
- Transgenic Core Facility, Mouse Clinic for Cancer and Aging (MCCA), the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands; ONCODE Institute, Utrecht, the Netherlands
| | - Gaetano Gargiulo
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany.
| | - Elisabetta Citterio
- Division of Molecular Genetics, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands; ONCODE Institute, Utrecht, the Netherlands.
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Sharma A, Almasan A. USP14 Regulates DNA Damage Response and Is a Target for Radiosensitization in Non-Small Cell Lung Cancer. Int J Mol Sci 2020; 21:E6383. [PMID: 32887472 PMCID: PMC7503721 DOI: 10.3390/ijms21176383] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 01/09/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) represents ~85% of the lung cancer cases. Despite recent advances in NSCLC treatment, the five-year survival rate is still around 23%. Radiotherapy is indicated in the treatment of both early and advanced stage NSCLC; however, treatment response in patients is heterogeneous. Thus, identification of new and more effective treatment combinations is warranted. We have identified Ubiquitin-specific protease 14 (USP14) s a regulator of major double-strand break (DSB) repair pathways in response to ionizing radiation (IR) by its impact on both non-homologous end joining (NHEJ) and homologous recombination (HR) in NSCLC. USP14 is a proteasomal deubiquitinase. IR treatment increases levels and DSB recruitment of USP14 in NSCLC cell lines. Genetic knockdown, using shUSP14 expression or pharmacological inhibition of USP14, using IU1, increases radiosensitization in NSCLC cell lines, as determined by a clonogenic survival assay. Moreover, shUSP14-expressing NSCLC cells show increased NHEJ efficiency, as indicated by chromatin recruitment of key NHEJ proteins, NHEJ reporter assay, and increased IR-induced foci formation by 53BP1 and pS2056-DNA-PKcs. Conversely, shUSP14-expressing NSCLC cells show decreased RPA32 and BRCA1 foci formation, suggesting HR-deficiency. These findings identify USP14 as an important determinant of DSB repair in response to radiotherapy and a promising target for NSCLC radiosensitization.
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Affiliation(s)
- Arishya Sharma
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Alexandru Almasan
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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Impact of Losing hRpn13 Pru or UCHL5 on Proteasome Clearance of Ubiquitinated Proteins and RA190 Cytotoxicity. Mol Cell Biol 2020; 40:MCB.00122-20. [PMID: 32631902 DOI: 10.1128/mcb.00122-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/26/2020] [Indexed: 01/18/2023] Open
Abstract
hRpn13/ADRM1 links substrate recruitment with deubiquitination at the proteasome through its proteasome- and ubiquitin-binding Pru domain and DEUBAD domain, which binds and activates deubiquitinating enzyme (DUB) UCHL5/Uch37. Here, we edit the HCT116 colorectal cancer cell line to delete part of the hRpn13 Pru, producing cells that express truncated hRpn13 (trRpn13), which is competent for UCHL5 binding but defective for proteasome interaction. trRpn13 cells demonstrate reduced levels of proteasome-bound ubiquitinated proteins, indicating that the loss of hRpn13 function at proteasomes cannot be fully compensated for by the two other dedicated substrate receptors (hRpn1 and hRpn10). Previous studies indicated that the loss of full-length hRpn13 causes a corresponding reduction of UCHL5. We find UCHL5 levels unaltered in trRpn13 cells, but hRpn11 is elevated in ΔhRpn13 and trRpn13 cells, perhaps from cell stress. Despite the ∼90 DUBs in human cells, including two others in addition to UCHL5 at the proteasome, we found deletion of UCHL5 from HCT116 cells to cause increased levels of ubiquitinated proteins in whole-cell extract and at proteasomes, suggesting that UCHL5 activity cannot be fully assumed by other DUBs. We also report anticancer molecule RA190, which binds covalently to hRpn13 and UCHL5, to require hRpn13 Pru and not UCHL5 for cytotoxicity.
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Dickson P, Simanski S, Ngundu JM, Kodadek T. Mechanistic Studies of the Multiple Myeloma and Melanoma Cell-Selective Toxicity of the Rpn13-Binding Peptoid KDT-11. Cell Chem Biol 2020; 27:1383-1395.e5. [PMID: 32857986 DOI: 10.1016/j.chembiol.2020.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/22/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022]
Abstract
We previously reported a peptoid ligand for the proteasomal ubiquitin receptor Rpn13 called KDT-11 and demonstrated that this compound is toxic to multiple myeloma cells, but not non-malignant cells. Here, we show that KDT-11 decreases the viability of a variety of cancer cell lines, especially melanomas and various blood cancers. The peptoid induces selective G1 cell-cycle arrest, resulting in eventual apoptosis. While KDT-11 does not antagonize any of the known protein-protein interactions involving Rpn13, the peptoid inhibits the ability of Rpn13 to stimulate the activity of an associated deubiquitylase Uch37/UCHL5 in vitro, suggesting a high level of Uch37 activity might be important for cancer cell proliferation. However, a variety of experiments in SK-MEL-5 melanoma cells suggest that KDT-11's cytotoxic effects are mediated by interactions with proteins other than Rpn13.
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Affiliation(s)
- Paige Dickson
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Scott Simanski
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - John Maina Ngundu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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Zhang T, Sun J, Cheng J, Yin W, Li J, Miller H, Herrada AA, Gu H, Song H, Chen Y, Gong Q, Liu C. The role of ubiquitinase in B cell development and function. J Leukoc Biol 2020; 109:395-405. [PMID: 32816356 DOI: 10.1002/jlb.1mr0720-185rr] [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: 08/01/2019] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 11/10/2022] Open
Abstract
Ubiquitinases are a select group of enzymes that modify target proteins through ubiquitination, which plays a crucial role in the regulation of protein degradation, location, and function. B lymphocytes that originated from bone marrow hematopoietic stem cells (HSC), exert humoral immune functions by differentiating into plasma cells and producing antibodies. Previous studies have shown that ubiquitination is involved in the regulation of the cell cycle and signal transduction important for B lymphocyte development and function. In this review, how ubiquitinases regulate B cell development, activation, apoptosis, and proliferation is discussed, which could help in understanding the physiological processes and diseases related to B cells and also provides potential new targets for further studies.
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Affiliation(s)
- Tong Zhang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianxuan Sun
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiali Cheng
- Department of hematology, Tongji Hospital, Tongji Medical college, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yin
- Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingwen Li
- Department of hematology, Wuhan Union Hospital, Tongji Medical college, Huazhong University of Science and Technology, Wuhan, China
| | - Heather Miller
- Department of Intracellular Pathogens, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Andrés A Herrada
- Lymphatic and Inflammation Research Laboratory, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Talca, Chile
| | - Heng Gu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongmei Song
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No 1, Shuaifuyuan, Dongcheng District, Beijing, China
| | - Yan Chen
- The Second Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Quan Gong
- Department of Immunology, School of Medicine, Yangtze University, Jingzhou, China.,Clinical Molecular Immunology Center, School of Medicine, Yangtze University, Jingzhou, China
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Regulation of Histone Ubiquitination in Response to DNA Double Strand Breaks. Cells 2020; 9:cells9071699. [PMID: 32708614 PMCID: PMC7407225 DOI: 10.3390/cells9071699] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic cells are constantly exposed to both endogenous and exogenous stressors that promote the induction of DNA damage. Of this damage, double strand breaks (DSBs) are the most lethal and must be efficiently repaired in order to maintain genomic integrity. Repair of DSBs occurs primarily through one of two major pathways: non-homologous end joining (NHEJ) or homologous recombination (HR). The choice between these pathways is in part regulated by histone post-translational modifications (PTMs) including ubiquitination. Ubiquitinated histones not only influence transcription and chromatin architecture at sites neighboring DSBs but serve as critical recruitment platforms for repair machinery as well. The reversal of these modifications by deubiquitinating enzymes (DUBs) is increasingly being recognized in a number of cellular processes including DSB repair. In this context, DUBs ensure proper levels of ubiquitin, regulate recruitment of downstream effectors, dictate repair pathway choice, and facilitate appropriate termination of the repair response. This review outlines the current understanding of histone ubiquitination in response to DSBs, followed by a comprehensive overview of the DUBs that catalyze the removal of these marks.
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Ubiquitylation-Mediated Fine-Tuning of DNA Double-Strand Break Repair. Cancers (Basel) 2020; 12:cancers12061617. [PMID: 32570875 PMCID: PMC7352447 DOI: 10.3390/cancers12061617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 01/04/2023] Open
Abstract
The proper function of DNA repair is indispensable for eukaryotic cells since accumulation of DNA damages leads to genome instability and is a major cause of oncogenesis. Ubiquitylation and deubiquitylation play a pivotal role in the precise regulation of DNA repair pathways by coordinating the recruitment and removal of repair proteins at the damaged site. Here, we summarize the most important post-translational modifications (PTMs) involved in DNA double-strand break repair. Although we highlight the most relevant PTMs, we focus principally on ubiquitylation-related processes since these are the most robust regulatory pathways among those of DNA repair.
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Matsui M, Sakasai R, Abe M, Kimura Y, Kajita S, Torii W, Katsuki Y, Ishiai M, Iwabuchi K, Takata M, Nishi R. USP42 enhances homologous recombination repair by promoting R-loop resolution with a DNA-RNA helicase DHX9. Oncogenesis 2020; 9:60. [PMID: 32541651 PMCID: PMC7296013 DOI: 10.1038/s41389-020-00244-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/21/2020] [Accepted: 05/29/2020] [Indexed: 01/05/2023] Open
Abstract
The nucleus of mammalian cells is compartmentalized by nuclear bodies such as nuclear speckles, however, involvement of nuclear bodies, especially nuclear speckles, in DNA repair has not been actively investigated. Here, our focused screen for nuclear speckle factors involved in homologous recombination (HR), which is a faithful DNA double-strand break (DSB) repair mechanism, identified transcription-related nuclear speckle factors as potential HR regulators. Among the top hits, we provide evidence showing that USP42, which is a hitherto unidentified nuclear speckles protein, promotes HR by facilitating BRCA1 recruitment to DSB sites and DNA-end resection. We further showed that USP42 localization to nuclear speckles is required for efficient HR. Furthermore, we established that USP42 interacts with DHX9, which possesses DNA-RNA helicase activity, and is required for efficient resolution of DSB-induced R-loop. In conclusion, our data propose a model in which USP42 facilitates BRCA1 loading to DSB sites, resolution of DSB-induced R-loop and preferential DSB repair by HR, indicating the importance of nuclear speckle-mediated regulation of DSB repair.
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Affiliation(s)
- Misaki Matsui
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Ryo Sakasai
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Masako Abe
- Department of Late Effects Studies, Radiation Biology Centre, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Yusuke Kimura
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Shoki Kajita
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Wakana Torii
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Yoko Katsuki
- Department of Late Effects Studies, Radiation Biology Centre, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Masamichi Ishiai
- Central Radioisotope Division, National Cancer Centre Research Institute, Chuoku, Tokyo, 104-0045, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Minoru Takata
- Department of Late Effects Studies, Radiation Biology Centre, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Ryotaro Nishi
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan. .,School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo, 192-0982, Japan.
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Zhang Z, Hu X, Kuang J, Liao J, Yuan Q. LncRNA DRAIC inhibits proliferation and metastasis of gastric cancer cells through interfering with NFRKB deubiquitination mediated by UCHL5. Cell Mol Biol Lett 2020; 25:29. [PMID: 32351584 PMCID: PMC7183705 DOI: 10.1186/s11658-020-00221-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 04/13/2020] [Indexed: 12/24/2022] Open
Abstract
Background Long non-coding RNA (lncRNA) as a widespread and pivotal epigenetic molecule participates in the occurrence and progression of malignant tumors. DRAIC, a kind of lncRNA whose coding gene location is on 15q23 chromatin, has been found to be weakly expressed in a variety of malignant tumors and acts as a suppressor, but its characteristics and role in gastric cancer (GC) remain to be elucidated. Methods Sixty-seven primary GC tissues and paired paracancerous normal tissues were collected. Bioinformatics is used to predict the interaction molecules of DRAIC. DRAIC and NFRKB were overexpressed or interfered exogenously in GC cells by lentivirus or transient transfection. Quantitative real-time PCR (qPCR) and western blotting were used to evaluate the expression of DRAIC, UCHL5 and NFRKB. The combinations of DRAIC and NFRKB or UCHL5 and NFRKB were verified by RNA-IP and Co-IP assays. Ubiquitination-IP and the treatment of MG132 and CHX were used to detect the ubiquitylation level of NFRKB. The CCK-8 and transwell invasion and migration assays measured the proliferation, migration and invasion of GC cells. Results DRAIC is down-regulated in GC tissues and cell lines while its potential interacting molecules UCHL5 and NFRKB are up-regulated, and DRAIC is positively correlated with NFRKB protein instead of mRNA. Lower DRAIC and higher UCHL5 and NFRKB indicated advanced progression of GC patients. DRAIC could increase NFRKB protein significantly instead of NFRKB mRNA and UCHL5, and bind to UCHL5. DRAIC combined with UCHL5 and attenuated binding of UCHL5 and NFRKB, meanwhile promoting the degradation of NFRKB via ubiquitination, and then inhibited the proliferation and metastasis of GC cells, which can be rescued by oeNFRKB. Conclusion DRAIC suppresses GC proliferation and metastasis via interfering with the combination of UCHL5 and NFRKB and mediating ubiquitination degradation.
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Affiliation(s)
- Zheng Zhang
- Department of Hepatopathy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000 Hunan Province China
| | - Xiaoxuan Hu
- Department of Hepatopathy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000 Hunan Province China
| | - Jia Kuang
- Department of Hepatopathy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000 Hunan Province China
| | - Jinmao Liao
- Department of Hepatopathy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000 Hunan Province China
| | - Qi Yuan
- Department of Hepatopathy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000 Hunan Province China
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Fiore A, Liang Y, Lin YH, Tung J, Wang H, Langlais D, Nijnik A. Deubiquitinase MYSM1 in the Hematopoietic System and beyond: A Current Review. Int J Mol Sci 2020; 21:ijms21083007. [PMID: 32344625 PMCID: PMC7216186 DOI: 10.3390/ijms21083007] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 01/21/2023] Open
Abstract
MYSM1 has emerged as an important regulator of hematopoietic stem cell function, blood cell production, immune response, and other aspects of mammalian physiology. It is a metalloprotease family protein with deubiquitinase catalytic activity, as well as SANT and SWIRM domains. MYSM1 normally localizes to the nucleus, where it can interact with chromatin and regulate gene expression, through deubiquitination of histone H2A and non-catalytic contacts with other transcriptional regulators. A cytosolic form of MYSM1 protein was also recently described and demonstrated to regulate signal transduction pathways of innate immunity, by promoting the deubiquitination of TRAF3, TRAF6, and RIP2. In this work we review the current knowledge on the molecular mechanisms of action of MYSM1 protein in transcriptional regulation, signal transduction, and potentially other cellular processes. The functions of MYSM1 in different cell types and aspects of mammalian physiology are also reviewed, highlighting the key checkpoints in hematopoiesis, immunity, and beyond regulated by MYSM1. Importantly, mutations in MYSM1 in human were recently linked to a rare hereditary disorder characterized by leukopenia, anemia, and other hematopoietic and developmental abnormalities. Our growing knowledge of MYSM1 functions and mechanisms of actions sheds important insights into its role in mammalian physiology and the etiology of the MYSM1-deficiency disorder in human.
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Affiliation(s)
- Amanda Fiore
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - Yue Liang
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - Yun Hsiao Lin
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - Jacky Tung
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
| | - HanChen Wang
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
- Department of Human Genetics, McGill University, Montreal, QC 3640, Canada
| | - David Langlais
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
- Department of Human Genetics, McGill University, Montreal, QC 3640, Canada
- McGill University Genome Centre, Montreal, QC 740, Canada
| | - Anastasia Nijnik
- Department of Physiology, McGill University, Montreal, QC 3655, Canada; (A.F.); (Y.L.); (Y.H.L.); (J.T.); (H.W.)
- Research Centre on Complex Traits, McGill University, Montreal, QC 3649, Canada;
- Correspondence: ; Tel.: +1-514-398-5567
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Lai KP, Chen J, Tse WKF. Role of Deubiquitinases in Human Cancers: Potential Targeted Therapy. Int J Mol Sci 2020; 21:ijms21072548. [PMID: 32268558 PMCID: PMC7177317 DOI: 10.3390/ijms21072548] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 02/06/2023] Open
Abstract
Deubiquitinases (DUBs) are involved in various cellular functions. They deconjugate ubiquitin (UBQ) from ubiquitylated substrates to regulate their activity and stability. Studies on the roles of deubiquitylation have been conducted in various cancers to identify the carcinogenic roles of DUBs. In this review, we evaluate the biological roles of DUBs in cancer, including proliferation, cell cycle control, apoptosis, the DNA damage response, tumor suppression, oncogenesis, and metastasis. This review mainly focuses on the regulation of different downstream effectors and pathways via biochemical regulation and posttranslational modifications. We summarize the relationship between DUBs and human cancers and discuss the potential of DUBs as therapeutic targets for cancer treatment. This review also provides basic knowledge of DUBs in the development of cancers and highlights the importance of DUBs in cancer biology.
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Affiliation(s)
- Keng Po Lai
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541004, China;
| | - Jian Chen
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541004, China;
- Correspondence: (J.C.); (W.K.F.T.); Tel.: +86-773-5895810 (J.C.); +81-92-802-4767 (W.K.F.T.)
| | - William Ka Fai Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
- Correspondence: (J.C.); (W.K.F.T.); Tel.: +86-773-5895810 (J.C.); +81-92-802-4767 (W.K.F.T.)
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Das S, Ramakrishna S, Kim KS. Critical Roles of Deubiquitinating Enzymes in the Nervous System and Neurodegenerative Disorders. Mol Cells 2020; 43:203-214. [PMID: 32133826 PMCID: PMC7103888 DOI: 10.14348/molcells.2020.2289] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/10/2020] [Accepted: 02/02/2020] [Indexed: 12/15/2022] Open
Abstract
Post-translational modifications play major roles in the stability, function, and localization of target proteins involved in the nervous system. The ubiquitin-proteasome pathway uses small ubiquitin molecules to degrade neuronal proteins. Deubiquitinating enzymes (DUBs) reverse this degradation and thereby control neuronal cell fate, synaptic plasticity,axonal growth, and proper function of the nervous system.Moreover, mutations or downregulation of certain DUBshave been found in several neurodegenerative diseases, as well as gliomas and neuroblastomas. Based on emerging findings, DUBs represent an important target for therapeutic intervention in various neurological disorders. Here, we summarize advances in our understanding of the roles of DUBs related to neurobiology.
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Affiliation(s)
- Soumyadip Das
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
- College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
- College of Medicine, Hanyang University, Seoul 04763, Korea
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Sen Nkwe N, Daou S, Uriarte M, Gagnon J, Iannantuono NV, Barbour H, Yu H, Masclef L, Fernández E, Zamorano Cuervo N, Mashtalir N, Binan L, Sergeev M, Bélanger F, Drobetsky E, Milot E, Wurtele H, Costantino S, Affar EB. A potent nuclear export mechanism imposes USP16 cytoplasmic localization during interphase. J Cell Sci 2020; 133:jcs239236. [PMID: 32005696 DOI: 10.1242/jcs.239236] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/13/2020] [Indexed: 01/09/2023] Open
Abstract
USP16 (also known as UBP-M) has emerged as a histone H2AK119 deubiquitylase (DUB) implicated in the regulation of chromatin-associated processes and cell cycle progression. Despite this, available evidence suggests that this DUB is also present in the cytoplasm. How the nucleo-cytoplasmic transport of USP16, and hence its function, is regulated has remained elusive. Here, we show that USP16 is predominantly cytoplasmic in all cell cycle phases. We identified the nuclear export signal (NES) responsible for maintaining USP16 in the cytoplasm. We found that USP16 is only transiently retained in the nucleus following mitosis and then rapidly exported from this compartment. We also defined a non-canonical nuclear localization signal (NLS) sequence that plays a minimal role in directing USP16 into the nucleus. We further established that this DUB does not accumulate in the nucleus following DNA damage. Instead, only enforced nuclear localization of USP16 abolishes DNA double-strand break (DSB) repair, possibly due to unrestrained DUB activity. Thus, in contrast to the prevailing view, our data indicate that USP16 is actively excluded from the nucleus and that this DUB might indirectly regulate DSB repair.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Nadine Sen Nkwe
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Salima Daou
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Maxime Uriarte
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Jessica Gagnon
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, QC H3T 1J4, Canada
| | - Nicholas Victor Iannantuono
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, QC H3T 1J4, Canada
| | - Haithem Barbour
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Helen Yu
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Louis Masclef
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Erlinda Fernández
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Natalia Zamorano Cuervo
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, QC H2X 0A9, Canada
| | - Nazar Mashtalir
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Loïc Binan
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Ophthalmology, University of Montréal, Montréal, Québec, Canada
| | - Mikhail Sergeev
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - François Bélanger
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Elliot Drobetsky
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Eric Milot
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Hugo Wurtele
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Santiago Costantino
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Ophthalmology, University of Montréal, Montréal, Québec, Canada
| | - El Bachir Affar
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
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43
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Garvin AJ. Beyond reversal: ubiquitin and ubiquitin-like proteases and the orchestration of the DNA double strand break repair response. Biochem Soc Trans 2019; 47:1881-1893. [PMID: 31769469 PMCID: PMC6925521 DOI: 10.1042/bst20190534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022]
Abstract
The cellular response to genotoxic DNA double strand breaks (DSBs) uses a multitude of post-translational modifications to localise, modulate and ultimately clear DNA repair factors in a timely and accurate manner. Ubiquitination is well established as vital to the DSB response, with a carefully co-ordinated pathway of histone ubiquitination events being a central component of DSB signalling. Other ubiquitin-like modifiers (Ubl) including SUMO and NEDD8 have since been identified as playing important roles in DSB repair. In the last five years ∼20 additional Ub/Ubl proteases have been implicated in the DSB response. The number of proteases identified highlights the complexity of the Ub/Ubl signal present at DSBs. Ub/Ubl proteases regulate turnover, activity and protein-protein interactions of DSB repair factors both catalytically and non-catalytically. This not only ensures efficient repair of breaks but has a role in channelling repair into the correct DSB repair sub-pathways. Ultimately Ub/Ubl proteases have essential roles in maintaining genomic stability. Given that deficiencies in many Ub/Ubl proteases promotes sensitivity to DNA damaging chemotherapies, they could be attractive targets for cancer treatment.
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Affiliation(s)
- Alexander J. Garvin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, U.K
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44
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Ting X, Xia L, Yang J, He L, Si W, Shang Y, Sun L. USP11 acts as a histone deubiquitinase functioning in chromatin reorganization during DNA repair. Nucleic Acids Res 2019; 47:9721-9740. [PMID: 31504778 PMCID: PMC6765148 DOI: 10.1093/nar/gkz726] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 08/03/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022] Open
Abstract
How chromatin dynamics is regulated to ensure efficient DNA repair remains to be understood. Here, we report that the ubiquitin-specific protease USP11 acts as a histone deubiquitinase to catalyze H2AK119 and H2BK120 deubiquitination. We showed that USP11 is physically associated with the chromatin remodeling NuRD complex and functionally involved in DNA repair process. We demonstrated that USP11-mediated histone deubiquitination and NuRD-associated histone deacetylation coordinate to allow timely termination of DNA repair and reorganization of the chromatin structure. As such, USP11 is involved in chromatin condensation, genomic stability, and cell survival. Together, these observations indicate that USP11 is a chromatin modifier critically involved in DNA damage response and the maintenance of genomic stability.
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Affiliation(s)
- Xia Ting
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lu Xia
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Wenzhe Si
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Yongfeng Shang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Luyang Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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45
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Li M, Huang T, Li MJ, Zhang CX, Yu XC, Yin YY, Liu C, Wang X, Feng HW, Zhang T, Liu MF, Han CS, Lu G, Li W, Ma JL, Chen ZJ, Liu HB, Liu K. The histone modification reader ZCWPW1 is required for meiosis prophase I in male but not in female mice. SCIENCE ADVANCES 2019; 5:eaax1101. [PMID: 31453335 PMCID: PMC6693912 DOI: 10.1126/sciadv.aax1101] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/08/2019] [Indexed: 05/12/2023]
Abstract
Meiosis is a specialized type of cell division that creates haploid germ cells and ensures their genetic diversity through homologous recombination. We show that the H3K4me3 reader ZCWPW1 is specifically required for meiosis prophase I progression in male but not in female germ cells in mice. Loss of Zcwpw1 in male mice caused a complete failure of synapsis, resulting in meiotic arrest at the zygotene to pachytene stage, accompanied by incomplete DNA double-strand break repair and lack of crossover formation, leading to male infertility. In oocytes, deletion of Zcwpw1 only somewhat slowed down meiosis prophase I progression; Zcwpw1-/- oocytes were able to complete meiosis, and Zcwpw1-/- female mice had normal fertility until mid-adulthood. We conclude that the H3K4me3 reader ZCWPW1 is indispensable for meiosis synapsis in males but is dispensable for females. Our results suggest that ZCWPW1 may represent a previously unknown, sex-dependent epigenetic regulator of germ cell meiosis in mammals.
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Affiliation(s)
- Miao Li
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Tao Huang
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Meng-Jing Li
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Chuan-Xin Zhang
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Xiao-Chen Yu
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Ying-Ying Yin
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hai-Wei Feng
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, Haiyuan First Road 1, Shenzhen, Guangdong 518053 China
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tuo Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Chun-Sheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Lu
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Long Ma
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University and Shanghai Key Laboratory of Assisted Reproduction and Reproductive Genetics, Shanghai 200031, China
| | - Hong-Bin Liu
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250001, China
- The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, Shandong 250001, China
- Corresponding author. (H.-B.L.); (K.L.)
| | - Kui Liu
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong-Shenzhen Hospital, Haiyuan First Road 1, Shenzhen, Guangdong 518053 China
- Department of Obstetrics and Gynecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Corresponding author. (H.-B.L.); (K.L.)
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Human MLL/KMT2A gene exhibits a second breakpoint cluster region for recurrent MLL-USP2 fusions. Leukemia 2019; 33:2306-2340. [PMID: 30899083 PMCID: PMC6756029 DOI: 10.1038/s41375-019-0451-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/15/2019] [Accepted: 03/08/2019] [Indexed: 01/10/2023]
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47
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Carter RJ, Nickson CM, Thompson JM, Kacperek A, Hill MA, Parsons JL. Characterisation of Deubiquitylating Enzymes in the Cellular Response to High-LET Ionizing Radiation and Complex DNA Damage. Int J Radiat Oncol Biol Phys 2019; 104:656-665. [PMID: 30851349 PMCID: PMC6542414 DOI: 10.1016/j.ijrobp.2019.02.053] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/31/2019] [Accepted: 02/26/2019] [Indexed: 12/11/2022]
Abstract
PURPOSE Ionizing radiation, particular high-linear energy transfer (LET) radiation, can induce complex DNA damage (CDD) wherein 2 or more DNA lesions are induced in close proximity, which contributes significantly to the cell killing effects. However, knowledge of the enzymes and mechanisms involved in coordinating the recognition and processing of CDD in cellular DNA are currently lacking. METHODS AND MATERIALS A small interfering RNA screen of deubiquitylation enzymes was conducted in HeLa cells irradiated with high-LET α-particles or protons, versus low-LET protons and x-rays, and cell survival was monitored by clonogenic assays. Candidates whose depletion led to decreased cell survival specifically in response to high-LET radiation were validated in both HeLa and oropharyngeal squamous cell carcinoma (UMSCC74A) cells, and the association with CDD repair was confirmed using an enzyme modified neutral comet assay. RESULTS Depletion of USP6 decreased cell survival specifically after high-LET α-particles and protons, but not low-LET protons or x-rays. USP6 depletion caused cell cycle arrest and a deficiency in CDD repair mediated through instability of poly(ADP-ribose) polymerase-1 (PARP-1) protein. Increased radiosensitivity of cells to high-LET protons as a consequence of defective CDD repair was furthermore mimicked using the PARP inhibitor olaparib, and through PARP-1 small interfering RNA. CONCLUSIONS USP6 controls cell survival in response to high-LET radiation by stabilizing PARP-1 protein levels, which is essential for CDD repair. We also describe synergy between CDD induced by high-LET protons and PARP inhibition, or PARP-1 depletion, in effective cancer cell killing.
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Affiliation(s)
- Rachel J Carter
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Catherine M Nickson
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - James M Thompson
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Gray Laboratories, Oxford, United Kingdom
| | - Andrzej Kacperek
- The National Eye Proton Therapy Centre, The Clatterbridge Cancer Centre NHS Foundation Trust, Bebington, United Kingdom
| | - Mark A Hill
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Gray Laboratories, Oxford, United Kingdom
| | - Jason L Parsons
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom.
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48
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Garvin AJ, Walker AK, Densham RM, Chauhan AS, Stone HR, Mackay HL, Jamshad M, Starowicz K, Daza-Martin M, Ronson GE, Lanz AJ, Beesley JF, Morris JR. The deSUMOylase SENP2 coordinates homologous recombination and nonhomologous end joining by independent mechanisms. Genes Dev 2019; 33:333-347. [PMID: 30796017 PMCID: PMC6411010 DOI: 10.1101/gad.321125.118] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/21/2018] [Indexed: 12/18/2022]
Abstract
SUMOylation (small ubiquitin-like modifier) in the DNA double-strand break (DSB) response regulates recruitment, activity, and clearance of repair factors. However, our understanding of a role for deSUMOylation in this process is limited. Here we identify different mechanistic roles for deSUMOylation in homologous recombination (HR) and nonhomologous end joining (NHEJ) through the investigation of the deSUMOylase SENP2. We found that regulated deSUMOylation of MDC1 prevents excessive SUMOylation and its RNF4-VCP mediated clearance from DSBs, thereby promoting NHEJ. In contrast, we show that HR is differentially sensitive to SUMO availability and SENP2 activity is needed to provide SUMO. SENP2 is amplified as part of the chromosome 3q amplification in many cancers. Increased SENP2 expression prolongs MDC1 focus retention and increases NHEJ and radioresistance. Collectively, our data reveal that deSUMOylation differentially primes cells for responding to DSBs and demonstrates the ability of SENP2 to tune DSB repair responses.
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Affiliation(s)
- Alexander J Garvin
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Alexandra K Walker
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Ruth M Densham
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Anoop Singh Chauhan
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Helen R Stone
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Hannah L Mackay
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Mohammed Jamshad
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Katarzyna Starowicz
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Manuel Daza-Martin
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - George E Ronson
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Alexander J Lanz
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - James F Beesley
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Joanna R Morris
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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Role of deubiquitinases in DNA damage response. DNA Repair (Amst) 2019; 76:89-98. [PMID: 30831436 DOI: 10.1016/j.dnarep.2019.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 12/13/2022]
Abstract
DNA damage response (DDR) serves as an integrated cellular network to detect cellular stress and react by activating pathways responsible for halting cell cycle progression, stimulating DNA damage repair, and initiating apoptosis. Efficient DDR protects cells from genomic instability while defective DDR can allow DNA lesions to go unrepaired, causing permanent mutations that will affect future generations of cells and possibly cause disease conditions such as cancer. Therefore, DDR mechanisms must be tightly regulated in order to ensure organismal health and viability. One major way of DDR regulation is ubiquitination, which has been long known to control DDR protein localization, activity, and stability. The reversal of this process, deubiquitination, has more recently come to the forefront of DDR research as an important new angle in ubiquitin-mediated regulation of DDR. As such, deubiquitinases have emerged as key factors in DDR. Importantly, deubiquitinases are attractive small-molecule drug targets due to their well-defined catalytic residues that provide a promising avenue for developing new cancer therapeutics. This review focuses on the emerging roles of deubiquitinases in various DNA repair pathways.
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Clague MJ, Urbé S, Komander D. Breaking the chains: deubiquitylating enzyme specificity begets function. Nat Rev Mol Cell Biol 2019; 20:338-352. [DOI: 10.1038/s41580-019-0099-1] [Citation(s) in RCA: 315] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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