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Andronikou C, Burdova K, Dibitetto D, Lieftink C, Malzer E, Kuiken HJ, Gogola E, Ray Chaudhuri A, Beijersbergen RL, Hanzlikova H, Jonkers J, Rottenberg S. PARG-deficient tumor cells have an increased dependence on EXO1/FEN1-mediated DNA repair. EMBO J 2024; 43:1015-1042. [PMID: 38360994 PMCID: PMC10943112 DOI: 10.1038/s44318-024-00043-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
Targeting poly(ADP-ribose) glycohydrolase (PARG) is currently explored as a therapeutic approach to treat various cancer types, but we have a poor understanding of the specific genetic vulnerabilities that would make cancer cells susceptible to such a tailored therapy. Moreover, the identification of such vulnerabilities is of interest for targeting BRCA2;p53-deficient tumors that have acquired resistance to poly(ADP-ribose) polymerase inhibitors (PARPi) through loss of PARG expression. Here, by performing whole-genome CRISPR/Cas9 drop-out screens, we identify various genes involved in DNA repair to be essential for the survival of PARG;BRCA2;p53-deficient cells. In particular, our findings reveal EXO1 and FEN1 as major synthetic lethal interactors of PARG loss. We provide evidence for compromised replication fork progression, DNA single-strand break repair, and Okazaki fragment processing in PARG;BRCA2;p53-deficient cells, alterations that exacerbate the effects of EXO1/FEN1 inhibition and become lethal in this context. Since this sensitivity is dependent on BRCA2 defects, we propose to target EXO1/FEN1 in PARPi-resistant tumors that have lost PARG activity. Moreover, EXO1/FEN1 targeting may be a useful strategy for enhancing the effect of PARG inhibitors in homologous recombination-deficient tumors.
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Affiliation(s)
- Christina Andronikou
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland
| | - Kamila Burdova
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Diego Dibitetto
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Elke Malzer
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Hendrik J Kuiken
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD, Rotterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Hana Hanzlikova
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands.
- Oncode Institute, Amsterdam, The Netherlands.
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland.
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands.
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland.
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2
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Vaitsiankova A, Burdova K, Sobol M, Gautam A, Benada O, Hanzlikova H, Caldecott KW. PARP inhibition impedes the maturation of nascent DNA strands during DNA replication. Nat Struct Mol Biol 2022; 29:329-338. [PMID: 35332322 PMCID: PMC9010290 DOI: 10.1038/s41594-022-00747-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is implicated in the detection and processing of unligated Okazaki fragments and other DNA replication intermediates, highlighting such structures as potential sources of genome breakage induced by PARP inhibition. Here, we show that PARP1 activity is greatly elevated in chicken and human S phase cells in which FEN1 nuclease is genetically deleted and is highest behind DNA replication forks. PARP inhibitor reduces the integrity of nascent DNA strands in both wild-type chicken and human cells during DNA replication, and does so in FEN1-/- cells to an even greater extent that can be detected as postreplicative single-strand nicks or gaps. Collectively, these data show that PARP inhibitors impede the maturation of nascent DNA strands during DNA replication, and implicate unligated Okazaki fragments and other nascent strand discontinuities in the cytotoxicity of these compounds.
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Affiliation(s)
- Alina Vaitsiankova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Kamila Burdova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Margarita Sobol
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Amit Gautam
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Oldrich Benada
- Laboratory of Molecular Structure Characterization, Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Hana Hanzlikova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, Czech Republic.
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, Czech Republic.
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3
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Adamowicz M, Hailstone R, Demin AA, Komulainen E, Hanzlikova H, Brazina J, Gautam A, Wells SE, Caldecott KW. XRCC1 protects transcription from toxic PARP1 activity during DNA base excision repair. Nat Cell Biol 2021; 23:1287-1298. [PMID: 34811483 PMCID: PMC8683375 DOI: 10.1038/s41556-021-00792-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022]
Abstract
Genetic defects in the repair of DNA single-strand breaks (SSBs) can result in neurological disease triggered by toxic activity of the single-strand-break sensor protein PARP1. However, the mechanism(s) by which this toxic PARP1 activity triggers cellular dysfunction are unclear. Here we show that human cells lacking XRCC1 fail to rapidly recover transcription following DNA base damage, a phenotype also observed in patient-derived fibroblasts with XRCC1 mutations and Xrcc1−/− mouse neurons. This defect is caused by excessive/aberrant PARP1 activity during DNA base excision repair, resulting from the loss of PARP1 regulation by XRCC1. We show that aberrant PARP1 activity suppresses transcriptional recovery during base excision repair by promoting excessive recruitment and activity of the ubiquitin protease USP3, which as a result reduces the level of monoubiquitinated histones important for normal transcriptional regulation. Importantly, inhibition and/or deletion of PARP1 or USP3 restores transcriptional recovery in XRCC1−/− cells, highlighting PARP1 and USP3 as possible therapeutic targets in neurological disease. Adamowicz et al. report that toxic PARP1 activity, induced by ataxia-associated mutations in XRCC1, impairs the recovery of global transcription during DNA base excision repair by promoting aberrant recruitment and activity of the histone ubiquitin protease USP3.
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Affiliation(s)
- Marek Adamowicz
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Richard Hailstone
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Annie A Demin
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Emilia Komulainen
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Hana Hanzlikova
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK.,Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Science, Prague, Czech Republic
| | - Jan Brazina
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Amit Gautam
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Sophie E Wells
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK. .,Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Science, Prague, Czech Republic.
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4
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Komulainen E, Badman J, Rey S, Rulten S, Ju L, Fennell K, Kalasova I, Ilievova K, McKinnon PJ, Hanzlikova H, Staras K, Caldecott KW. Parp1 hyperactivity couples DNA breaks to aberrant neuronal calcium signalling and lethal seizures. EMBO Rep 2021; 22:e51851. [PMID: 33932076 PMCID: PMC8097344 DOI: 10.15252/embr.202051851] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/21/2022] Open
Abstract
Defects in DNA single-strand break repair (SSBR) are linked with neurological dysfunction but the underlying mechanisms remain poorly understood. Here, we show that hyperactivity of the DNA strand break sensor protein Parp1 in mice in which the central SSBR protein Xrcc1 is conditionally deleted (Xrcc1Nes-Cre ) results in lethal seizures and shortened lifespan. Using electrophysiological recording and synaptic imaging approaches, we demonstrate that aberrant Parp1 activation triggers seizure-like activity in Xrcc1-defective hippocampus ex vivo and deregulated presynaptic calcium signalling in isolated hippocampal neurons in vitro. Moreover, we show that these defects are prevented by Parp1 inhibition or deletion and, in the case of Parp1 deletion, that the lifespan of Xrcc1Nes-Cre mice is greatly extended. This is the first demonstration that lethal seizures can be triggered by aberrant Parp1 activity at unrepaired SSBs, highlighting PARP inhibition as a possible therapeutic approach in hereditary neurological disease.
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Affiliation(s)
- Emilia Komulainen
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
| | - Jack Badman
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
- Sussex NeuroscienceSchool of Life SciencesUniversity of SussexBrightonUK
| | - Stephanie Rey
- Sussex NeuroscienceSchool of Life SciencesUniversity of SussexBrightonUK
| | - Stuart Rulten
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
| | - Limei Ju
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
| | - Kate Fennell
- Sussex NeuroscienceSchool of Life SciencesUniversity of SussexBrightonUK
| | - Ilona Kalasova
- Department of Genome DynamicsInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Kristyna Ilievova
- Department of Genome DynamicsInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Peter J McKinnon
- Department of GeneticsSt Jude Children’s Research HospitalMemphisTNUSA
| | - Hana Hanzlikova
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
- Department of Genome DynamicsInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Kevin Staras
- Sussex NeuroscienceSchool of Life SciencesUniversity of SussexBrightonUK
| | - Keith W Caldecott
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
- Department of Genome DynamicsInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
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5
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Wu W, Hill SE, Nathan WJ, Paiano J, Callen E, Wang D, Shinoda K, van Wietmarschen N, Colón-Mercado JM, Zong D, De Pace R, Shih HY, Coon S, Parsadanian M, Pavani R, Hanzlikova H, Park S, Jung SK, McHugh PJ, Canela A, Chen C, Casellas R, Caldecott KW, Ward ME, Nussenzweig A. Neuronal enhancers are hotspots for DNA single-strand break repair. Nature 2021; 593:440-444. [PMID: 33767446 PMCID: PMC9827709 DOI: 10.1038/s41586-021-03468-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023]
Abstract
Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons1,2. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breaks (SSBs) at specific sites within the genome. Genome-wide mapping reveals that SSBs are located within enhancers at or near CpG dinucleotides and sites of DNA demethylation. These SSBs are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair increase DNA repair synthesis at neuronal enhancers, whereas defects in long-patch repair reduce synthesis. The high levels of SSB repair in neuronal enhancers are therefore likely to be sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell-type-specific SSB repair, revealing unexpected levels of localized and continuous DNA breakage in neurons. In addition, they suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.
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Affiliation(s)
- Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sarah E Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - William J Nathan
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.,Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jacob Paiano
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Dongpeng Wang
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kenta Shinoda
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | - Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Raffaella De Pace
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Han-Yu Shih
- National Eye Institute, NIH, Bethesda, MD, USA
| | - Steve Coon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Maia Parsadanian
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Hana Hanzlikova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Solji Park
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Seol Kyoung Jung
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Andres Canela
- The Hakubi Center for Advanced Research and Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Chongyi Chen
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Keith W Caldecott
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic. .,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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6
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Kalasova I, Hailstone R, Bublitz J, Bogantes J, Hofmann W, Leal A, Hanzlikova H, Caldecott KW. Pathological mutations in PNKP trigger defects in DNA single-strand break repair but not DNA double-strand break repair. Nucleic Acids Res 2020; 48:6672-6684. [PMID: 32504494 PMCID: PMC7337934 DOI: 10.1093/nar/gkaa489] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/30/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
Hereditary mutations in polynucleotide kinase-phosphatase (PNKP) result in a spectrum of neurological pathologies ranging from neurodevelopmental dysfunction in microcephaly with early onset seizures (MCSZ) to neurodegeneration in ataxia oculomotor apraxia-4 (AOA4) and Charcot-Marie-Tooth disease (CMT2B2). Consistent with this, PNKP is implicated in the repair of both DNA single-strand breaks (SSBs) and DNA double-strand breaks (DSBs); lesions that can trigger neurodegeneration and neurodevelopmental dysfunction, respectively. Surprisingly, however, we did not detect a significant defect in DSB repair (DSBR) in primary fibroblasts from PNKP patients spanning the spectrum of PNKP-mutated pathologies. In contrast, the rate of SSB repair (SSBR) is markedly reduced. Moreover, we show that the restoration of SSBR in patient fibroblasts collectively requires both the DNA kinase and DNA phosphatase activities of PNKP, and the fork-head associated (FHA) domain that interacts with the SSBR protein, XRCC1. Notably, however, the two enzymatic activities of PNKP appear to affect different aspects of disease pathology, with reduced DNA phosphatase activity correlating with neurodevelopmental dysfunction and reduced DNA kinase activity correlating with neurodegeneration. In summary, these data implicate reduced rates of SSBR, not DSBR, as the source of both neurodevelopmental and neurodegenerative pathology in PNKP-mutated disease, and the extent and nature of this reduction as the primary determinant of disease severity.
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Affiliation(s)
- Ilona Kalasova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Richard Hailstone
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Janin Bublitz
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Jovel Bogantes
- Servicio de Cirugía Reconstructiva, Hospital Rafael Ángel Calderón Guardia, Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Alejandro Leal
- Section of Genetics and Biotechnology, School of Biology, University of Costa Rica, San José, Costa Rica
| | - Hana Hanzlikova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic.,Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Keith W Caldecott
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic.,Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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7
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Hanzlikova H, Prokhorova E, Krejcikova K, Cihlarova Z, Kalasova I, Kubovciak J, Sachova J, Hailstone R, Brazina J, Ghosh S, Cirak S, Gleeson JG, Ahel I, Caldecott KW. Pathogenic ARH3 mutations result in ADP-ribose chromatin scars during DNA strand break repair. Nat Commun 2020; 11:3391. [PMID: 32636369 PMCID: PMC7341855 DOI: 10.1038/s41467-020-17069-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/08/2020] [Indexed: 12/31/2022] Open
Abstract
Neurodegeneration is a common hallmark of individuals with hereditary defects in DNA single-strand break repair; a process regulated by poly(ADP-ribose) metabolism. Recently, mutations in the ARH3 (ADPRHL2) hydrolase that removes ADP-ribose from proteins have been associated with neurodegenerative disease. Here, we show that ARH3-mutated patient cells accumulate mono(ADP-ribose) scars on core histones that are a molecular memory of recently repaired DNA single-strand breaks. We demonstrate that the ADP-ribose chromatin scars result in reduced endogenous levels of important chromatin modifications such as H3K9 acetylation, and that ARH3 patient cells exhibit measurable levels of deregulated transcription. Moreover, we show that the mono(ADP-ribose) scars are lost from the chromatin of ARH3-defective cells in the prolonged presence of PARP inhibition, and concomitantly that chromatin acetylation is restored to normal. Collectively, these data indicate that ARH3 can act as an eraser of ADP-ribose chromatin scars at sites of PARP activity during DNA single-strand break repair.
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Affiliation(s)
- Hana Hanzlikova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic.
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Katerina Krejcikova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Zuzana Cihlarova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Ilona Kalasova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Jan Kubovciak
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Jana Sachova
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Richard Hailstone
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Jan Brazina
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Shereen Ghosh
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, 92093, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Sebahattin Cirak
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, 50931, Germany
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50931, Germany
- Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50931, Germany
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, 92093, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Keith W Caldecott
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic.
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
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8
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Mahjoub A, Cihlarova Z, Tétreault M, MacNeil L, Sondheimer N, Caldecott KW, Hanzlikova H, Yoon G. Homozygous pathogenic variant in BRAT1 associated with nonprogressive cerebellar ataxia. Neurol Genet 2019; 5:e359. [PMID: 31742228 PMCID: PMC6773431 DOI: 10.1212/nxg.0000000000000359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/29/2019] [Indexed: 11/16/2022]
Abstract
Objective To investigate the pathogenicity of a novel homozygous BRAT1 variant in 2 siblings with nonprogressive cerebellar ataxia (NPCA) through functional studies on primary and immortalized patient cell lines. Methods BRAT1 protein levels and ataxia-telangiectasia mutated (ATM) kinase activity in patient-derived and control cell lines were assessed by Western blotting. The impact of the novel BRAT1 variants on mitochondrial function was also assessed, by comparing patient and control cell lines for rates of oxygen consumption and for phosphorylation (S293) of the E1⍺ subunit of pyruvate dehydrogenase (PDH). Results Two male siblings with NPCA, mild intellectual disability, and isolated cerebellar atrophy were found to be homozygous for a c.185T>A (p.Val62Glu) variant in BRAT1 by whole exome sequencing. Western blotting revealed markedly decreased BRAT1 protein levels in lymphocytes and/or fibroblast cells from both affected siblings compared to control cell lines. There were no differences between the patient and control cells in ATM kinase activation, following ionizing radiation. Mitochondrial studies were initially suggestive of a defect in regulation of PDH activity, but there was no evidence of increased phosphorylation of the E1⍺ subunit of the PDH complex. Measurement of oxygen consumption rates similarly failed to identify differences between patient and control cells. Conclusions Biallelic pathogenic variants in BRAT1 can be associated with NPCA, a phenotype considerably milder than previously reported. Surprisingly, despite the molecular role currently proposed for BRAT1 in ATM regulation, this disorder is unlikely to result from defective ATM kinase or mitochondrial dysfunction.
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Affiliation(s)
- Areej Mahjoub
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Zuzana Cihlarova
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Martine Tétreault
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Lauren MacNeil
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Neal Sondheimer
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Keith W Caldecott
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Hana Hanzlikova
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Grace Yoon
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
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9
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Abstract
Accurate copying of DNA during S phase is essential for genome stability and cell viability. During genome duplication, the progression of the DNA replication machinery is challenged by limitations in nucleotide supply and physical barriers in the DNA template that include naturally occurring DNA lesions and secondary structures that are difficult to replicate. To ensure correct and complete replication of the genome, cells have evolved several mechanisms that protect DNA replication forks and thus maintain genome integrity and stability during S phase. One class of enzymes that have recently emerged as important in this process, and therefore as promising targets in anticancer therapy, are the poly(ADP-ribose) polymerases (PARPs). We review here the roles of these enzymes during DNA replication as well as their impact on genome stability and cellular viability in normal and cancer cells.
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Affiliation(s)
- Hana Hanzlikova
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, 4, Czech Republic.
| | - Keith W Caldecott
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, 4, Czech Republic.
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10
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Vancurova M, Hanzlikova H, Knoblochova L, Kosla J, Majera D, Mistrik M, Burdova K, Hodny Z, Bartek J. PML nuclear bodies are recruited to persistent DNA damage lesions in an RNF168-53BP1 dependent manner and contribute to DNA repair. DNA Repair (Amst) 2019; 78:114-127. [PMID: 31009828 DOI: 10.1016/j.dnarep.2019.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/07/2019] [Accepted: 04/01/2019] [Indexed: 11/29/2022]
Abstract
The bulk of DNA damage caused by ionizing radiation (IR) is generally repaired within hours, yet a subset of DNA lesions may persist even for long periods of time. Such persisting IR-induced foci (pIRIF) co-associate with PML nuclear bodies (PML-NBs) and are among the characteristics of cellular senescence. Here we addressed some fundamental questions concerning the nature and determinants of this co-association, the role of PML-NBs at such sites, and the reason for the persistence of DNA damage in human primary cells. We show that the persistent DNA lesions are devoid of homologous recombination (HR) proteins BRCA1 and Rad51. Our super-resolution microscopy-based analysis showed that PML-NBs are juxtaposed to and partially overlap with the pIRIFs. Notably, depletion of 53BP1 resulted in decreased intersection between PML-NBs and pIRIFs implicating the RNF168-53BP1 pathway in their interaction. To test whether the formation and persistence of IRIFs is PML-dependent and to investigate the role of PML in the context of DNA repair and senescence, we genetically deleted PML in human hTERT-RPE-1 cells. Unexpectedly, upon high-dose IR treatment, cells displayed similar DNA damage signalling, repair dynamics and kinetics of cellular senescence regardless of the presence or absence of PML. In contrast, the PML knock-out cells showed increased sensitivity to low doses of IR and DNA-damaging agents mitomycin C, cisplatin and camptothecin that all cause DNA lesions requiring repair by HR. These results, along with enhanced sensitivity of the PML knock-out cells to DNA-PK and PARP inhibitors implicate PML as a factor contributing to HR-mediated DNA repair.
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Affiliation(s)
- Marketa Vancurova
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Hana Hanzlikova
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lucie Knoblochova
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Kosla
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Dusana Majera
- Laboratory of Genome Integrity, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - Martin Mistrik
- Laboratory of Genome Integrity, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - Kamila Burdova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| | - Jiri Bartek
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic; Laboratory of Genome Integrity, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic; Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21, Stockholm, Sweden.
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11
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Kalasova I, Hanzlikova H, Gupta N, Li Y, Altmüller J, Reynolds JJ, Stewart GS, Wollnik B, Yigit G, Caldecott KW. Novel PNKP mutations causing defective DNA strand break repair and PARP1 hyperactivity in MCSZ. Neurol Genet 2019; 5:e320. [PMID: 31041400 PMCID: PMC6454307 DOI: 10.1212/nxg.0000000000000320] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/07/2019] [Indexed: 11/29/2022]
Abstract
Objective To address the relationship between novel mutations in polynucleotide 5'-kinase 3'-phosphatase (PNKP), DNA strand break repair, and neurologic disease. Methods We have employed whole-exome sequencing, Sanger sequencing, and molecular/cellular biology. Results We describe here a patient with microcephaly with early onset seizures (MCSZ) from the Indian sub-continent harboring 2 novel mutations in PNKP, including a pathogenic mutation in the fork-head associated domain. In addition, we confirm that MCSZ is associated with hyperactivation of the single-strand break sensor protein protein poly (ADP-ribose) polymerase 1 (PARP1) following the induction of abortive topoisomerase I activity, a source of DNA strand breakage associated previously with neurologic disease. Conclusions These data expand the spectrum of PNKP mutations associated with MCSZ and show that PARP1 hyperactivation at unrepaired topoisomerase-induced DNA breaks is a molecular feature of this disease.
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Affiliation(s)
- Ilona Kalasova
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Hana Hanzlikova
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Neerja Gupta
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Yun Li
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Janine Altmüller
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - John J Reynolds
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Grant S Stewart
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Bernd Wollnik
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Gökhan Yigit
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Keith W Caldecott
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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12
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Hanzlikova H, Kalasova I, Demin AA, Pennicott LE, Cihlarova Z, Caldecott KW. The Importance of Poly(ADP-Ribose) Polymerase as a Sensor of Unligated Okazaki Fragments during DNA Replication. Mol Cell 2018; 71:319-331.e3. [PMID: 29983321 PMCID: PMC6060609 DOI: 10.1016/j.molcel.2018.06.004] [Citation(s) in RCA: 220] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/11/2018] [Accepted: 06/01/2018] [Indexed: 01/08/2023]
Abstract
Poly(ADP-ribose) is synthesized by PARP enzymes during the repair of stochastic DNA breaks. Surprisingly, however, we show that most if not all endogenous poly(ADP-ribose) is detected in normal S phase cells at sites of DNA replication. This S phase poly(ADP-ribose) does not result from damaged or misincorporated nucleotides or from DNA replication stress. Rather, perturbation of the DNA replication proteins LIG1 or FEN1 increases S phase poly(ADP-ribose) more than 10-fold, implicating unligated Okazaki fragments as the source of S phase PARP activity. Indeed, S phase PARP activity is ablated by suppressing Okazaki fragment formation with emetine, a DNA replication inhibitor that selectively inhibits lagging strand synthesis. Importantly, PARP activation during DNA replication recruits the single-strand break repair protein XRCC1, and human cells lacking PARP activity and/or XRCC1 are hypersensitive to FEN1 perturbation. Collectively, our data indicate that PARP1 is a sensor of unligated Okazaki fragments during DNA replication and facilitates their repair.
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Affiliation(s)
- Hana Hanzlikova
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic.
| | - Ilona Kalasova
- Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic
| | - Annie A Demin
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Lewis E Pennicott
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Zuzana Cihlarova
- Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic
| | - Keith W Caldecott
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic.
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13
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Hanzlikova H, Gittens W, Krejcikova K, Zeng Z, Caldecott KW. Overlapping roles for PARP1 and PARP2 in the recruitment of endogenous XRCC1 and PNKP into oxidized chromatin. Nucleic Acids Res 2017; 45:2546-2557. [PMID: 27965414 PMCID: PMC5389470 DOI: 10.1093/nar/gkw1246] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/11/2016] [Indexed: 01/01/2023] Open
Abstract
A critical step of DNA single-strand break repair is the rapid recruitment of the scaffold protein XRCC1 that interacts with, stabilizes and stimulates multiple enzymatic components of the repair process. XRCC1 recruitment is promoted by PARP1, an enzyme that is activated following DNA damage and synthesizes ADP-ribose polymers that XRCC1 binds directly. However, cells possess two other DNA strand break-induced PARP enzymes, PARP2 and PARP3, for which the roles are unclear. To address their involvement in the recruitment of endogenous XRCC1 into oxidized chromatin we have established ‘isogenic’ human diploid cells in which PARP1 and/or PARP2, or PARP3 are deleted. Surprisingly, we show that either PARP1 or PARP2 are sufficient for near-normal XRCC1 recruitment at oxidative single-strand breaks (SSBs) as indicated by the requirement for loss of both proteins to greatly reduce or ablate XRCC1 chromatin binding following H2O2 treatment. Similar results were observed for PNKP; an XRCC1 protein partner important for repair of oxidative SSBs. Notably, concentrations of PARP inhibitor >1000-fold higher than the IC50 were required to ablate both ADP-ribosylation and XRCC1 chromatin binding following H2O2 treatment. These results demonstrate that very low levels of ADP-ribosylation, synthesized by either PARP1 or PARP2, are sufficient for XRCC1 recruitment following oxidative stress.
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Affiliation(s)
- Hana Hanzlikova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - William Gittens
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Katerina Krejcikova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | | | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
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14
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Hoch N, Hanzlikova H, Rulten SL, Tétreault M, Koumulainen E, Ju L, Hornyak P, Zeng Z, Gittens W, Rey S, Staras K, Mancini GM, McKinnon PJ, Wang ZQ, Wagner J, Yoon G, Caldecott KW. XRCC1 mutation is associated with PARP1 hyperactivation and cerebellar ataxia. Nature 2017; 541:87-91. [PMID: 28002403 PMCID: PMC5218588 DOI: 10.1038/nature20790] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 11/15/2016] [Indexed: 01/14/2023]
Abstract
XRCC1 is a molecular scaffold protein that assembles multi-protein complexes involved in DNA single-strand break repair. Here we show that biallelic mutations in the human XRCC1 gene are associated with ocular motor apraxia, axonal neuropathy, and progressive cerebellar ataxia. Cells from a patient with mutations in XRCC1 exhibited not only reduced rates of single-strand break repair but also elevated levels of protein ADP-ribosylation. This latter phenotype is recapitulated in a related syndrome caused by mutations in the XRCC1 partner protein PNKP and implicates hyperactivation of poly(ADP-ribose) polymerase/s as a cause of cerebellar ataxia. Indeed, remarkably, genetic deletion of Parp1 rescued normal cerebellar ADP-ribose levels and reduced the loss of cerebellar neurons and ataxia in Xrcc1-defective mice, identifying a molecular mechanism by which endogenous single-strand breaks trigger neuropathology. Collectively, these data establish the importance of XRCC1 protein complexes for normal neurological function and identify PARP1 as a therapeutic target in DNA strand break repair-defective disease.
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Affiliation(s)
- Nicolas Hoch
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
- CAPES Foundation, Ministry of Education of Brazil, Brasilia/DF 70040-020, Brazil
| | - Hana Hanzlikova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Stuart L. Rulten
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Martine Tétreault
- Department of Human Genetics, McGill University and Genome Québec Innovation Centre, Montréal, Québec, H3A 0G4, Canada
| | - Emilia Koumulainen
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Limei Ju
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Peter Hornyak
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Zhihong Zeng
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - William Gittens
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Stephanie Rey
- Neuroscience, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Kevin Staras
- Neuroscience, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Grazia M.S. Mancini
- Department of Clinical Genetics, Erasmus MC, P.O. Box 2040, 3000 CA, Rotterdam, the Netherlands
| | | | - Zhao-Qi Wang
- Leibniz Institute for Age Research, Fritz Lipmann Institute, 1107745 Jena, Germany
| | - Justin Wagner
- The Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1L 8H1, Canada
| | | | - Grace Yoon
- Division of Clinical and Metabolic Genetics, and Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, M5G 1X8, Canada
| | - Keith W. Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
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15
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Zarska M, Novotny F, Havel F, Sramek M, Babelova A, Benada O, Novotny M, Saran H, Kuca K, Musilek K, Hvezdova Z, Dzijak R, Vancurova M, Krejcikova K, Gabajova B, Hanzlikova H, Kyjacova L, Bartek J, Proska J, Hodny Z. Two-Step Mechanism of Cellular Uptake of Cationic Gold Nanoparticles Modified by (16-Mercaptohexadecyl)trimethylammonium Bromide. Bioconjug Chem 2016; 27:2558-2574. [PMID: 27602782 DOI: 10.1021/acs.bioconjchem.6b00491] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cationic colloidal gold nanorods (GNRs) have a great potential as a theranostic tool for diverse medical applications. GNRs' properties such as cellular internalization and stability are determined by physicochemical characteristics of their surface coating. GNRs modified by (16-mercaptohexadecyl)trimethylammonium bromide (MTAB), MTABGNRs, show excellent cellular uptake. Despite their promise for biomedicine, however, relatively little is known about the cellular pathways that facilitate the uptake of GNRs, their subcellular fate and intracellular persistence. Here we studied the mechanism of cellular internalization and long-term fate of GNRs coated with MTAB, for which the synthesis was optimized to give higher yield, in various human cell types including normal diploid versus cancerous, and dividing versus nondividing (senescent) cells. The process of MTABGNRs internalization into their final destination in lysosomes proceeds in two steps: (1) fast passive adhesion to cell membrane mediated by sulfated proteoglycans occurring within minutes and (2) slower active transmembrane and intracellular transport of individual nanorods via clathrin-mediated endocytosis and of aggregated nanorods via macropinocytosis. The expression of sulfated proteoglycans was the major factor determining the extent of uptake by the respective cell types. Upon uptake into proliferating cells, MTABGNRs were diluted equally and relatively rapidly into daughter cells; however, in nondividing/senescent cells the loss of MTABGNRs was gradual and very modest, attributable mainly to exocytosis. Exocytosed MTABGNRs can again be internalized. These findings broaden our knowledge about cellular uptake of gold nanorods, a crucial prerequisite for future successful engineering of nanoparticles for biomedical applications such as photothermal cancer therapy or elimination of senescent cells as part of the emerging rejuvenation approach.
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Affiliation(s)
- Monika Zarska
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic
| | - Filip Novotny
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic.,Department of Physical Electronics, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague , CZ-115 19 Prague 1, Czech Republic
| | - Filip Havel
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic.,Department of Physical Electronics, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague , CZ-115 19 Prague 1, Czech Republic
| | - Michal Sramek
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic
| | - Andrea Babelova
- Laboratory of Mutagenesis and Carcinogenesis, Cancer Research Institute BMC, Slovak Academy of Sciences , 945 05 Bratislava, Slovakia
| | - Oldrich Benada
- Laboratory of Molecular Structure Characterization, Institute of Microbiology of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic
| | - Michal Novotny
- Department of Chemistry, Faculty of Science, University of Hradec Kralove , 500 03 Hradec Kralove, Czech Republic.,Biomedical Research Center, University Hospital , CZ-500 05 Hradec Kralove, Czech Republic
| | - Hilal Saran
- Department of Chemistry, Faculty of Science, University of Hradec Kralove , 500 03 Hradec Kralove, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove , 500 03 Hradec Kralove, Czech Republic.,Biomedical Research Center, University Hospital , CZ-500 05 Hradec Kralove, Czech Republic
| | - Kamil Musilek
- Department of Chemistry, Faculty of Science, University of Hradec Kralove , 500 03 Hradec Kralove, Czech Republic.,Biomedical Research Center, University Hospital , CZ-500 05 Hradec Kralove, Czech Republic
| | - Zuzana Hvezdova
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic
| | - Rastislav Dzijak
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic
| | - Marketa Vancurova
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic
| | - Katerina Krejcikova
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic
| | - Blanka Gabajova
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic
| | - Hana Hanzlikova
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic
| | - Lenka Kyjacova
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic
| | - Jiri Bartek
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic.,Genome Integrity Unit, Danish Cancer Society Research Center , DK-2100 Copenhagen, Denmark.,Department of Medical Biochemistry and Biophysics, Science For Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institute , 17121 Solna, Sweden
| | - Jan Proska
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic.,Department of Physical Electronics, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague , CZ-115 19 Prague 1, Czech Republic
| | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics of the CAS, v.v.i. , CZ-142 20 Prague 4, Czech Republic
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16
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Mistrik M, Vesela E, Furst T, Hanzlikova H, Frydrych I, Gursky J, Majera D, Bartek J. Cells and Stripes: A novel quantitative photo-manipulation technique. Sci Rep 2016; 6:19567. [PMID: 26777522 PMCID: PMC4726120 DOI: 10.1038/srep19567] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/10/2015] [Indexed: 12/17/2022] Open
Abstract
Laser micro-irradiation is a technology widely used in the DNA damage response, checkpoint signaling, chromatin remodeling and related research fields, to assess chromatin modifications and recruitment of diverse DNA damage sensors, mediators and repair proteins to sites of DNA lesions. While this approach has aided numerous discoveries related to cell biology, maintenance of genome integrity, aging and cancer, it has so far been limited by a tedious manual definition of laser-irradiated subcellular regions, with the ensuing restriction to only a small number of cells treated and analyzed in a single experiment. Here, we present an improved and versatile alternative to the micro-irradiation approach: Quantitative analysis of photo-manipulated samples using innovative settings of standard laser-scanning microscopes. Up to 200 cells are simultaneously exposed to a laser beam in a defined pattern of collinear rays. The induced striation pattern is then automatically evaluated by a simple algorithm, which provides a quantitative assessment of various laser-induced phenotypes in live or fixed cells. Overall, this new approach represents a more robust alternative to existing techniques, and provides a versatile tool for a wide range of applications in biomedicine.
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Affiliation(s)
- Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Eva Vesela
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Tomas Furst
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Hana Hanzlikova
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic
| | - Ivo Frydrych
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Jan Gursky
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Dusana Majera
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Jiri Bartek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.,Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic.,Danish Cancer Society Research Center, Copenhagen, Denmark
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17
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Svadlenka J, Brazina J, Hanzlikova H, Cermak L, Andera L. Multifunctional adaptor protein Daxx interacts with chromatin-remodelling ATPase Brg1. Biochem Biophys Rep 2015; 5:246-252. [PMID: 28955830 PMCID: PMC5600331 DOI: 10.1016/j.bbrep.2015.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 11/25/2015] [Accepted: 12/28/2015] [Indexed: 01/22/2023] Open
Abstract
Multifunctional adapter and chaperone protein Daxx participates in the regulation of a number of mainly transcription-related processes. Most notably in a complex with chromatin-remodelling ATPase ATRX, Daxx serves as a histone H3.3 chaperone at telomeric regions and certain genes. In this report we document that Daxx interacts with another chromatin-remodelling, ATPase Brg1. We confirm the Daxx-Brg1 association both in vitro and in cells and show that Daxx interacts with Brg1 in high-molecular-weight complexes. Ectopic co-expression of Daxx with Brg1 and PML could shift disperse nuclear localisation of Brg1 into PML bodies. Mapping the Daxx-Brg1 interaction revealed that Daxx preferentially binds the region between Brg1 N-terminal QLQ and HSA domains, but also weakly interacts with its C-terminal part. Brg1 interacted with both the central and N-terminal parts of Daxx. SiRNA-mediated down-regulation of Daxx in SW13 adrenal carcinoma cells markedly enhanced expression of Brg1-activated genes CD44 or SCEL, suggesting that Daxx either directly through Brg1 and/or indirectly via other factors is a negative regulator of their transcription. Our findings point to Brg1 as another chromatin-remodelling protein that might similarly, as ATRX, target Daxx to specific chromatin regions where it can carry out its chromatin- and transcription-regulating functions.
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Affiliation(s)
- Jan Svadlenka
- Institute of Molecular Genetics AS CR, Czech Republic
| | - Jan Brazina
- Institute of Molecular Genetics AS CR, Czech Republic
| | | | - Lukas Cermak
- Department of Pathology, New York University School of Medicine, New York, USA
| | - Ladislav Andera
- Institute of Molecular Genetics AS CR, Czech Republic.,Institute of Biotechnology AS CR, Prague, Czech Republic
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18
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Brazina J, Svadlenka J, Macurek L, Andera L, Hodny Z, Bartek J, Hanzlikova H. DNA damage-induced regulatory interplay between DAXX, p53, ATM kinase and Wip1 phosphatase. Cell Cycle 2015; 14:375-87. [PMID: 25659035 PMCID: PMC4353233 DOI: 10.4161/15384101.2014.988019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Death domain-associated protein 6 (DAXX) is a histone chaperone, putative regulator of apoptosis and transcription, and candidate modulator of p53-mediated gene expression following DNA damage. DAXX becomes phosphorylated upon DNA damage, however regulation of this modification, and its relationship to p53 remain unclear. Here we show that in human cells exposed to ionizing radiation or genotoxic drugs etoposide and neocarzinostatin, DAXX became rapidly phosphorylated in an ATM kinase-dependent manner. Our deletion and site-directed mutagenesis experiments identified Serine 564 (S564) as the dominant ATM-targeted site of DAXX, and immunofluorescence experiments revealed localization of S564-phosphorylated DAXX to PML nuclear bodies. Furthermore, using a panel of human cell types, we identified the p53-regulated Wip1 protein phosphatase as a key negative regulator of DAXX phosphorylation at S564, both in vitro and in cells. Consistent with the emerging oncogenic role of Wip1, its DAXX-dephosphorylating impact was most apparent in cancer cell lines harboring gain-of-function mutant and/or overexpressed Wip1. Unexpectedly, while Wip1 depletion increased DAXX phosphorylation both before and after DNA damage and increased p53 stability and transcriptional activity, knock-down of DAXX impacted neither p53 stabilization nor p53-mediated expression of Gadd45a, Noxa, Mdm2, p21, Puma, Sesn2, Tigar or Wip1. Consistently, analyses of cells with genetic, TALEN-mediated DAXX deletion corroborated the notion that neither phosphorylated nor non-phosphorylated DAXX is required for p53-mediated gene expression upon DNA damage. Overall, we identify ATM kinase and Wip1 phosphatase as opposing regulators of DAXX-S564 phosphorylation, and propose that the role of DAXX phosphorylation and DAXX itself are independent of p53-mediated gene expression.
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Affiliation(s)
- Jan Brazina
- a Department of Cell Signaling and Apoptosis
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19
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Breslin C, Hornyak P, Ridley A, Rulten SL, Hanzlikova H, Oliver AW, Caldecott KW. The XRCC1 phosphate-binding pocket binds poly (ADP-ribose) and is required for XRCC1 function. Nucleic Acids Res 2015; 43:6934-44. [PMID: 26130715 PMCID: PMC4538820 DOI: 10.1093/nar/gkv623] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 12/29/2022] Open
Abstract
Poly (ADP-ribose) is synthesized at DNA single-strand breaks and can promote the recruitment of the scaffold protein, XRCC1. However, the mechanism and importance of this process has been challenged. To address this issue, we have characterized the mechanism of poly (ADP-ribose) binding by XRCC1 and examined its importance for XRCC1 function. We show that the phosphate-binding pocket in the central BRCT1 domain of XRCC1 is required for selective binding to poly (ADP-ribose) at low levels of ADP-ribosylation, and promotes interaction with cellular PARP1. We also show that the phosphate-binding pocket is required for EGFP-XRCC1 accumulation at DNA damage induced by UVA laser, H2O2, and at sites of sub-nuclear PCNA foci, suggesting that poly (ADP-ribose) promotes XRCC1 recruitment both at single-strand breaks globally across the genome and at sites of DNA replication stress. Finally, we show that the phosphate-binding pocket is required following DNA damage for XRCC1-dependent acceleration of DNA single-strand break repair, DNA base excision repair, and cell survival. These data support the hypothesis that poly (ADP-ribose) synthesis promotes XRCC1 recruitment at DNA damage sites and is important for XRCC1 function.
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Affiliation(s)
- Claire Breslin
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Peter Hornyak
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Andrew Ridley
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Stuart L Rulten
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Hana Hanzlikova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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20
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Andrs M, Korabecny J, Nepovimova E, Jun D, Hodny Z, Moravcova S, Hanzlikova H, Kuca K. The development of ataxia telangiectasia mutated kinase inhibitors. Mini Rev Med Chem 2014. [DOI: 10.2174/1389557514666141013140217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Andrs M, Korabecny J, Nepovimova E, Jun D, Hodny Z, Moravcova S, Hanzlikova H, Kuca K. The development of ataxia telangiectasia mutated kinase inhibitors. Mini Rev Med Chem 2014:MRMC-EPUB-62785. [PMID: 25307308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 08/16/2014] [Accepted: 09/22/2014] [Indexed: 06/04/2023]
Abstract
Radiation and genotoxic drugs are two of the cornerstones of current cancer treatment strategy. However, this type of therapy often suffers from radio- or chemo-resistance caused by DNA repair mechanisms. With the aim of increasing the efficacy of these treatments, there has been great interest in studying DNA damage responses (DDR). Among the plethora of signal and effector proteins involved in DDR, three related kinases ATM (ataxia telangiectasia mutated), ATR (ATM and Rad3-related) and DNA-PK (DNA-dependent protein kinase) play the main roles in initiation and regulation of signaling pathways in response to DNA double and single strand breaks (DSB and SSB). ATM inhibitors, as well as those of ATR and DNA-PK, provide an opportunity to sensitize cancer cells to therapy. Moreover, they can lead to selective killing of cancer cells, exploiting a concept known as synthetic lethality. However, only a very few selective inhibitors have been identified to this date. This mini-review is focused both on the development of selective inhibitors of ATM and other inhibitors which have ATM as one of their targets.
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Affiliation(s)
| | | | | | | | | | | | | | - Kamil Kuca
- University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic..
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22
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Andrs M, Korabecny J, Nepovimova E, Jun D, Hodny Z, Moravcova S, Hanzlikova H, Kuca K. The development of ataxia telangiectasia mutated kinase inhibitors. Mini Rev Med Chem 2014; 14:805-811. [PMID: 25138084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 08/16/2014] [Accepted: 08/16/2014] [Indexed: 06/03/2023]
Abstract
Radiation and genotoxic drugs are two of the cornerstones of current cancer treatment strategy. However, this type of therapy often suffers from radio- or chemo-resistance caused by DNA repair mechanisms. With the aim of increasing the efficacy of these treatments, there has been great interest in studying DNA damage responses (DDR). Among the plethora of signal and effector proteins involved in DDR, three related kinases ATM (ataxia telangiectasia mutated), ATR (ATM and Rad3-related) and DNA-PK (DNA-dependent protein kinase) play the main roles in initiation and regulation of signaling pathways in response to DNA double and single strand breaks (DSB and SSB). ATM inhibitors, as well as those of ATR and DNA-PK, provide an opportunity to sensitize cancer cells to therapy. Moreover, they can lead to selective killing of cancer cells, exploiting a concept known as synthetic lethality. However, only a very few selective inhibitors have been identified to this date. This mini-review is focused both on the development of selective inhibitors of ATM and other inhibitors which have ATM as one of their targets.
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Affiliation(s)
| | | | | | | | | | | | | | - Kamil Kuca
- University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
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23
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Moudry P, Lukas C, Macurek L, Hanzlikova H, Hodny Z, Lukas J, Bartek J. Ubiquitin-activating enzyme UBA1 is required for cellular response to DNA damage. Cell Cycle 2012; 11:1573-82. [PMID: 22456334 DOI: 10.4161/cc.19978] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The cellular DNA damage response (DDR) machinery that maintains genomic integrity and prevents severe pathologies, including cancer, is orchestrated by signaling through protein modifications. Protein ubiquitylation regulates repair of DNA double-strand breaks (DSBs), toxic lesions caused by various metabolic as well as environmental insults such as ionizing radiation (IR). Whereas several components of the DSB-evoked ubiquitylation cascade have been identified, including RNF168 and BRCA1 ubiquitin ligases, whose genetic defects predispose to a syndrome mimicking ataxia-telangiectasia and cancer, respectively, the identity of the apical E1 enzyme involved in DDR has not been established. Here, we identify ubiquitin-activating enzyme UBA1 as the E1 enzyme required for responses to IR and replication stress in human cells. We show that siRNA-mediated knockdown of UBA1, but not of another UBA family member UBA6, impaired formation of both ubiquitin conjugates at the sites of DNA damage and IR-induced foci (IRIF) by the downstream components of the DSB response pathway, 53BP1 and BRCA1. Furthermore, chemical inhibition of UBA1 prevented IRIF formation and severely impaired DSB repair and formation of 53BP1 bodies in G 1, a marker of response to replication stress. In contrast, the upstream steps of DSB response, such as phosphorylation of histone H2AX and recruitment of MDC1, remained unaffected by UBA1 depletion. Overall, our data establish UBA1 as the apical enzyme critical for ubiquitylation-dependent signaling of both DSBs and replication stress in human cells, with implications for maintenance of genomic integrity, disease pathogenesis and cancer treatment.
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Affiliation(s)
- Pavel Moudry
- Department of Genome Integrity, Institute of Molecular Genetics of the ASCR, v.v.i., Prague, Czech Republic
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24
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Hubackova S, Novakova Z, Krejcikova K, Kosar M, Dobrovolna J, Duskova P, Hanzlikova H, Vancurova M, Barath P, Bartek J, Hodny Z. Regulation of the PML tumor suppressor in drug-induced senescence of human normal and cancer cells by JAK/STAT-mediated signaling. Cell Cycle 2010; 9:3085-99. [PMID: 20699642 DOI: 10.4161/cc.9.15.12521] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Promyelocytic leukemia protein (PML) tumor suppressor is upregulated in several forms of cellular senescence, however the mechanism of its induction is elusive. Here we show that genotoxic drugs that induce senescence, such as 5-bromo-2'deoxyuridine (BrdU), thymidine (TMD), distamycin A (DMA), aphidicolin (APH), etoposide (ET) and camptothecin (CPT) all evoke expansion of PML nuclear compartment and its association with persistent DNA lesions in several human cancer cell lines and normal diploid fibroblasts. This phenomenon was accompanied by elevation of PML transcripts after treatment with BrdU, TMD, DMA and CPT. Chemical inhibition of all JAK kinases and RNAi-mediated knock-down of JAK1 suppressed PML expression, implicating JAK/STAT-mediated signaling in regulation of the PML gene. As PML protein stability remained unchanged after drug treatment, decreased protein turnover was unlikely to explain the senescence-associated increased abundance of PML. Furthermore, binding activity of Interferon Stimulated Response Element (ISRE) within the PML gene promoter, and suppression of reporter gene activity after deletion of ISRE from the PML promoter region suggested that drug-induced PML transcription is controlled via transcription factors interacting with this element. Collectively, our data show that upregulation of the PML tumor suppressor in cellular senescence triggered by diverse drugs including clinically used anti-cancer chemotherapeutics relies on stimulation of PML transcription by JAK/STAT-mediated signaling, possibly evoked by the autocrine/paracrine activities of senescence-associated cytokines.
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Affiliation(s)
- Sona Hubackova
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
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