1
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Kar P, Chatrin C, Đukić N, Suyari O, Schuller M, Zhu K, Prokhorova E, Bigot N, Ahel J, Elsborg JD, Nielsen ML, Clausen T, Huet S, Niepel M, Sanyal S, Ahel D, Smith R, Ahel I. PARP14 and PARP9/DTX3L regulate interferon-induced ADP-ribosylation. EMBO J 2024:10.1038/s44318-024-00126-0. [PMID: 38834853 DOI: 10.1038/s44318-024-00126-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024] Open
Abstract
PARP-catalysed ADP-ribosylation (ADPr) is important in regulating various cellular pathways. Until recently, PARP-dependent mono-ADP-ribosylation has been poorly understood due to the lack of sensitive detection methods. Here, we utilised an improved antibody to detect mono-ADP-ribosylation. We visualised endogenous interferon (IFN)-induced ADP-ribosylation and show that PARP14 is a major enzyme responsible for this modification. Fittingly, this signalling is reversed by the macrodomain from SARS-CoV-2 (Mac1), providing a possible mechanism by which Mac1 counteracts the activity of antiviral PARPs. Our data also elucidate a major role of PARP9 and its binding partner, the E3 ubiquitin ligase DTX3L, in regulating PARP14 activity through protein-protein interactions and by the hydrolytic activity of PARP9 macrodomain 1. Finally, we also present the first visualisation of ADPr-dependent ubiquitylation in the IFN response. These approaches should further advance our understanding of IFN-induced ADPr and ubiquitin signalling processes and could shed light on how different pathogens avoid such defence pathways.
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Affiliation(s)
- Pulak Kar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
- Department of Biological Sciences, SRM University-AP, Amaravati, 522502, India
| | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Nina Đukić
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Osamu Suyari
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Nicolas Bigot
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT - UMS3480, F-35000, Rennes, France
| | - Juraj Ahel
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Jonas Damgaard Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT - UMS3480, F-35000, Rennes, France
| | | | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Rebecca Smith
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
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2
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Ribeiro VC, Russo LC, Hoch NC. PARP14 is regulated by the PARP9/DTX3L complex and promotes interferon γ-induced ADP-ribosylation. EMBO J 2024:10.1038/s44318-024-00125-1. [PMID: 38834852 DOI: 10.1038/s44318-024-00125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024] Open
Abstract
Protein ADP-ribosylation plays important but ill-defined roles in antiviral signalling cascades such as the interferon response. Several viruses of clinical interest, including coronaviruses, express hydrolases that reverse ADP-ribosylation catalysed by host enzymes, suggesting an important role for this modification in host-pathogen interactions. However, which ADP-ribosyltransferases mediate host ADP-ribosylation, what proteins and pathways they target and how these modifications affect viral infection and pathogenesis is currently unclear. Here we show that host ADP-ribosyltransferase activity induced by IFNγ signalling depends on PARP14 catalytic activity and that the PARP9/DTX3L complex is required to uphold PARP14 protein levels via post-translational mechanisms. Both the PARP9/DTX3L complex and PARP14 localise to IFNγ-induced cytoplasmic inclusions containing ADP-ribosylated proteins, and both PARP14 itself and DTX3L are likely targets of PARP14 ADP-ribosylation. We provide evidence that these modifications are hydrolysed by the SARS-CoV-2 Nsp3 macrodomain, shedding light on the intricate cross-regulation between IFN-induced ADP-ribosyltransferases and the potential roles of the coronavirus macrodomain in counteracting their activity.
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Affiliation(s)
| | | | - Nícolas Carlos Hoch
- Department of Biochemistry, University of São Paulo, São Paulo, 05508-000, Brazil.
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3
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Saleh H, Liloglou T, Rigden DJ, Parsons JL, Grundy GJ. KH-like Domains in PARP9/DTX3L and PARP14 Coordinate Protein-Protein Interactions to Promote Cancer Cell Survival. J Mol Biol 2024; 436:168434. [PMID: 38182103 PMCID: PMC11080071 DOI: 10.1016/j.jmb.2023.168434] [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: 09/18/2023] [Revised: 12/12/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
Certain members of the ADP-ribosyltransferase superfamily (ARTD or PARP enzymes) catalyse ADP-ribosylation in response to cellular stress, DNA damage and viral infection and are upregulated in various tumours. PARP9, its binding partner DTX3L and PARP14 protein levels are significantly correlated in head and neck squamous cell carcinoma (HNSCC) and other tumour types though a mechanism where PARP9/DTX3L regulates PARP14 post-transcriptionally. Depleting PARP9, DTX3L or PARP14 expression in HNSCC or HeLa cell lines decreases cell survival through a reduction of proliferation and an increase in apoptosis. A partial rescue of survival was achieved by expressing a PARP14 truncation containing a predicted eukaryotic type I KH domain. KH-like domains were also found in PARP9 and in DTX3L and contributed to protein-protein interactions between PARP9-DTX3L and PARP14-DTX3L. Homodimerization of DTX3L was also coordinated by a KH-like domain and was disrupted by site-specific mutation. Although, cell survival promoted by PARP14 did not require ADP-ribosyltransferase activity, interaction of DTX3L in vitro suppressed PARP14 auto-ADP-ribosylation and promoted trans-ADP-ribosylation of PARP9 and DTX3L. In summary, we characterised PARP9-DTX3L-PARP14 interactions important to pro-survival signalling in HNSCC cells, albeit in PARP14 catalytically independent fashion.
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Affiliation(s)
- Hadil Saleh
- University of Liverpool, Department of Molecular and Clinical Cancer Medicine, 6 West Derby St, Liverpool L7 8TX, UK
| | - Triantafillos Liloglou
- Edge Hill University, Faculty of Health, Social Care & Medicine, St Helens Road, Ormskirk, Lancashire L39 4QP, UK
| | - Daniel J Rigden
- University of Liverpool, Department of Biochemistry, Cell and Systems Biology, Liverpool L69 7ZB, UK
| | - Jason L Parsons
- University of Birmingham, Institute of Cancer and Genomic Sciences, IBR West, Birmingham B15 2TT, UK
| | - Gabrielle J Grundy
- University of Liverpool, Department of Molecular and Clinical Cancer Medicine, 6 West Derby St, Liverpool L7 8TX, UK.
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4
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Vela-Rodríguez C, Scarpulla I, Ashok Y, Lehtiö L. Discovery of DTX3L inhibitors through a homogeneous FRET-based assay that monitors formation and removal of poly-ubiquitin chains. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:365-375. [PMID: 37579950 DOI: 10.1016/j.slasd.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
Ubiquitination is a reversible protein post-translational modification in which consequent enzymatic activity results in the covalent linking of ubiquitin to a target protein. Once ubiquitinated, a protein can undergo multiple rounds of ubiquitination on multiple sites or form poly-ubiquitin chains. Ubiquitination regulates various cellular processes, and dysregulation of ubiquitination has been associated with more than one type of cancer. Therefore, efforts have been carried out to identify modulators of the ubiquitination cascade. Herein, we present the development of a FRET-based assay that allows us to monitor ubiquitination activity of DTX3L, a RING-type E3 ubiquitin ligase. Our method shows a good signal window with a robust average Z' factor of 0.76 on 384-well microplates, indicating a good assay for screening inhibitors in a high-throughput setting. From a validatory screening experiment, we have identified the first molecules that inhibit DTX3L with potencies in the low micromolar range. We also demonstrate that the method can be expanded to study deubiquitinases, such as USP28, that reduce FRET due to hydrolysis of fluorescent poly-ubiquitin chains.
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Affiliation(s)
- Carlos Vela-Rodríguez
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Ilaria Scarpulla
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Yashwanth Ashok
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.
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5
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Scalia P, Williams SJ, Suma A, Carnevale V. The DTX Protein Family: An Emerging Set of E3 Ubiquitin Ligases in Cancer. Cells 2023; 12:1680. [PMID: 37443713 PMCID: PMC10340142 DOI: 10.3390/cells12131680] [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: 05/18/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Until recently, Deltex (DTX) proteins have been considered putative E3 ligases, based on the presence of an E3 RING domain in their protein coding sequence. The human DTX family includes DTX1, DTX2, DTX3, DTX3L and DTX4. Despite the fact that our knowledge of this class of E3-ubiquitin ligases is still at an early stage, our understanding of their role in oncogenesis is beginning to unfold. In fact, recently published studies allow us to define specific biological scenarios and further consolidate evidence-based working hypotheses. According to the current evidence, all DTX family members are involved in the regulation of Notch signaling, suggesting a phylogenetically conserved role in the regulation of this pathway. Indeed, additional evidence reveals a wider involvement of these proteins in other signaling complexes and cancer-promoting mechanisms beyond NOTCH signaling. DTX3, in particular, had been known to express two isoform variants (DTX3a and DTX3b). The recent identification and cloning of a third isoform variant in cancer (DTX3c), and its specific involvement in EphB4 degradation in cancer cells, sheds further light on this group of proteins and their specific role in cancer. Herein, we review the cumulative knowledge of this family of E3 Ubiquitin ligases with a specific focus on the potential oncogenic role of DTX isoforms in light of the rapidly expanding findings regarding this protein family's cellular targets and regulated signaling pathways. Furthermore, using a comparative and bioinformatic approach, we here disclose a new putative motif of a member of this family which may help in understanding the biological and contextual differences between the members of these proteins.
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Affiliation(s)
- Pierluigi Scalia
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA 19102, USA; 93100 Caltanissetta, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Stephen J. Williams
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA 19102, USA; 93100 Caltanissetta, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Antonio Suma
- Institute of Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Vincenzo Carnevale
- Institute of Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
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6
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Thirunavukkarasu S, Ahmed M, Rosa BA, Boothby M, Cho SH, Rangel-Moreno J, Mbandi SK, Schreiber V, Gupta A, Zuniga J, Mitreva M, Kaushal D, Scriba TJ, Khader SA. Poly(ADP-ribose) polymerase 9 mediates early protection against Mycobacterium tuberculosis infection by regulating type I IFN production. J Clin Invest 2023; 133:e158630. [PMID: 37200107 PMCID: PMC10266794 DOI: 10.1172/jci158630] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/19/2023] [Indexed: 05/20/2023] Open
Abstract
The ADP ribosyltransferases (PARPs 1-17) regulate diverse cellular processes, including DNA damage repair. PARPs are classified on the basis of their ability to catalyze poly-ADP-ribosylation (PARylation) or mono-ADP-ribosylation (MARylation). Although PARP9 mRNA expression is significantly increased in progressive tuberculosis (TB) in humans, its participation in host immunity to TB is unknown. Here, we show that PARP9 mRNA encoding the MARylating PARP9 enzyme was upregulated during TB in humans and mice and provide evidence of a critical modulatory role for PARP9 in DNA damage, cyclic GMP-AMP synthase (cGAS) expression, and type I IFN production during TB. Thus, Parp9-deficient mice were susceptible to Mycobacterium tuberculosis infection and exhibited increased TB disease, cGAS and 2'3'-cyclic GMP-AMP (cGAMP) expression, and type I IFN production, along with upregulation of complement and coagulation pathways. Enhanced M. tuberculosis susceptibility is type I IFN dependent, as blockade of IFN α receptor (IFNAR) signaling reversed the enhanced susceptibility of Parp9-/- mice. Thus, in sharp contrast to PARP9 enhancement of type I IFN production in viral infections, this member of the MAR family plays a protective role by limiting type I IFN responses during TB.
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Affiliation(s)
| | | | - Bruce A. Rosa
- McDonnell Genome Institute, and
- Division of Infectious Diseases, Department of Internal Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Mark Boothby
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sung Hoon Cho
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Javier Rangel-Moreno
- Department of Medicine, Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Stanley K. Mbandi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Valérie Schreiber
- Biotechnology and Cell Signaling, CNRS UMR7242, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch, France
| | | | - Joaquin Zuniga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Makedonka Mitreva
- McDonnell Genome Institute, and
- Division of Infectious Diseases, Department of Internal Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
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7
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Goekeri C, Pennitz P, Groenewald W, Behrendt U, Kirsten H, Zobel CM, Berger S, Heinz GA, Mashreghi MF, Wienhold SM, Dietert K, Dorhoi A, Gruber AD, Scholz M, Rohde G, Suttorp N, Witzenrath M, Nouailles G. MicroRNA-223 Dampens Pulmonary Inflammation during Pneumococcal Pneumonia. Cells 2023; 12:cells12060959. [PMID: 36980300 PMCID: PMC10047070 DOI: 10.3390/cells12060959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Community-acquired pneumonia remains a major contributor to global communicable disease-mediated mortality. Neutrophils play a leading role in trying to contain bacterial lung infection, but they also drive detrimental pulmonary inflammation, when dysregulated. Here we aimed at understanding the role of microRNA-223 in orchestrating pulmonary inflammation during pneumococcal pneumonia. Serum microRNA-223 was measured in patients with pneumococcal pneumonia and in healthy subjects. Pulmonary inflammation in wild-type and microRNA-223-knockout mice was assessed in terms of disease course, histopathology, cellular recruitment and evaluation of inflammatory protein and gene signatures following pneumococcal infection. Low levels of serum microRNA-223 correlated with increased disease severity in pneumococcal pneumonia patients. Prolonged neutrophilic influx into the lungs and alveolar spaces was detected in pneumococci-infected microRNA-223-knockout mice, possibly accounting for aggravated histopathology and acute lung injury. Expression of microRNA-223 in wild-type mice was induced by pneumococcal infection in a time-dependent manner in whole lungs and lung neutrophils. Single-cell transcriptome analyses of murine lungs revealed a unique profile of antimicrobial and cellular maturation genes that are dysregulated in neutrophils lacking microRNA-223. Taken together, low levels of microRNA-223 in human pneumonia patient serum were associated with increased disease severity, whilst its absence provoked dysregulation of the neutrophil transcriptome in murine pneumococcal pneumonia.
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Affiliation(s)
- Cengiz Goekeri
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Faculty of Medicine, Cyprus International University, 99040 Nicosia, Cyprus
- Correspondence: (C.G.); (G.N.)
| | - Peter Pennitz
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Wibke Groenewald
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Ulrike Behrendt
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics, and Epidemiology, Universität Leipzig, 04107 Leipzig, Germany
| | - Christian M. Zobel
- Department of Internal Medicine, Bundeswehrkrankenhaus Berlin, 10115 Berlin, Germany
| | - Sarah Berger
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Gitta A. Heinz
- Therapeutic Gene Regulation, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Institut der Leibniz-Gemeinschaft, 10117 Berlin, Germany
| | - Mir-Farzin Mashreghi
- Therapeutic Gene Regulation, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Institut der Leibniz-Gemeinschaft, 10117 Berlin, Germany
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
| | - Sandra-Maria Wienhold
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Kristina Dietert
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Anca Dorhoi
- Institute of Immunology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
- Faculty of Mathematics and Natural Sciences, University of Greifswald, 17489 Greifswald, Germany
| | - Achim D. Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics, and Epidemiology, Universität Leipzig, 04107 Leipzig, Germany
| | - Gernot Rohde
- Department of Respiratory Medicine, Medical Clinic I, Goethe-Universität Frankfurt am Main, 60596 Frankfurt am Main, Germany
- CAPNETZ STIFTUNG, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- CAPNETZ STIFTUNG, 30625 Hannover, Germany
- German Center for Lung Research (DZL), 10117 Berlin, Germany
| | | | - Martin Witzenrath
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- CAPNETZ STIFTUNG, 30625 Hannover, Germany
- German Center for Lung Research (DZL), 10117 Berlin, Germany
| | - Geraldine Nouailles
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Correspondence: (C.G.); (G.N.)
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8
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ADP-Ribosylation in Antiviral Innate Immune Response. Pathogens 2023; 12:pathogens12020303. [PMID: 36839575 PMCID: PMC9964302 DOI: 10.3390/pathogens12020303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Adenosine diphosphate (ADP)-ribosylation is a reversible post-translational modification catalyzed by ADP-ribosyltransferases (ARTs). ARTs transfer one or more ADP-ribose from nicotinamide adenine dinucleotide (NAD+) to the target substrate and release the nicotinamide (Nam). Accordingly, it comes in two forms: mono-ADP-ribosylation (MARylation) and poly-ADP-ribosylation (PARylation). ADP-ribosylation plays important roles in many biological processes, such as DNA damage repair, gene regulation, and energy metabolism. Emerging evidence demonstrates that ADP-ribosylation is implicated in host antiviral immune activity. Here, we summarize and discuss ADP-ribosylation modifications that occur on both host and viral proteins and their roles in host antiviral response.
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9
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Jiang C, Zhou Y, Yan L, Zheng J, Wang X, Li J, Jiang X. A prognostic NAD+ metabolism-related gene signature for predicting response to immune checkpoint inhibitor in glioma. Front Oncol 2023; 13:1051641. [PMID: 36845744 PMCID: PMC9945104 DOI: 10.3389/fonc.2023.1051641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Background Nicotinamide adenine dinucleotide (NAD+) metabolism is involved in a series of cancer pathogenesis processes, and is considered a promising therapeutic target for cancer treatment. However, a comprehensive analysis of NAD+ metabolism events on immune regulation and cancer survival has not yet been conducted. Here, we constructed a prognostic NAD+ metabolism-related gene signature (NMRGS) associated with immune checkpoint inhibitor (ICI) efficacy in glioma. Methods 40 NAD+ metabolism-related genes (NMRGs) were obtained from the Reactome database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Glioma cases with transcriptome data and clinical information were obtained from Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA). NMRGS was constructed based on the calculated risk score using univariate analysis, Kaplan-Meier analysis, multivariate Cox regression, and nomogram. This NMRGS was verified in training (CGGA693) and validation (TCGA and CGGA325) cohorts. The immune characteristics, mutation profile, and response to ICI therapy were subsequently analyzed for different NMRGS subgroups. Results Six NAD+ metabolism-related genes, including CD38, nicotinamide adenine dinucleotide kinase (NADK), nicotinate phosphoribosyltransferase (NAPRT), nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 (NMNAT3), poly(ADP-Ribose) polymerase family member 6 (PARP6), and poly(ADP-Ribose) polymerase family member 9 (PARP9), were ultimately used to construct a comprehensive risk model for glioma patients. Patients in the NMRGS-high group showed a poorer survival outcome than those in the NMRGS-low group. The area under curve (AUC) indicated that NMRGS has good potential in glioma prognostic prediction. A nomogram with improved accuracy was established based on independent prognostic factors (NMRGS score, 1p19q codeletion status, and WHO grade). Furthermore, patients in the NMRGS-high group showed a more immunosuppressive microenvironment, higher tumor mutation burden (TMB), higher human leucocyte antigen (HLA) expression and a more therapeutic response to ICI therapy. Conclusions This study constructed a prognostic NAD+ metabolism-related signature associated with the immune landscape in glioma, which can be used for guiding individualized ICI therapy.
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Affiliation(s)
- Cheng Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yujie Zhou
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lizhao Yan
- Department of Hand Surgery, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianglin Zheng
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuan Wang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junjun Li
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,*Correspondence: Junjun Li, ; Xiaobing Jiang,
| | - Xiaobing Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,*Correspondence: Junjun Li, ; Xiaobing Jiang,
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10
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Hu W, Hu Y, Pei Y, Li R, Xu F, Chi X, Mi J, Bergquist J, Lu L, Zhang L, Yang C. Silencing DTX3L Inhibits the Progression of Cervical Carcinoma by Regulating PI3K/AKT/mTOR Signaling Pathway. Int J Mol Sci 2023; 24:ijms24010861. [PMID: 36614304 PMCID: PMC9821498 DOI: 10.3390/ijms24010861] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/04/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023] Open
Abstract
Cervical carcinoma (CC) is the second most prevalent gynecologic cancer in females across the world. To obtain a better understanding of the mechanisms underlying the development of CC, high-resolution label-free mass spectrometry was performed on CC and adjacent normal tissues from eight patients. A total of 2631 proteins were identified, and 46 significant differently expressed proteins (DEPs) were found between CC and normal tissues (p < 0.01, fold change >10 or <0.1). Ingenuity pathway analysis revealed that the majority of the proteins were involved in the regulation of eIF4 and p70S6K signaling and mTOR signaling. Among 46 DEPs, Integrinβ6 (ITGB6), PPP1CB, TMPO, PTGES3 (P23) and DTX3L were significantly upregulated, while Desmin (DES) was significantly downregulated in CC tissues compared with the adjacent normal tissues. In in vivo and in vitro experiments, DTX3L knockdown suppressed CC cell proliferation, migration, invasion and xenograft tumorigenesis, and enhanced cell apoptosis. Combination of silencing DTX3L and cisplatin treatment induced higher apoptosis percentage compared to cisplatin treatment alone. Moreover, DTX3L silencing inhibited the PI3K/AKT/mTOR signal pathway. Thus, our results suggested DTX3L could regulate CC progression through the PI3K/AKT/mTOR signal pathway and is potentially a novel biomarker and therapeutic target for CC.
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Affiliation(s)
- Wei Hu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai 264000, China
| | - Yaorui Hu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai 264000, China
- School of Basic Medicine, Binzhou Medical University, Yantai 264000, China
| | - Yao Pei
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai 264000, China
| | - Rongrong Li
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai 264000, China
- School of Basic Medicine, Binzhou Medical University, Yantai 264000, China
| | - Fuyi Xu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai 264000, China
| | - Xiaodong Chi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai 264000, China
| | - Jia Mi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai 264000, China
| | - Jonas Bergquist
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai 264000, China
- Department of Chemistry—BMC, Analytical Chemistry and Neurochemistry, Uppsala University, 75124 Uppsala, Sweden
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Luping Zhang
- School of Basic Medicine, Binzhou Medical University, Yantai 264000, China
- Correspondence: (L.Z.); (C.Y.)
| | - Chunhua Yang
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai 264000, China
- Correspondence: (L.Z.); (C.Y.)
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11
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Activities and binding partners of E3 ubiquitin ligase DTX3L and its roles in cancer. Biochem Soc Trans 2022; 50:1683-1692. [DOI: 10.1042/bst20220501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/27/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022]
Abstract
Ubiquitination is a protein post-translational modification that affects protein localisation, stability and interactions. E3 ubiquitin ligases regulate the final step of the ubiquitination reaction by recognising target proteins and mediating the ubiquitin transfer from an E2 enzyme. DTX3L is a multi-domain E3 ubiquitin ligase in which the N-terminus mediates protein oligomerisation, a middle D3 domain mediates the interaction with PARP9, a RING domain responsible for recognising E2 ∼ Ub and a DTC domain has the dual activity of ADP-ribosylating ubiquitin and mediating ubiquitination. The activity of DTX3L is known to be modulated by at least two different factors: the concentration of NAD+, which dictates if the enzyme acts as a ligase or as an ADP-ribosyltransferase, and its binding partners, which affect DTX3L activity through yet unknown mechanisms. In light of recent findings it is possible that DTX3L could ubiquitinate ADP-ribose attached to proteins. Different DTX3L–protein complexes have been found to be part of multiple signalling pathways through which they promote the adhesion, proliferation, migration and chemoresistance of e.g. lymphoma, glioma, melanoma, and prostate cancer. In this review, we have covered the literature available for the molecular functions of DTX3L especially in the context of cancer biology, different pathways it regulates and how these relate to its function as an oncoprotein.
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12
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Bińkowski J, Taryma-Leśniak O, Łuczkowska K, Niedzwiedź A, Lechowicz K, Strapagiel D, Jarczak J, Davalos V, Pujol A, Esteller M, Kotfis K, Machaliński B, Parczewski M, Wojdacz TK. Epigenetic activation of antiviral sensors and effectors of interferon response pathways during SARS-CoV-2 infection. Biomed Pharmacother 2022; 153:113396. [PMID: 36076479 PMCID: PMC9271528 DOI: 10.1016/j.biopha.2022.113396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/15/2022] Open
Abstract
Recent studies have shown that methylation changes identified in blood cells of COVID-19 patients have a potential to be used as biomarkers of SARS-CoV-2 infection outcomes. However, different studies have reported different subsets of epigenetic lesions that stratify patients according to the severity of infection symptoms, and more importantly, the significance of those epigenetic changes in the pathology of the infection is still not clear. We used methylomics and transcriptomics data from the largest so far cohort of COVID-19 patients from four geographically distant populations, to identify casual interactions of blood cells’ methylome in pathology of the COVID-19 disease. We identified a subset of methylation changes that is uniformly present in all COVID-19 patients regardless of symptoms. Those changes are not present in patients suffering from upper respiratory tract infections with symptoms similar to COVID-19. Most importantly, the identified epigenetic changes affect the expression of genes involved in interferon response pathways and the expression of those genes differs between patients admitted to intensive care units and only hospitalized. In conclusion, the DNA methylation changes involved in pathophysiology of SARS-CoV-2 infection, which are specific to COVID-19 patients, can not only be utilized as biomarkers in the disease management but also present a potential treatment target.
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13
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Gan Y, Sha H, Zou R, Xu M, Zhang Y, Feng J, Wu J. Research Progress on Mono-ADP-Ribosyltransferases in Human Cell Biology. Front Cell Dev Biol 2022; 10:864101. [PMID: 35652091 PMCID: PMC9149570 DOI: 10.3389/fcell.2022.864101] [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: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
ADP-ribosylation is a well-established post-translational modification that is inherently connected to diverse processes, including DNA repair, transcription, and cell signaling. The crucial roles of mono-ADP-ribosyltransferases (mono-ARTs) in biological processes have been identified in recent years by the comprehensive use of genetic engineering, chemical genetics, and proteomics. This review provides an update on current methodological advances in the study of these modifiers. Furthermore, the review provides details on the function of mono ADP-ribosylation. Several mono-ARTs have been implicated in the development of cancer, and this review discusses the role and therapeutic potential of some mono-ARTs in cancer.
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Affiliation(s)
- Yujie Gan
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Huanhuan Sha
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Renrui Zou
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Miao Xu
- Nanjing Medical University, Nanjing, China
| | - Yuan Zhang
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Jifeng Feng
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
- *Correspondence: Jifeng Feng,
| | - Jianzhong Wu
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
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14
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Lüscher B, Verheirstraeten M, Krieg S, Korn P. Intracellular mono-ADP-ribosyltransferases at the host-virus interphase. Cell Mol Life Sci 2022; 79:288. [PMID: 35536484 PMCID: PMC9087173 DOI: 10.1007/s00018-022-04290-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 01/22/2023]
Abstract
The innate immune system, the primary defense mechanism of higher organisms against pathogens including viruses, senses pathogen-associated molecular patterns (PAMPs). In response to PAMPs, interferons (IFNs) are produced, allowing the host to react swiftly to viral infection. In turn the expression of IFN-stimulated genes (ISGs) is induced. Their products disseminate the antiviral response. Among the ISGs conserved in many species are those encoding mono-ADP-ribosyltransferases (mono-ARTs). This prompts the question whether, and if so how, mono-ADP-ribosylation affects viral propagation. Emerging evidence demonstrates that some mono-ADP-ribosyltransferases function as PAMP receptors and modify both host and viral proteins relevant for viral replication. Support for mono-ADP-ribosylation in virus–host interaction stems from the findings that some viruses encode mono-ADP-ribosylhydrolases, which antagonize cellular mono-ARTs. We summarize and discuss the evidence linking mono-ADP-ribosylation and the enzymes relevant to catalyze this reversible modification with the innate immune response as part of the arms race between host and viruses.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
| | - Maud Verheirstraeten
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
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15
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Weidle UH, Sela T, Brinkmann U, Niewoehner J. Circular RNAs With Efficacy in Preclinical In Vitro and In Vivo Models of Esophageal Squamous Cell Carcinoma. Cancer Genomics Proteomics 2022; 19:283-298. [PMID: 35430563 DOI: 10.21873/cgp.20320] [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: 01/27/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 02/06/2023] Open
Abstract
Esophageal cancer is associated with a dismal prognosis. The armamentarium of approved drugs is focused on chemotherapy with modest therapeutic benefit. Recently, checkpoint inhibitory monoclonal antibody Pembrolizumab was approved. In order to identify new targets and modalities for the treatment of esophagus squamous cell carcinoma (ESCC) we searched the literature for circRNAs involved in the pathogenesis of ESCC. We identified two down-regulated and 17 up-regulated circRNAs as well as a synthetic circRNA with efficacy in preclinical in vivo systems. Down-regulated circRNAs sponge microRNAs directed against tumor suppressor genes. Up-regulated circRNAs sponge microRNAs directed against mRNAs, which encode proteins with pro-tumoral functions. We discuss issues such as reconstitution of down-regulated circRNAs and inhibition of up-regulated circRNAs with short interfering RNA (siRNA)- related entities. Also, we address druggability issues of the identified targets.
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Affiliation(s)
- Ulrich H Weidle
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Tatjana Sela
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Jens Niewoehner
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
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16
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E3 Ubiquitin Ligase Regulators of Notch Receptor Endocytosis: From Flies to Humans. Biomolecules 2022; 12:biom12020224. [PMID: 35204725 PMCID: PMC8961608 DOI: 10.3390/biom12020224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Notch is a developmental receptor, conserved in the evolution of the metazoa, which regulates cell fate proliferation and survival in numerous developmental contexts, and also regulates tissue renewal and repair in adult organisms. Notch is activated by proteolytic removal of its extracellular domain and the subsequent release of its intracellular domain, which then acts in the nucleus as part of a transcription factor complex. Numerous regulatory mechanisms exist to tune the amplitude, duration and spatial patterning of this core signalling mechanism. In Drosophila, Deltex (Dx) and Suppressor of dx (Su(dx)) are E3 ubiquitin ligases which interact with the Notch intracellular domain to regulate its endocytic trafficking, with impacts on both ligand-dependent and ligand-independent signal activation. Homologues of Dx and Su(dx) have been shown to also interact with one or more of the four mammalian Notch proteins and other target substrates. Studies have shown similarities, specialisations and diversifications of the roles of these Notch regulators. This review collates together current research on vertebrate Dx and Su(dx)-related proteins, provides an overview of their various roles, and discusses their contributions to cell fate regulation and disease.
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17
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Reconstitution of the DTX3L-PARP9 complex reveals determinants for high affinity heterodimerization and multimeric assembly. Biochem J 2022; 479:289-304. [PMID: 35037691 DOI: 10.1042/bcj20210722] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/07/2022] [Accepted: 01/17/2022] [Indexed: 11/17/2022]
Abstract
Ubiquitination and ADP-ribosylation are post-translational modifications that play major roles in pathways including the DNA damage response and viral infection. The enzymes responsible for these modifications are therefore potential targets for therapeutic intervention. DTX3L is an E3 Ubiquitin ligase that forms a heterodimer with PARP9. In addition to its ubiquitin ligase activity, DTX3L-PARP9 also acts as an ADP-ribosyl transferase for Gly76 on the C-terminus of ubiquitin. NAD+-dependent ADP-ribosylation of ubiquitin by DTX3L-PARP9 prevents ubiquitin from conjugating to protein substrates. To gain insight into how DTX3L-PARP9 generates these post-translational modifications, we have generated recombinant forms of DTX3L and PARP9 and studied their physical interactions. We show the DTX3L D3 domain (230-510) mediates the interaction with PARP9 with nanomolar affinity and an apparent 1:1 stoichiometry. We also show that DTX3L and PARP9 assemble into a higher molecular weight oligomer, and that this is mediated by the DTX3L N-terminal region (1-200). Lastly, we show that ADP-ribosylation of ubiquitin at Gly76 is reversible in vitro by several Macrodomain-type hydrolases. Our study provides a framework to understand how DTX3L-PARP9 mediates ADP-ribosylation and ubiquitination through both intra- and inter-subunit interactions.
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18
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Sha H, Gan Y, Zou R, Wu J, Feng J. Research Advances in the Role of the Poly ADP Ribose Polymerase Family in Cancer. Front Oncol 2022; 11:790967. [PMID: 34976832 PMCID: PMC8716401 DOI: 10.3389/fonc.2021.790967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/24/2021] [Indexed: 12/27/2022] Open
Abstract
Poly ADP ribose polymerases (PARPs) catalyze the modification of acceptor proteins, DNA, or RNA with ADP-ribose, which plays an important role in maintaining genomic stability and regulating signaling pathways. The rapid development of PARP1/2 inhibitors for the treatment of ovarian and breast cancers has advanced research on other PARP family members for the treatment of cancer. This paper reviews the role of PARP family members (except PARP1/2 and tankyrases) in cancer and the underlying regulatory mechanisms, which will establish a molecular basis for the clinical application of PARPs in the future.
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Affiliation(s)
- Huanhuan Sha
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yujie Gan
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Renrui Zou
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jianzhong Wu
- Research Center of Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jifeng Feng
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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19
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Boehi F, Manetsch P, Hottiger MO. Interplay between ADP-ribosyltransferases and essential cell signaling pathways controls cellular responses. Cell Discov 2021; 7:104. [PMID: 34725336 PMCID: PMC8560908 DOI: 10.1038/s41421-021-00323-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
Signaling cascades provide integrative and interactive frameworks that allow the cell to respond to signals from its environment and/or from within the cell itself. The dynamic regulation of mammalian cell signaling pathways is often modulated by cascades of protein post-translational modifications (PTMs). ADP-ribosylation is a PTM that is catalyzed by ADP-ribosyltransferases and manifests as mono- (MARylation) or poly- (PARylation) ADP-ribosylation depending on the addition of one or multiple ADP-ribose units to protein substrates. ADP-ribosylation has recently emerged as an important cell regulator that impacts a plethora of cellular processes, including many intracellular signaling events. Here, we provide an overview of the interplay between the intracellular diphtheria toxin-like ADP-ribosyltransferase (ARTD) family members and five selected signaling pathways (including NF-κB, JAK/STAT, Wnt-β-catenin, MAPK, PI3K/AKT), which are frequently described to control or to be controlled by ADP-ribosyltransferases and how these interactions impact the cellular responses.
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Affiliation(s)
- Flurina Boehi
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Cancer Biology PhD Program of the Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Patrick Manetsch
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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20
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Wu Z, Sainz AG, Shadel GS. Mitochondrial DNA: cellular genotoxic stress sentinel. Trends Biochem Sci 2021; 46:812-821. [PMID: 34088564 PMCID: PMC9809014 DOI: 10.1016/j.tibs.2021.05.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/24/2021] [Accepted: 05/08/2021] [Indexed: 02/08/2023]
Abstract
High copy number, damage prone, and lean on repair mechanisms are unique features of mitochondrial DNA (mtDNA) that are hard to reconcile with its essentiality for oxidative phosphorylation, the primary function ascribed to this maternally inherited component of our genome. We propose that mtDNA is also a genotoxic stress sentinel, as well as a direct second messenger of this type of cellular stress. Here, we discuss existing evidence for this sentinel/effector role through the ability of mtDNA to escape the confines of the mitochondrial matrix and activate nuclear DNA damage/repair responses via interferon-stimulated gene products and other downstream effectors. However, this arrangement may come at a cost, leading to cancer chemoresistance and contributing to inflammation, disease pathology, and aging.
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Affiliation(s)
- Zheng Wu
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA,Graduate Program in Genetics, Yale School of Medicine, New Haven, CT 06437, USA,These authors contributed equally to this work
| | - Alva G. Sainz
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA,Graduate Program in Experimental Pathology, Yale School of Medicine, New Haven, CT 06437, USA,These authors contributed equally to this work
| | - Gerald S. Shadel
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA,Correspondence: (G.S. Shadel)
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21
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Wang L, Sun X, He J, Liu Z. Functions and Molecular Mechanisms of Deltex Family Ubiquitin E3 Ligases in Development and Disease. Front Cell Dev Biol 2021; 9:706997. [PMID: 34513839 PMCID: PMC8424196 DOI: 10.3389/fcell.2021.706997] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/05/2021] [Indexed: 12/14/2022] Open
Abstract
Ubiquitination is a posttranslational modification of proteins that significantly affects protein stability and function. The specificity of substrate recognition is determined by ubiquitin E3 ligase during ubiquitination. Human Deltex (DTX) protein family, which functions as ubiquitin E3 ligases, comprises five members, namely, DTX1, DTX2, DTX3, DTX3L, and DTX4. The characteristics and functional diversity of the DTX family proteins have attracted significant attention over the last decade. DTX proteins have several physiological and pathological roles and are closely associated with cell signal transduction, growth, differentiation, and apoptosis, as well as the occurrence and development of various tumors. Although they have been extensively studied in various species, data on structural features, biological functions, and potential mechanisms of action of the DTX family proteins remain limited. In this review, recent research progress on each member of the DTX family is summarized, providing insights into future research directions and potential strategies in disease diagnosis and therapy.
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Affiliation(s)
- Lidong Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaodan Sun
- Postdoctoral Research Workstation, Jilin Cancer Hospital, Changchun, China
| | - Jingni He
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhen Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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22
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Hoch NC. Host ADP-ribosylation and the SARS-CoV-2 macrodomain. Biochem Soc Trans 2021; 49:1711-1721. [PMID: 34351418 PMCID: PMC8421052 DOI: 10.1042/bst20201212] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 11/29/2022]
Abstract
The COVID-19 pandemic has prompted intense research efforts into elucidating mechanisms of coronavirus pathogenesis and to propose antiviral interventions. The interferon (IFN) response is the main antiviral component of human innate immunity and is actively suppressed by several non-structural SARS-CoV-2 proteins, allowing viral replication within human cells. Differences in IFN signalling efficiency and timing have emerged as central determinants of the variability of COVID-19 disease severity between patients, highlighting the need for an improved understanding of host-pathogen interactions that affect the IFN response. ADP-ribosylation is an underexplored post-translational modification catalyzed by ADP-ribosyl transferases collectively termed poly(ADP-ribose) polymerases (PARPs). Several human PARPs are induced by the IFN response and participate in antiviral defences by regulating IFN signalling itself, modulating host processes such as translation and protein trafficking, as well as directly modifying and inhibiting viral target proteins. SARS-CoV-2 and other viruses encode a macrodomain that hydrolyzes ADP-ribose modifications, thus counteracting antiviral PARP activity. This mini-review provides a brief overview of the known targets of IFN-induced ADP-ribosylation and the functions of viral macrodomains, highlighting several open questions in the field.
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Affiliation(s)
- Nicolas C. Hoch
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
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23
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Ahmad SS, Samia NSN, Khan AS, Turjya RR, Khan MAAK. Bidirectional promoters: an enigmatic genome architecture and their roles in cancers. Mol Biol Rep 2021; 48:6637-6644. [PMID: 34378109 DOI: 10.1007/s11033-021-06612-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Bidirectional promoters are the transcription regulatory regions of genes positioned head-to-head on opposite strands. Specific sequence signals, chromatin modifications and three-dimensional structures of the transcription site facilitate the unconventional yet tightly regulated transcription proceeding in both directions from these promoters. Mutations or aberrant epigenetic changes can lead to abnormal enhanced or reduced expression from either of the bidirectionally transcribed genes resulting in tumorigenesis. Moreover, bidirectionally transcribed genes might also contribute towards the immune regulation in tumor microenvironment. In this review, we aimed to expound the characteristic features of bidirectional promoters alongside their transcriptional regulations, and ultimately, the association of these enigmatic genomic elements in different cancers.
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Affiliation(s)
- Sheikh Shafin Ahmad
- Department of Mathematics and Natural Sciences, Brac University, Dhaka, Bangladesh
| | | | - Auroni Semonti Khan
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Rafeed Rahman Turjya
- Department of Mathematics and Natural Sciences, Brac University, Dhaka, Bangladesh
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24
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Russo LC, Tomasin R, Matos IA, Manucci AC, Sowa ST, Dale K, Caldecott KW, Lehtiö L, Schechtman D, Meotti FC, Bruni-Cardoso A, Hoch NC. The SARS-CoV-2 Nsp3 macrodomain reverses PARP9/DTX3L-dependent ADP-ribosylation induced by interferon signaling. J Biol Chem 2021; 297:101041. [PMID: 34358560 PMCID: PMC8332738 DOI: 10.1016/j.jbc.2021.101041] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/16/2021] [Accepted: 08/02/2021] [Indexed: 11/26/2022] Open
Abstract
SARS-CoV-2 nonstructural protein 3 (Nsp3) contains a macrodomain that is essential for coronavirus pathogenesis and is thus an attractive target for drug development. This macrodomain is thought to counteract the host interferon (IFN) response, an important antiviral signalling cascade, via the reversal of protein ADP-ribosylation, a posttranslational modification catalyzed by host poly(ADP-ribose) polymerases (PARPs). However, the main cellular targets of the coronavirus macrodomain that mediate this effect are currently unknown. Here, we use a robust immunofluorescence-based assay to show that activation of the IFN response induces ADP-ribosylation of host proteins and that ectopic expression of the SARS-CoV-2 Nsp3 macrodomain reverses this modification in human cells. We further demonstrate that this assay can be used to screen for on-target and cell-active macrodomain inhibitors. This IFN-induced ADP-ribosylation is dependent on PARP9 and its binding partner DTX3L, but surprisingly the expression of the Nsp3 macrodomain or the deletion of either PARP9 or DTX3L does not impair IFN signaling or the induction of IFN-responsive genes. Our results suggest that PARP9/DTX3L-dependent ADP-ribosylation is a downstream effector of the host IFN response and that the cellular function of the SARS-CoV-2 Nsp3 macrodomain is to hydrolyze this end product of IFN signaling, rather than to suppress the IFN response itself.
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Affiliation(s)
- Lilian Cristina Russo
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Rebeka Tomasin
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Isaac Araújo Matos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Antonio Carlos Manucci
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Sven T Sowa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Katie Dale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Deborah Schechtman
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Flavia C Meotti
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Alexandre Bruni-Cardoso
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Nicolas Carlos Hoch
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.
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25
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Yang CS, Jividen K, Kamata T, Dworak N, Oostdyk L, Remlein B, Pourfarjam Y, Kim IK, Du KP, Abbas T, Sherman NE, Wotton D, Paschal BM. Androgen signaling uses a writer and a reader of ADP-ribosylation to regulate protein complex assembly. Nat Commun 2021; 12:2705. [PMID: 33976187 PMCID: PMC8113490 DOI: 10.1038/s41467-021-23055-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/14/2021] [Indexed: 02/03/2023] Open
Abstract
Androgen signaling through the androgen receptor (AR) directs gene expression in both normal and prostate cancer cells. Androgen regulates multiple aspects of the AR life cycle, including its localization and post-translational modification, but understanding how modifications are read and integrated with AR activity has been difficult. Here, we show that ADP-ribosylation regulates AR through a nuclear pathway mediated by Parp7. We show that Parp7 mono-ADP-ribosylates agonist-bound AR, and that ADP-ribosyl-cysteines within the N-terminal domain mediate recruitment of the E3 ligase Dtx3L/Parp9. Molecular recognition of ADP-ribosyl-cysteine is provided by tandem macrodomains in Parp9, and Dtx3L/Parp9 modulates expression of a subset of AR-regulated genes. Parp7, ADP-ribosylation of AR, and AR-Dtx3L/Parp9 complex assembly are inhibited by Olaparib, a compound used clinically to inhibit poly-ADP-ribosyltransferases Parp1/2. Our study reveals the components of an androgen signaling axis that uses a writer and reader of ADP-ribosylation to regulate protein-protein interactions and AR activity.
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Affiliation(s)
- Chun-Song Yang
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Kasey Jividen
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
| | - Teddy Kamata
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Natalia Dworak
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
| | - Luke Oostdyk
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Bartlomiej Remlein
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Yasin Pourfarjam
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - In-Kwon Kim
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Kang-Ping Du
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA, USA
| | - Tarek Abbas
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA, USA
| | - Nicholas E Sherman
- W. M. Keck Biomedical Mass Spectrometry Laboratory, University of Virginia, Charlottesville, VA, USA
| | - David Wotton
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Bryce M Paschal
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA.
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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26
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Malgras M, Garcia M, Jousselin C, Bodet C, Lévêque N. The Antiviral Activities of Poly-ADP-Ribose Polymerases. Viruses 2021; 13:v13040582. [PMID: 33808354 PMCID: PMC8066025 DOI: 10.3390/v13040582] [Citation(s) in RCA: 22] [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: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023] Open
Abstract
The poly-adenosine diphosphate (ADP)-ribose polymerases (PARPs) are responsible for ADP-ribosylation, a reversible post-translational modification involved in many cellular processes including DNA damage repair, chromatin remodeling, regulation of translation and cell death. In addition to these physiological functions, recent studies have highlighted the role of PARPs in host defenses against viruses, either by direct antiviral activity, targeting certain steps of virus replication cycle, or indirect antiviral activity, via modulation of the innate immune response. This review focuses on the antiviral activity of PARPs, as well as strategies developed by viruses to escape their action.
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Affiliation(s)
- Mathilde Malgras
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
| | - Magali Garcia
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, 86021 Poitiers, France
| | - Clément Jousselin
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, 86021 Poitiers, France
| | - Charles Bodet
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
| | - Nicolas Lévêque
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, 86021 Poitiers, France
- Correspondence: nicolas.lévê; Tel.: +33-(0)5-49-44-38-17
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27
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Hopp AK, Hottiger MO. Uncovering the Invisible: Mono-ADP-ribosylation Moved into the Spotlight. Cells 2021; 10:680. [PMID: 33808662 PMCID: PMC8003356 DOI: 10.3390/cells10030680] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Adenosine diphosphate (ADP)-ribosylation is a nicotinamide adenine dinucleotide (NAD+)-dependent post-translational modification that is found on proteins as well as on nucleic acids. While ARTD1/PARP1-mediated poly-ADP-ribosylation has extensively been studied in the past 60 years, comparably little is known about the physiological function of mono-ADP-ribosylation and the enzymes involved in its turnover. Promising technological advances have enabled the development of innovative tools to detect NAD+ and NAD+/NADH (H for hydrogen) ratios as well as ADP-ribosylation. These tools have significantly enhanced our current understanding of how intracellular NAD dynamics contribute to the regulation of ADP-ribosylation as well as to how mono-ADP-ribosylation integrates into various cellular processes. Here, we discuss the recent technological advances, as well as associated new biological findings and concepts.
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Affiliation(s)
| | - Michael O. Hottiger
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland;
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28
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Schenkel LB, Molina JR, Swinger KK, Abo R, Blackwell DJ, Lu AZ, Cheung AE, Church WD, Kunii K, Kuplast-Barr KG, Majer CR, Minissale E, Mo JR, Niepel M, Reik C, Ren Y, Vasbinder MM, Wigle TJ, Richon VM, Keilhack H, Kuntz KW. A potent and selective PARP14 inhibitor decreases protumor macrophage gene expression and elicits inflammatory responses in tumor explants. Cell Chem Biol 2021; 28:1158-1168.e13. [PMID: 33705687 DOI: 10.1016/j.chembiol.2021.02.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/18/2020] [Accepted: 02/11/2021] [Indexed: 11/28/2022]
Abstract
PARP14 has been implicated by genetic knockout studies to promote protumor macrophage polarization and suppress the antitumor inflammatory response due to its role in modulating interleukin-4 (IL-4) and interferon-γ signaling pathways. Here, we describe structure-based design efforts leading to the discovery of a potent and highly selective PARP14 chemical probe. RBN012759 inhibits PARP14 with a biochemical half-maximal inhibitory concentration of 0.003 μM, exhibits >300-fold selectivity over all PARP family members, and its profile enables further study of PARP14 biology and disease association both in vitro and in vivo. Inhibition of PARP14 with RBN012759 reverses IL-4-driven protumor gene expression in macrophages and induces an inflammatory mRNA signature similar to that induced by immune checkpoint inhibitor therapy in primary human tumor explants. These data support an immune suppressive role of PARP14 in tumors and suggest potential utility of PARP14 inhibitors in the treatment of cancer.
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Affiliation(s)
- Laurie B Schenkel
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; MOMA Therapeutics, Cambridge, MA 02142, USA
| | - Jennifer R Molina
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Kerren K Swinger
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; Xilio Therapeutics, Waltham, MA 02451, USA
| | - Ryan Abo
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; Obsidian Therapeutics, Cambridge, MA 02138, USA
| | - Danielle J Blackwell
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Alvin Z Lu
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Anne E Cheung
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; A2Empowerment, Arlington, MA 02474, USA
| | - W David Church
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Kaiko Kunii
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Kristy G Kuplast-Barr
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Christina R Majer
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Elena Minissale
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Jan-Rung Mo
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Mario Niepel
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Christopher Reik
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; Bain & Company, Boston, MA 02116, USA
| | - Yue Ren
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Melissa M Vasbinder
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Tim J Wigle
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Victoria M Richon
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA; Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Heike Keilhack
- Department of Biological Sciences, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Kevin W Kuntz
- Department of Molecular Discovery, Ribon Therapeutics, Inc., Cambridge, MA 02140, USA.
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29
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Xu H, Chai S, Wang Y, Wang J, Xiao D, Li J, Xiong N. Molecular and clinical characterization of PARP9 in gliomas: A potential immunotherapeutic target. CNS Neurosci Ther 2020; 26:804-814. [PMID: 32678519 PMCID: PMC7366751 DOI: 10.1111/cns.13380] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/29/2020] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Glioma is a primary malignancy of the central nervous system (CNS). As biomedicine advances, an efficient molecular target is urgently needed for the diagnosis and treatment of glioma. Meanwhile, several studies have demonstrated that glioma development is closely related to immunity. PARP9 is an inactive mono-ADP-ribosyltransferase belonging to the poly-ADP ribosyltransferase (ARTD) family. In this article, we aimed to reveal the relationship between PARP9 and glioma and explore the potential prognostic value and immunotherapeutic targetability of PARP9 in glioma. METHODS PARP9 transcript levels were analyzed with TCGA and GEO databases. The clinicopathological information of patients with glioma in the TCGA database and gene expression profiles were analyzed to determine the relationship between the expression of PARP9 and clinicopathologic characteristics. Kaplan-Meier survival analysis, univariate Cox regression analysis, and multivariate Cox regression analysis were used for survival analysis. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used for bioinformatics analysis. Correlation analysis explored the relationships between PARP9, infiltrating inflammatory immune cells, and immune checkpoint molecules. RESULTS PARP9 is highly expressed in glioma, and high expression of PARP9 is associated with poor prognosis and advanced clinicopathological features. Bioinformatics analysis showed that some immune-related pathways were closely associated with high expression of PARP9. Correlation analysis indicated that PARP9 was closely related to inflammatory and immune responses, high immune cell infiltration, and immune checkpoint molecules. CONCLUSIONS PARP9 may serve as an unfavorable prognosis predictor for glioma and a potential immunotherapeutic target.
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Affiliation(s)
- Hao Xu
- Department of NeurosurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Songshan Chai
- Department of NeurosurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yihao Wang
- Department of NeurosurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Jiajing Wang
- Department of NeurosurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Dongdong Xiao
- Department of NeurosurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Junjun Li
- Department of NeurosurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Nanxiang Xiong
- Department of NeurosurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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30
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Xu L, Yu D, Peng L, Wu Y, Fan Y, Gu T, Yao YL, Zhong J, Chen X, Yao YG. An Alternative Splicing of Tupaia STING Modulated Anti-RNA Virus Responses by Targeting MDA5-LGP2 and IRF3. THE JOURNAL OF IMMUNOLOGY 2020; 204:3191-3204. [DOI: 10.4049/jimmunol.1901320] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/15/2020] [Indexed: 01/01/2023]
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31
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Tian Q, Zhao H, Ling H, Sun L, Xiao C, Yin G, Wang X, Wu G, Yang C, Chen M, Jin S, Yang X, Wang J. Poly(ADP-Ribose) Polymerase Enhances Infiltration of Mononuclear Cells in Primary Sjögren's Syndrome Through Interferon-Induced Protein With Tetratricopeptide Repeats 1-Mediated Up-Regulation of CXCL10. Arthritis Rheumatol 2020; 72:1003-1012. [PMID: 31876388 DOI: 10.1002/art.41195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/19/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVE Mononuclear cell infiltration and type I interferon (IFN) system activation play an important role in primary Sjögren's syndrome (SS). We undertook this study to investigate the mechanism of poly(ADP-ribose) polymerase family member 9 (PARP-9) on mononuclear cell infiltration triggered by type I IFN. METHODS A proteomic study was conducted in peripheral blood mononuclear cells from patients with primary SS (n = 30) and healthy controls (n = 30) to determine differentially expressed proteins (DEPs) (P < 0.05; fold change >1.20). Labial salivary glands (LSGs) were isolated for hematoxylin and eosin staining and immunohistochemical analysis. CD19+ B cells were purified by magnetic cell sorting for immunofluorescence staining, lentivirus-PARP-9 transfection, and IFNα treatment experiments. PARP-9 small interfering RNA (siRNA) and DTX3L siRNA were delivered into female NOD/LtJ female mice to determine their effect. RESULTS The overexpression of PARP-9 and CXCL10 as well as their colocalization was confirmed in primary SS. PARP-9 levels in LSGs rose with increased Chisholm scores in patients with primary SS. PARP-9 and DTX3L were present in the infiltrating mononuclear cells from salivary glands in female NOD/LtJ mouse models. Additionally, Ingenuity Pathway Analysis networks of DEPs demonstrated that PARP-9, STAT1, and IFN-induced protein with tetratricopeptide repeats 1 (IFIT-1) participated in the IFN-related pathway. Furthermore, PARP-9 could up-regulate the expression of IFIT1 and CXCL10 in B cells. Moreover, PARP-9 and CXCL10 could be induced by IFNα in B cells. CONCLUSION This study is the first to implicate PARP-9 as a regulator of infiltration of mononuclear cells in primary SS progression and to reveal that PARP-9 increases CXCL10 expression through up-regulating IFIT-1, which is mediated by the phosphorylation of STAT1. PARP-9 might therefore be a novel therapeutic target for primary SS.
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Affiliation(s)
| | - Han Zhao
- Wenzhou Medical University, Wenzhou, China
| | | | - Li Sun
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | | | - Guoyu Yin
- Wenzhou Medical University, Wenzhou, China
| | - Xiaobing Wang
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Gan Wu
- Wenzhou Medical University, Wenzhou, China
| | | | - Mu Chen
- Wenzhou Medical University, Wenzhou, China
| | - Shengwei Jin
- The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xinyu Yang
- Wenzhou Medical University, Wenzhou, China
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32
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Abstract
ADP-ribosylation is an intricate and versatile posttranslational modification involved in the regulation of a vast variety of cellular processes in all kingdoms of life. Its complexity derives from the varied range of different chemical linkages, including to several amino acid side chains as well as nucleic acids termini and bases, it can adopt. In this review, we provide an overview of the different families of (ADP-ribosyl)hydrolases. We discuss their molecular functions, physiological roles, and influence on human health and disease. Together, the accumulated data support the increasingly compelling view that (ADP-ribosyl)hydrolases are a vital element within ADP-ribosyl signaling pathways and they hold the potential for novel therapeutic approaches as well as a deeper understanding of ADP-ribosylation as a whole.
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Affiliation(s)
| | - Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, 80145 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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33
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Fehr AR, Singh SA, Kerr CM, Mukai S, Higashi H, Aikawa M. The impact of PARPs and ADP-ribosylation on inflammation and host-pathogen interactions. Genes Dev 2020; 34:341-359. [PMID: 32029454 PMCID: PMC7050484 DOI: 10.1101/gad.334425.119] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Poly-adenosine diphosphate-ribose polymerases (PARPs) promote ADP-ribosylation, a highly conserved, fundamental posttranslational modification (PTM). PARP catalytic domains transfer the ADP-ribose moiety from NAD+ to amino acid residues of target proteins, leading to mono- or poly-ADP-ribosylation (MARylation or PARylation). This PTM regulates various key biological and pathological processes. In this review, we focus on the roles of the PARP family members in inflammation and host-pathogen interactions. Here we give an overview the current understanding of the mechanisms by which PARPs promote or suppress proinflammatory activation of macrophages, and various roles PARPs play in virus infections. We also demonstrate how innovative technologies, such as proteomics and systems biology, help to advance this research field and describe unanswered questions.
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Affiliation(s)
- Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Catherine M Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Shin Mukai
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hideyuki Higashi
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Center for Excellence in Vascular Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Human Pathology, I.M. Sechenov First Moscow State Medical University of the Ministry of Health, Moscow 119146, Russian Federation
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34
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Wigle TJ, Church WD, Majer CR, Swinger KK, Aybar D, Schenkel LB, Vasbinder MM, Brendes A, Beck C, Prahm M, Wegener D, Chang P, Kuntz KW. Forced Self-Modification Assays as a Strategy to Screen MonoPARP Enzymes. SLAS DISCOVERY 2019; 25:241-252. [PMID: 31855104 PMCID: PMC7036481 DOI: 10.1177/2472555219883623] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mono(ADP-ribosylation) (MARylation) and poly(ADP-ribosylation) (PARylation) are
posttranslational modifications found on multiple amino acids. There are 12
enzymatically active mono(ADP-ribose) polymerase (monoPARP) enzymes and 4
enzymatically active poly(ADP-ribose) polymerase (polyPARP) enzymes that use
nicotinamide adenine dinucleotide (NAD+) as the ADP-ribose donating
substrate to generate these modifications. While there are approved drugs and
clinical trials ongoing for the enzymes that perform PARylation, MARylation is
gaining recognition for its role in immune function, inflammation, and cancer.
However, there is a lack of chemical probes to study the function of monoPARPs
in cells and in vivo. An important first step to generating chemical probes for
monoPARPs is to develop biochemical assays to enable hit finding, and
determination of the potency and selectivity of inhibitors. Complicating the
development of enzymatic assays is that it is poorly understood how monoPARPs
engage their substrates. To overcome this, we have developed a family-wide
approach to developing robust high-throughput monoPARP assays where the enzymes
are immobilized and forced to self-modify using biotinylated-NAD+,
which is detected using a dissociation-enhanced lanthanide fluorescence
immunoassay (DELFIA) readout. Herein we describe the development of assays for
12 monoPARPs and 3 polyPARPs and apply them to understand the potency and
selectivity of a focused library of inhibitors across this family.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Paul Chang
- Ribon Therapeutics Inc., Cambridge, MA, USA
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35
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Palazzo L, Mikolčević P, Mikoč A, Ahel I. ADP-ribosylation signalling and human disease. Open Biol 2019; 9:190041. [PMID: 30991935 PMCID: PMC6501648 DOI: 10.1098/rsob.190041] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023] Open
Abstract
ADP-ribosylation (ADPr) is a reversible post-translational modification of proteins, which controls major cellular and biological processes, including DNA damage repair, cell proliferation and differentiation, metabolism, stress and immune responses. In order to maintain the cellular homeostasis, diverse ADP-ribosyl transferases and hydrolases are involved in the fine-tuning of ADPr systems. The control of ADPr network is vital, and dysregulation of enzymes involved in the regulation of ADPr signalling has been linked to a number of inherited and acquired human diseases, such as several neurological disorders and in cancer. Conversely, the therapeutic manipulation of ADPr has been shown to ameliorate several disorders in both human and animal models. These include cardiovascular, inflammatory, autoimmune and neurological disorders. Herein, we summarize the recent findings in the field of ADPr, which support the impact of this modification in human pathophysiology and highlight the curative potential of targeting ADPr for translational and molecular medicine.
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Affiliation(s)
- Luca Palazzo
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Petra Mikolčević
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
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Poly(ADP-Ribose) Polymerases in Host-Pathogen Interactions, Inflammation, and Immunity. Microbiol Mol Biol Rev 2018; 83:83/1/e00038-18. [PMID: 30567936 DOI: 10.1128/mmbr.00038-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The literature review presented here details recent research involving members of the poly(ADP-ribose) polymerase (PARP) family of proteins. Among the 17 recognized members of the family, the human enzyme PARP1 is the most extensively studied, resulting in a number of known biological and metabolic roles. This review is focused on the roles played by PARP enzymes in host-pathogen interactions and in diseases with an associated inflammatory response. In mammalian cells, several PARPs have specific roles in the antiviral response; this is perhaps best illustrated by PARP13, also termed the zinc finger antiviral protein (ZAP). Plant stress responses and immunity are also regulated by poly(ADP-ribosyl)ation. PARPs promote inflammatory responses by stimulating proinflammatory signal transduction pathways that lead to the expression of cytokines and cell adhesion molecules. Hence, PARP inhibitors show promise in the treatment of inflammatory disorders and conditions with an inflammatory component, such as diabetes, arthritis, and stroke. These functions are correlated with the biophysical characteristics of PARP family enzymes. This work is important in providing a comprehensive understanding of the molecular basis of pathogenesis and host responses, as well as in the identification of inhibitors. This is important because the identification of inhibitors has been shown to be effective in arresting the progression of disease.
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Palazzo L, Ahel I. PARPs in genome stability and signal transduction: implications for cancer therapy. Biochem Soc Trans 2018; 46:1681-1695. [PMID: 30420415 PMCID: PMC6299239 DOI: 10.1042/bst20180418] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/15/2018] [Accepted: 09/21/2018] [Indexed: 01/03/2023]
Abstract
The poly(ADP-ribose) polymerase (PARP) superfamily of enzymes catalyses the ADP-ribosylation (ADPr) of target proteins by using nicotinamide adenine dinucleotide (NAD+) as a donor. ADPr reactions occur either in the form of attachment of a single ADP-ribose nucleotide unit on target proteins or in the form of ADP-ribose chains, with the latter called poly(ADP-ribosyl)ation. PARPs regulate many cellular processes, including the maintenance of genome stability and signal transduction. In this review, we focus on the PARP family members that possess the ability to modify proteins by poly(ADP-ribosyl)ation, namely PARP1, PARP2, Tankyrase-1, and Tankyrase-2. Here, we detail the cellular functions of PARP1 and PARP2 in the regulation of DNA damage response and describe the function of Tankyrases in Wnt-mediated signal transduction. Furthermore, we discuss how the understanding of these pathways has provided some major breakthroughs in the treatment of human cancer.
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Affiliation(s)
- Luca Palazzo
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K.
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Zhu H, Wu LF, Mo XB, Lu X, Tang H, Zhu XW, Xia W, Guo YF, Wang MJ, Zeng KQ, Wu J, Qiu YH, Lin X, Zhang YH, Liu YZ, Yi NJ, Deng FY, Lei SF. Rheumatoid arthritis–associated DNA methylation sites in peripheral blood mononuclear cells. Ann Rheum Dis 2018; 78:36-42. [DOI: 10.1136/annrheumdis-2018-213970] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/28/2018] [Accepted: 09/12/2018] [Indexed: 12/26/2022]
Abstract
ObjectivesTo identify novel DNA methylation sites significant for rheumatoid arthritis (RA) and comprehensively understand their underlying pathological mechanism.MethodsWe performed (1) genome-wide DNA methylation and mRNA expression profiling in peripheral blood mononuclear cells from RA patients and health controls; (2) correlation analysis and causal inference tests for DNA methylation and mRNA expression data; (3) differential methylation genes regulatory network construction; (4) validation tests of 10 differential methylation positions (DMPs) of interest and corresponding gene expressions; (5) correlation between PARP9 methylation and its mRNA expression level in Jurkat cells and T cells from patients with RA; (6) testing the pathological functions of PARP9 in Jurkat cells.ResultsA total of 1046 DNA methylation positions were associated with RA. The identified DMPs have regulatory effects on mRNA expressions. Causal inference tests identified six DNA methylation–mRNA–RA regulatory chains (eg, cg00959259-PARP9-RA). The identified DMPs and genes formed an interferon-inducible gene interaction network (eg, MX1, IFI44L, DTX3L and PARP9). Key DMPs and corresponding genes were validated their differences in additional samples. Methylation of PARP9 was correlated with mRNA level in Jurkat cells and T lymphocytes isolated from patients with RA. The PARP9 gene exerted significant effects on Jurkat cells (eg, cell cycle, cell proliferation, cell activation and expression of inflammatory factor IL-2).ConclusionsThis multistage study identified an interferon-inducible gene interaction network associated with RA and highlighted the importance of PARP9 gene in RA pathogenesis. The results enhanced our understanding of the important role of DNA methylation in pathology of RA.
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Tang X, Zhang H, Long Y, Hua H, Jiang Y, Jing J. PARP9 is overexpressed in human breast cancer and promotes cancer cell migration. Oncol Lett 2018; 16:4073-4077. [PMID: 30128030 DOI: 10.3892/ol.2018.9124] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/01/2018] [Indexed: 02/05/2023] Open
Abstract
Poly(ADP-Ribose) polymerase family member 9 (PARP9) promotes the proliferation, survival and chemotherapy resistance in lymphoma and prostate cancer. The expression and function of PARP9 in human breast cancer remains unknown. In the present study, it was demonstrated that PARP9 is frequently overexpressed in human breast cancer. In 57 normal breast tissues, the expression of PARP9 was not detected in 43 cases (75.4%), but low levels of PARP9 were detected in 13 cases (22.8%), and modest levels of PARP9 (PARP9/GAPDH ratio ~1:1) were detected in only 1 case (1.7%). In contrast, the expression of PARP9 was detected in all 57 breast cancer tissues, in which the levels of PARP9 were higher than that in paired normal breast tissues. In addition, high levels of PARP9 were detected in 43.8% of breast cancer tissues. Overexpression of PARP9 was negatively associated with estrogen receptor expression, and positively associated with axillary lymph node metastasis. However, PARP9 expression was not associated with other clinicopathological parameters, including age, HER-2 and tumor size. Furthermore, PARP9-knockdown inhibited breast cancer cell migration. These data indicate that PARP9 may promote breast cancer progression.
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Affiliation(s)
- Xinghong Tang
- Department of Thyroid and Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Hongying Zhang
- Laboratory of Oncogene, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yan Long
- Laboratory of Oncogene, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Hui Hua
- Laboratory of Stem Cell Biology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yangfu Jiang
- Laboratory of Oncogene, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jing Jing
- Department of Thyroid and Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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Becker AC, Gannagé M, Giese S, Hu Z, Abou-Eid S, Roubaty C, Paul P, Bühler L, Gretzmeier C, Dumit VI, Kaeser-Pebernard S, Schwemmle M, Münz C, Dengjel J. Influenza A Virus Induces Autophagosomal Targeting of Ribosomal Proteins. Mol Cell Proteomics 2018; 17:1909-1921. [PMID: 29980615 PMCID: PMC6166674 DOI: 10.1074/mcp.ra117.000364] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 07/04/2018] [Indexed: 12/24/2022] Open
Abstract
Seasonal epidemics of influenza A virus are a major cause of severe illness and are of high socio-economic relevance. For the design of effective antiviral therapies, a detailed knowledge of pathways perturbed by virus infection is critical. We performed comprehensive expression and organellar proteomics experiments to study the cellular consequences of influenza A virus infection using three human epithelial cell lines derived from human lung carcinomas: A549, Calu-1 and NCI-H1299. As a common response, the type I interferon pathway was up-regulated upon infection. Interestingly, influenza A virus infection led to numerous cell line-specific responses affecting both protein abundance as well as subcellular localization. In A549 cells, the vesicular compartment appeared expanded after virus infection. The composition of autophagsomes was altered by targeting of ribosomes, viral mRNA and proteins to these double membrane vesicles. Thus, autophagy may support viral protein translation by promoting the clustering of the respective molecular machinery in autophagosomes in a cell line-dependent manner.
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Affiliation(s)
- Andrea C Becker
- From the ‡Department of Dermatology, Medical Center University of Freiburg, Hauptstr. 7, 79104 Freiburg, Germany.,§Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany
| | - Monique Gannagé
- ¶Department of Pathology and Immunology, School of Medicine, University of Geneva, 1 rue Michel Servet, 1211 Geneva, Switzerland
| | - Sebastian Giese
- §Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany.,‖Institute for Virology, Medical Center, University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany
| | - Zehan Hu
- From the ‡Department of Dermatology, Medical Center University of Freiburg, Hauptstr. 7, 79104 Freiburg, Germany.,§Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany.,§§Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Shadi Abou-Eid
- §§Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Carole Roubaty
- §§Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Petra Paul
- **Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lea Bühler
- From the ‡Department of Dermatology, Medical Center University of Freiburg, Hauptstr. 7, 79104 Freiburg, Germany.,§Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany
| | - Christine Gretzmeier
- From the ‡Department of Dermatology, Medical Center University of Freiburg, Hauptstr. 7, 79104 Freiburg, Germany.,§Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany
| | - Veronica I Dumit
- ‡‡Core Facility Proteomics, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | | | - Martin Schwemmle
- §Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany.,‖Institute for Virology, Medical Center, University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany
| | - Christian Münz
- **Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jörn Dengjel
- From the ‡Department of Dermatology, Medical Center University of Freiburg, Hauptstr. 7, 79104 Freiburg, Germany; .,§Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany.,§§Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
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Zeng Z, Liu H, Yuan J, Ren X, Deng Y, Dai W, Wu Y, Huang Y, Huang R, Liu J, Huang H, Hu J. Poly (ADP-ribose) glycohydrolase silencing-mediated maintenance of H2A and downregulation of H2AK9me protect human bronchial epithelial cells from benzo(a)pyrene-induced carcinogenesis. Toxicol Lett 2018; 295:270-276. [PMID: 29981922 DOI: 10.1016/j.toxlet.2018.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 05/31/2018] [Accepted: 07/04/2018] [Indexed: 01/15/2023]
Abstract
Poly (ADP-ribosylation) is a key post-translational modification (PTM), and poly (ADP-ribose) glycohydrolase (PARG) is the main enzyme that hydrolyzes poly (ADP-ribose) in eukaryotic organisms. Our previous findings suggested that knockdown of PARG attenuates benzo(a)pyrene (BaP) carcinogenesis. However, the mechanisms underlying PARG-mediated protective effects remain limited. In this study, the expression levels of histones were analyzed by Western blotting and immunofluorescence. Histone H2A levels were abnormally decreased by BaP-induced carcinogenesis, but were maintained by knockdown of PARG in the 16HBE human bronchial epithelial cell line. The interaction between poly (ADP-ribose) and H2A was confirmed by co-immunoprecipitation. PARG-related modifications in H2A were profiled by immune antibody enrichment coupled with mass spectrometry. H2AK5ac, H2AK9ac, H2AK13ac, H2A.ZK4K7K11ac, and H2AK9me were expressed in BaP-transformed 16HBE (BTC-16HBE) cells, but were not detectable in normal 16HBE or BaP-transformed 16HBE cells with knockdown of PARG (BTC-shPARG). Further verification by Western blotting indicated that H2AK9me was elevated in BTC-16HBE cells but decreased in BTC-shPARG cells. These findings suggest that knockdown of PARG protects against BaP-induced carcinogenesis in 16HBE cells by downregulating H2AK9me. Our in vivo studies confirmed that PARG silencing decreased H2AK9me levels, thereby countering the carcinogenic teratogenic effects induced by BaP.
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Affiliation(s)
- Zhuoying Zeng
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, China; Institude of Toxicology, Shenzhen Center for Disease Control and Prevention, China
| | - Hailong Liu
- Institude of Toxicology, Shenzhen Center for Disease Control and Prevention, China
| | - Jianhui Yuan
- Institude of Toxicology, Shenzhen Center for Disease Control and Prevention, China
| | - Xiaohu Ren
- Institude of Toxicology, Shenzhen Center for Disease Control and Prevention, China
| | - Yanxia Deng
- Institude of Toxicology, Shenzhen Center for Disease Control and Prevention, China
| | - Wenjuan Dai
- Institude of Toxicology, Shenzhen Center for Disease Control and Prevention, China
| | - Yue Wu
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, China
| | - Yun Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, China
| | - Ruixue Huang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, China
| | - Jiaofeng Liu
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, China
| | - Haiyan Huang
- Institude of Toxicology, Shenzhen Center for Disease Control and Prevention, China.
| | - Jian'an Hu
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, China.
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Caprara G, Prosperini E, Piccolo V, Sigismondo G, Melacarne A, Cuomo A, Boothby M, Rescigno M, Bonaldi T, Natoli G. PARP14 Controls the Nuclear Accumulation of a Subset of Type I IFN-Inducible Proteins. THE JOURNAL OF IMMUNOLOGY 2018; 200:2439-2454. [PMID: 29500242 DOI: 10.4049/jimmunol.1701117] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 01/29/2018] [Indexed: 12/20/2022]
Abstract
The enzymes of the poly-ADP-ribose polymerase (PARP) superfamily control many relevant cellular processes, but a precise understanding of their activities in different physiological or disease contexts is largely incomplete. We found that transcription of several Parp genes was dynamically regulated upon murine macrophage activation by endotoxin. PARP14 was strongly induced by several inflammatory stimuli and translocated into the nucleus of stimulated cells. Quantitative mass spectrometry analysis showed that PARP14 bound to a group of IFN-stimulated gene (ISG)-encoded proteins, most with an unknown function, and it was required for their nuclear accumulation. Moreover, PARP14 depletion attenuated transcription of primary antiviral response genes regulated by the IFN regulatory transcription factor 3, including Ifnb1, thus reducing IFN-β production and activation of ISGs involved in the secondary antiviral response. In agreement with the above-mentioned data, PARP14 hindered Salmonella typhimurium proliferation in murine macrophages. Overall, these data hint at a role of PARP14 in the control of antimicrobial responses and specifically in nuclear activities of a subgroup of ISG-encoded proteins.
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Affiliation(s)
- Greta Caprara
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milan, Italy;
| | - Elena Prosperini
- Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Viviana Piccolo
- Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | | | - Alessia Melacarne
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milan, Italy
| | - Mark Boothby
- Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Maria Rescigno
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milan, Italy.,Department of Biosciences, University of Milan, 20133 Milan, Italy; and
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milan, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milan, Italy; .,Humanitas University, 20089 Rozzano, Milan, Italy
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Lo PK, Yao Y, Lee JS, Zhang Y, Huang W, Kane MA, Zhou Q. LIPG signaling promotes tumor initiation and metastasis of human basal-like triple-negative breast cancer. eLife 2018; 7:31334. [PMID: 29350614 PMCID: PMC5809145 DOI: 10.7554/elife.31334] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/18/2018] [Indexed: 12/29/2022] Open
Abstract
Current understanding of aggressive human basal-like triple-negative breast cancer (TNBC) remains incomplete. In this study, we show endothelial lipase (LIPG) is aberrantly overexpressed in basal-like TNBCs. We demonstrate that LIPG is required for in vivo tumorigenicity and metastasis of TNBC cells. LIPG possesses a lipase-dependent function that supports cancer cell proliferation and a lipase-independent function that promotes invasiveness, stemness and basal/epithelial-mesenchymal transition features of TNBC. Mechanistically, LIPG executes its oncogenic function through its involvement in interferon-related DTX3L-ISG15 signaling, which regulates protein function and stability by ISGylation. We show that DTX3L, an E3-ubiquitin ligase, is required for maintaining LIPG protein levels in TNBC cells by inhibiting proteasome-mediated LIPG degradation. Inactivation of LIPG impairs DTX3L-ISG15 signaling, indicating the existence of DTX3L-LIPG-ISG15 signaling. We further reveal LIPG-ISG15 signaling is lipase-independent. We demonstrate that DTX3L-LIPG-ISG15 signaling is essential for malignancies of TNBC cells. Targeting this pathway provides a novel strategy for basal-like TNBC therapy.
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Affiliation(s)
- Pang-Kuo Lo
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, United States
| | - Yuan Yao
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, United States
| | - Ji Shin Lee
- Department of Pathology, Chonnam National University Medical School, Gwangju, Korea
| | - Yongshu Zhang
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, United States
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, United States
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, United States
| | - Qun Zhou
- Department of Biochemistry and Molecular Biology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, United States
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44
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Yang CS, Jividen K, Spencer A, Dworak N, Ni L, Oostdyk LT, Chatterjee M, Kuśmider B, Reon B, Parlak M, Gorbunova V, Abbas T, Jeffery E, Sherman NE, Paschal BM. Ubiquitin Modification by the E3 Ligase/ADP-Ribosyltransferase Dtx3L/Parp9. Mol Cell 2017; 66:503-516.e5. [PMID: 28525742 DOI: 10.1016/j.molcel.2017.04.028] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/18/2017] [Accepted: 04/28/2017] [Indexed: 10/19/2022]
Abstract
ADP-ribosylation of proteins is emerging as an important regulatory mechanism. Depending on the family member, ADP-ribosyltransferases either conjugate a single ADP-ribose to a target or generate ADP-ribose chains. Here we characterize Parp9, a mono-ADP-ribosyltransferase reported to be enzymatically inactive. Parp9 undergoes heterodimerization with Dtx3L, a histone E3 ligase involved in DNA damage repair. We show that the Dtx3L/Parp9 heterodimer mediates NAD+-dependent mono-ADP-ribosylation of ubiquitin, exclusively in the context of ubiquitin processing by E1 and E2 enzymes. Dtx3L/Parp9 ADP-ribosylates the carboxyl group of Ub Gly76. Because Gly76 is normally used for Ub conjugation to substrates, ADP-ribosylation of the Ub carboxyl terminus precludes ubiquitylation. Parp9 ADP-ribosylation activity therefore restrains the E3 function of Dtx3L. Mutation of the NAD+ binding site in Parp9 increases the DNA repair activity of the heterodimer. Moreover, poly(ADP-ribose) binding to the Parp9 macrodomains increases E3 activity. Dtx3L heterodimerization with Parp9 enables NAD+ and poly(ADP-ribose) regulation of E3 activity.
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Affiliation(s)
- Chun-Song Yang
- Center for Cell Signaling, University of Virginia, West Complex, 1335 Lee Street, Charlottesville, VA 22908, USA
| | - Kasey Jividen
- Center for Cell Signaling, University of Virginia, West Complex, 1335 Lee Street, Charlottesville, VA 22908, USA
| | - Adam Spencer
- Center for Cell Signaling, University of Virginia, West Complex, 1335 Lee Street, Charlottesville, VA 22908, USA
| | - Natalia Dworak
- Center for Cell Signaling, University of Virginia, West Complex, 1335 Lee Street, Charlottesville, VA 22908, USA
| | - Li Ni
- Center for Cell Signaling, University of Virginia, West Complex, 1335 Lee Street, Charlottesville, VA 22908, USA
| | - Luke T Oostdyk
- Center for Cell Signaling, University of Virginia, West Complex, 1335 Lee Street, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, PO Box 800733, Charlottesville, VA 22908, USA
| | - Mandovi Chatterjee
- Center for Cell Signaling, University of Virginia, West Complex, 1335 Lee Street, Charlottesville, VA 22908, USA
| | - Beata Kuśmider
- Center for Cell Signaling, University of Virginia, West Complex, 1335 Lee Street, Charlottesville, VA 22908, USA
| | - Brian Reon
- Department of Biochemistry and Molecular Genetics, University of Virginia, PO Box 800733, Charlottesville, VA 22908, USA
| | - Mahmut Parlak
- Department of Radiation Oncology, University of Virginia, PO Box 800383, Charlottesville, VA 22908, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, 434 Hutchison Hall, Rochester, NY 14627, USA
| | - Tarek Abbas
- Center for Cell Signaling, University of Virginia, West Complex, 1335 Lee Street, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, PO Box 800733, Charlottesville, VA 22908, USA; Department of Radiation Oncology, University of Virginia, PO Box 800383, Charlottesville, VA 22908, USA
| | - Erin Jeffery
- W. M. Keck Biomedical Mass Spectrometry Laboratory, University of Virginia, Pinn Hall, Room 1034, Charlottesville, VA 22908, USA
| | - Nicholas E Sherman
- W. M. Keck Biomedical Mass Spectrometry Laboratory, University of Virginia, Pinn Hall, Room 1034, Charlottesville, VA 22908, USA
| | - Bryce M Paschal
- Center for Cell Signaling, University of Virginia, West Complex, 1335 Lee Street, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, PO Box 800733, Charlottesville, VA 22908, USA.
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Xu P, Tao X, Zhao C, Huang Q, Chang H, Ban N, Bei Y, Xia X, Shen C, Wang K, Xu L, Wu P, Ren J, Wang D. DTX3L is upregulated in glioma and is associated with glioma progression. Int J Mol Med 2017. [PMID: 28627634 DOI: 10.3892/ijmm.2017.3023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Gliomas are the most common primary brain tumors of the central nervous system (CNS). Due to the poor prognosis of glioma patients, it is urgent to develop more effective therapies. Deltex-3-like (DTX3L), also known as B-lymphoma and BAL-associated protein (BBAP), has been reported to play an important role in the progression of many tumors. This study aimed to investigate the clinical significance and biological function of DTX3L in human glioma. Clinically, the protein expression level of DTX3L is increased in glioma tissues compared with that observed in normal brain tissues. Immunohistochemical analysis demonstrated that DTX3L was highly expressed in the glioma tissues and its level was correlated with the grade of malignancy. Multivariate analysis revealed the association between high expression of DTX3L and the poor prognosis of glioma patients. In addition, knockdown of DTX3L by siRNA transfection increased glioma cell apoptosis. Moreover, suppression of DTX3L expression was shown to significantly inhibit the migration and invasion of glioma cells. These data indicate that DTX3L plays an important role in the pathogenic process of glioma, suggesting that DTX3L could be a potential prognostic biomarker for glioma.
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Affiliation(s)
- Peng Xu
- Department of Pathology, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xuelei Tao
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Targets, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Chengjin Zhao
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Targets, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Qingfeng Huang
- Department of Neurosurgery, The Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Hao Chang
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Targets, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Na Ban
- Department of Pathology, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yuanqi Bei
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Targets, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Xiaojie Xia
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Targets, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Chaoyan Shen
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Targets, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Kun Wang
- Department of Pathology, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Li Xu
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Targets, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Peizhang Wu
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Targets, Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Jianbing Ren
- Department of Neurosurgery, The Second People's Hospital of Nantong, Nantong, Jiangsu 226001, P.R. China
| | - Donglin Wang
- Department of Pathology, Nantong University, Nantong, Jiangsu 226001, P.R. China
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46
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Robert I, Gaudot L, Yélamos J, Noll A, Wong HK, Dantzer F, Schreiber V, Reina-San-Martin B. Robust immunoglobulin class switch recombination and end joining in Parp9-deficient mice. Eur J Immunol 2017; 47:665-676. [PMID: 28105679 DOI: 10.1002/eji.201646757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/16/2016] [Accepted: 01/18/2017] [Indexed: 12/15/2022]
Abstract
To mount highly specific and adapted immune responses, B lymphocytes assemble and diversify their antibody repertoire through mechanisms involving the formation of programmed DNA damage. Immunoglobulin class switch recombination (CSR) is triggered by DNA lesions induced by activation-induced cytidine deaminase, which are processed to double-stranded DNA break (DSB) intermediates. These DSBs activate the cellular DNA damage response and enroll numerous DNA repair factors, involving poly(ADP-ribose) polymerases Parp1, Parp2, and Parp3 to promote appropriate DNA repair and efficient long-range recombination. The macroParp Parp9, which is overexpressed in certain lymphomas, has been recently implicated in DSB repair, acting together with Parp1. Here, we examine the contribution of Parp9 to the resolution of physiological DSBs incurred during V(D)J recombination and CSR by generating Parp9-/- mice. We find that Parp9-deficient mice are viable, fertile, and do not show any overt phenotype. Moreover, we find that Parp9 is dispensable for B-cell development. Finally, we show that CSR and DNA end-joining are robust in the absence of Parp9, indicating that Parp9 is not essential in vivo to achieve physiological DSB repair, or that strong compensatory mechanisms exist.
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Affiliation(s)
- Isabelle Robert
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Centre National de Recherche Scientifique, UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Léa Gaudot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Centre National de Recherche Scientifique, UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Department of Immunology, Hospital del Mar, Barcelona, Spain.,Network Center for Biomedical Research on Hepatic and Digestive Diseases, Madrid, Spain
| | - Aurélia Noll
- Centre National de Recherche Scientifique, UMR7242, Illkirch, France.,Laboratoire d'Excellence Medalis, Université de Strasbourg, Illkirch, France.,Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, Illkirch, France.,Ecole Supérieure de Biotechnologie de Strasbourg, Illkirch, France
| | - Heng-Kuan Wong
- Centre National de Recherche Scientifique, UMR7242, Illkirch, France.,Laboratoire d'Excellence Medalis, Université de Strasbourg, Illkirch, France.,Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, Illkirch, France.,Ecole Supérieure de Biotechnologie de Strasbourg, Illkirch, France
| | - Françoise Dantzer
- Centre National de Recherche Scientifique, UMR7242, Illkirch, France.,Laboratoire d'Excellence Medalis, Université de Strasbourg, Illkirch, France.,Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, Illkirch, France.,Ecole Supérieure de Biotechnologie de Strasbourg, Illkirch, France
| | - Valérie Schreiber
- Centre National de Recherche Scientifique, UMR7242, Illkirch, France.,Laboratoire d'Excellence Medalis, Université de Strasbourg, Illkirch, France.,Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, Illkirch, France.,Ecole Supérieure de Biotechnologie de Strasbourg, Illkirch, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Centre National de Recherche Scientifique, UMR7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
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47
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Thang ND, Minh NV, Huong PT. Translocation of BBAP from the cytoplasm to the nucleus reduces the metastatic ability of vemurafenib-resistant SKMEL28 cells. Mol Med Rep 2016; 15:317-322. [PMID: 27922665 DOI: 10.3892/mmr.2016.5976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 11/01/2016] [Indexed: 11/06/2022] Open
Abstract
To the best of our knowledge, the present study is the first to demonstrate that treatment of vemurafenib-resistant SKMEL28 (SKMEL28-R) cells with paclitaxel leads to a shift in localization of the E3-ligase BBAP from the cytoplasm to the nucleus, consequently decreasing the metastatic ability of this cell line. The present study revealed that the movement of BBAP from the cytoplasm to nucleus initiated a change in cell morphology. In addition, the translocation of BBAP led to a decrease of metastatic characteristics in SKMEL28‑R cells, including migration and invasion via downregulation of the phosphorylated form of focal adhesion kinase and N‑cadherin, as well as an upregulation of p21 and E-cadherin. The results of the present study suggested that BBAP may not only be a novel biomarker for melanoma, but also a novel therapeutic target for treatment of metastatic melanoma.
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Affiliation(s)
- Nguyen Dinh Thang
- Department of Biochemistry and Plant Physiology, Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi 120564, Vietnam
| | - Nguyen Van Minh
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi 120564, Vietnam
| | - Pham Thu Huong
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, Vietnam National University, Hanoi 120564, Vietnam
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48
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Grinchuk OV, Motakis E, Yenamandra SP, Ow GS, Jenjaroenpun P, Tang Z, Yarmishyn AA, Ivshina AV, Kuznetsov VA. Sense-antisense gene-pairs in breast cancer and associated pathological pathways. Oncotarget 2016; 6:42197-221. [PMID: 26517092 PMCID: PMC4747219 DOI: 10.18632/oncotarget.6255] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 09/30/2015] [Indexed: 01/04/2023] Open
Abstract
More than 30% of human protein-coding genes form hereditary complex genome architectures composed of sense-antisense (SA) gene pairs (SAGPs) transcribing their RNAs from both strands of a given locus. Such architectures represent important novel components of genome complexity contributing to gene expression deregulation in cancer cells. Therefore, the architectures might be involved in cancer pathways and, in turn, be used for novel drug targets discovery. However, the global roles of SAGPs in cancer pathways has not been studied. Here we investigated SAGPs associated with breast cancer (BC)-related pathways using systems biology, prognostic survival and experimental methods. Gene expression analysis identified 73 BC-relevant SAGPs that are highly correlated in BC. Survival modelling and metadata analysis of the 1161 BC patients allowed us to develop a novel patient prognostic grouping method selecting the 12 survival-significant SAGPs. The qRT-PCR-validated 12-SAGP prognostic signature reproducibly stratified BC patients into low- and high-risk prognostic subgroups. The 1381 SAGP-defined differentially expressed genes common across three studied cohorts were identified. The functional enrichment analysis of these genes revealed the GABPA gene network, including BC-relevant SAGPs, specific gene sets involved in cell cycle, spliceosomal and proteasomal pathways. The co-regulatory function of GABPA in BC cells was supported using siRNA knockdown studies. Thus, we demonstrated SAGPs as the synergistically functional genome architectures interconnected with cancer-related pathways and associated with BC patient clinical outcomes. Taken together, SAGPs represent an important component of genome complexity which can be used to identify novel aspects of coordinated pathological gene networks in cancers.
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Affiliation(s)
- Oleg V Grinchuk
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Efthymios Motakis
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore.,Current address: RIKEN, Japan
| | - Surya Pavan Yenamandra
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Ghim Siong Ow
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Piroon Jenjaroenpun
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Zhiqun Tang
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Aliaksandr A Yarmishyn
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Anna V Ivshina
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Vladimir A Kuznetsov
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore.,School of Computing Engineering, Nanyang Technological University, Singapore
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49
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Posavec Marjanović M, Crawford K, Ahel I. PARP, transcription and chromatin modeling. Semin Cell Dev Biol 2016; 63:102-113. [PMID: 27677453 DOI: 10.1016/j.semcdb.2016.09.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/14/2016] [Accepted: 09/23/2016] [Indexed: 12/21/2022]
Abstract
Compaction mode of chromatin and chromatin highly organised structures regulate gene expression. Posttranslational modifications, histone variants and chromatin remodelers modulate the compaction, structure and therefore function of specific regions of chromatin. The generation of poly(ADP-ribose) (PAR) is emerging as one of the key signalling events on sites undergoing chromatin structure modulation. PAR is generated locally in response to stresses. These include genotoxic stress but also differentiation signals, metabolic and hormonal cues. A pictures emerges in which transient PAR formation is essential to orchestrate chromatin remodelling and transcription factors allowing the cell to adapt to alteration in its environment. This review summarizes the diverse factors of ADP-ribosylation in the adaptive regulation of chromatin structure and transcription.
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Affiliation(s)
| | - Kerryanne Crawford
- Sir William Dunn School of Pathology, University of Oxford, S Parks Rd, Oxford OX1 3RE, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, S Parks Rd, Oxford OX1 3RE, UK,.
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50
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Sanchez N, Chapdelaine P, Rousseau J, Raymond F, Corbeil J, Tremblay JP. Characterization of frataxin gene network in Friedreich's ataxia fibroblasts using the RNA-Seq technique. Mitochondrion 2016; 30:59-66. [PMID: 27350085 DOI: 10.1016/j.mito.2016.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 06/11/2016] [Accepted: 06/15/2016] [Indexed: 11/25/2022]
Affiliation(s)
- Noëlia Sanchez
- Axe neurosciences, Centre de recherche du CHUL, Université Laval, Québec City, QC, Canada.
| | - Pierre Chapdelaine
- Axe neurosciences, Centre de recherche du CHUL, Université Laval, Québec City, QC, Canada.
| | - Joël Rousseau
- Axe neurosciences, Centre de recherche du CHUL, Université Laval, Québec City, QC, Canada.
| | - Frédéric Raymond
- Axe maladies infectieuses et immunitaires, Centre de recherche du CHUL, Université Laval, Québec City, QC, Canada.
| | - Jacques Corbeil
- Axe maladies infectieuses et immunitaires, Centre de recherche du CHUL, Université Laval, Québec City, QC, Canada.
| | - Jacques P Tremblay
- Axe neurosciences, Centre de recherche du CHUL, Université Laval, Québec City, QC, Canada.
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