1
|
Dabin J, Giacomini G, Petit E, Polo SE. New facets in the chromatin-based regulation of genome maintenance. DNA Repair (Amst) 2024; 140:103702. [PMID: 38878564 DOI: 10.1016/j.dnarep.2024.103702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 07/13/2024]
Abstract
The maintenance of genome integrity by DNA damage response machineries is key to protect cells against pathological development. In cell nuclei, these genome maintenance machineries operate in the context of chromatin, where the DNA wraps around histone proteins. Here, we review recent findings illustrating how the chromatin substrate modulates genome maintenance mechanisms, focusing on the regulatory role of histone variants and post-translational modifications. In particular, we discuss how the pre-existing chromatin landscape impacts DNA damage formation and guides DNA repair pathway choice, and how DNA damage-induced chromatin alterations control DNA damage signaling and repair, and DNA damage segregation through cell divisions. We also highlight that pathological alterations of histone proteins may trigger genome instability by impairing chromosome segregation and DNA repair, thus defining new oncogenic mechanisms and opening up therapeutic options.
Collapse
Affiliation(s)
- Juliette Dabin
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France
| | - Giulia Giacomini
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France
| | - Eliane Petit
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France.
| |
Collapse
|
2
|
Özdemir C, Purkey LR, Sanchez A, Miller KM. PARticular MARks: Histone ADP-ribosylation and the DNA damage response. DNA Repair (Amst) 2024; 140:103711. [PMID: 38924925 DOI: 10.1016/j.dnarep.2024.103711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/04/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
Cellular and molecular responses to DNA damage are highly orchestrated and dynamic, acting to preserve the maintenance and integrity of the genome. Histone proteins bind DNA and organize the genome into chromatin. Post-translational modifications of histones have been shown to play an essential role in orchestrating the chromatin response to DNA damage by regulating the DNA damage response pathway. Among the histone modifications that contribute to this intricate network, histone ADP-ribosylation (ADPr) is emerging as a pivotal component of chromatin-based DNA damage response (DDR) pathways. In this review, we survey how histone ADPr is regulated to promote the DDR and how it impacts chromatin and other histone marks. Recent advancements have revealed histone ADPr effects on chromatin structure and the regulation of DNA repair factor recruitment to DNA lesions. Additionally, we highlight advancements in technology that have enabled the identification and functional validation of histone ADPr in cells and in response to DNA damage. Given the involvement of DNA damage and epigenetic regulation in human diseases including cancer, these findings have clinical implications for histone ADPr, which are also discussed. Overall, this review covers the involvement of histone ADPr in the DDR and highlights potential future investigations aimed at identifying mechanisms governed by histone ADPr that participate in the DDR, human diseases, and their treatments.
Collapse
Affiliation(s)
- Cem Özdemir
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Laura R Purkey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
3
|
Zhang H, Zha S. The dynamics and regulation of PARP1 and PARP2 in response to DNA damage and during replication. DNA Repair (Amst) 2024; 140:103690. [PMID: 38823186 DOI: 10.1016/j.dnarep.2024.103690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/14/2024] [Accepted: 04/29/2024] [Indexed: 06/03/2024]
Abstract
DNA strand breaks activate Poly(ADP-ribose) polymerase (PARP) 1 and 2, which use NAD+ as the substrate to covalently conjugate ADP-ribose on themselves and other proteins (e.g., Histone) to promote chromatin relaxation and recruit additional DNA repair factors. Enzymatic inhibitors of PARP1 and PARP2 (PARPi) are promising cancer therapy agents that selectively target BRCA1- or BRCA2- deficient cancers. As immediate early responders to DNA strand breaks with robust activities, PARP1 and PARP2 normally form transient foci (<10 minutes) at the micro-irradiation-induced DNA lesions. In addition to enzymatic inhibition, PARPi also extend the presence of PARP1 and PARP2 at DNA lesions, including at replication forks, where they may post a physical block for subsequent repair and DNA replication. The dynamic nature of PARP1 and PARP2 foci made live cell imaging a unique platform to detect subtle changes and the functional interaction among PARP1, PARP2, and their regulators. Recent imaging studies have provided new understandings of the biological consequence of PARP inhibition and uncovered functional interactions between PARP1 and PARP2 and new regulators (e.g., histone poly(ADP-ribosylation) factor). Here, we review recent advances in dissecting the temporal and spatial Regulation of PARP1 and PARP2 at DNA lesions and discuss their physiological implications on both cancer and normal cells.
Collapse
Affiliation(s)
- Hanwen Zhang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, USA; Department of Pathology and Cell Biology, Herbert Irvine Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, USA; Division of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, USA; Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, USA.
| |
Collapse
|
4
|
Zentout S, Imburchia V, Chapuis C, Duma L, Schützenhofer K, Prokhorova E, Ahel I, Smith R, Huet S. Histone ADP-ribosylation promotes resistance to PARP inhibitors by facilitating PARP1 release from DNA lesions. Proc Natl Acad Sci U S A 2024; 121:e2322689121. [PMID: 38865276 PMCID: PMC11194589 DOI: 10.1073/pnas.2322689121] [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: 12/22/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) has emerged as a central target for cancer therapies due to the ability of PARP inhibitors to specifically kill tumors deficient for DNA repair by homologous recombination. Upon DNA damage, PARP1 quickly binds to DNA breaks and triggers ADP-ribosylation signaling. ADP-ribosylation is important for the recruitment of various factors to sites of damage, as well as for the timely dissociation of PARP1 from DNA breaks. Indeed, PARP1 becomes trapped at DNA breaks in the presence of PARP inhibitors, a mechanism underlying the cytotoxitiy of these inhibitors. Therefore, any cellular process influencing trapping is thought to impact PARP inhibitor efficiency, potentially leading to acquired resistance in patients treated with these drugs. There are numerous ADP-ribosylation targets after DNA damage, including PARP1 itself as well as histones. While recent findings reported that the automodification of PARP1 promotes its release from the DNA lesions, the potential impact of other ADP-ribosylated proteins on this process remains unknown. Here, we demonstrate that histone ADP-ribosylation is also crucial for the timely dissipation of PARP1 from the lesions, thus contributing to cellular resistance to PARP inhibitors. Considering the crosstalk between ADP-ribosylation and other histone marks, our findings open interesting perspectives for the development of more efficient PARP inhibitor-driven cancer therapies.
Collapse
Affiliation(s)
- Siham Zentout
- University of Rennes, CNRS, Institut de génétique et développement de Rennes–UMR 6290, Biologie, Santé, Innovation Technologique (BIOSIT)–UMS3480, RennesF-35000, France
| | - Victor Imburchia
- University of Rennes, CNRS, Institut de génétique et développement de Rennes–UMR 6290, Biologie, Santé, Innovation Technologique (BIOSIT)–UMS3480, RennesF-35000, France
| | - Catherine Chapuis
- University of Rennes, CNRS, Institut de génétique et développement de Rennes–UMR 6290, Biologie, Santé, Innovation Technologique (BIOSIT)–UMS3480, RennesF-35000, France
| | - Lena Duma
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Kira Schützenhofer
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Rebecca Smith
- University of Rennes, CNRS, Institut de génétique et développement de Rennes–UMR 6290, Biologie, Santé, Innovation Technologique (BIOSIT)–UMS3480, RennesF-35000, France
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Sébastien Huet
- University of Rennes, CNRS, Institut de génétique et développement de Rennes–UMR 6290, Biologie, Santé, Innovation Technologique (BIOSIT)–UMS3480, RennesF-35000, France
| |
Collapse
|
5
|
Liu Z, Ajit K, Wu Y, Zhu WG, Gullerova M. The GATAD2B-NuRD complex drives DNA:RNA hybrid-dependent chromatin boundary formation upon DNA damage. EMBO J 2024; 43:2453-2485. [PMID: 38719994 PMCID: PMC11183058 DOI: 10.1038/s44318-024-00111-7] [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: 11/10/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/19/2024] Open
Abstract
Double-strand breaks (DSBs) are the most lethal form of DNA damage. Transcriptional activity at DSBs, as well as transcriptional repression around DSBs, are both required for efficient DNA repair. The chromatin landscape defines and coordinates these two opposing events. However, how the open and condensed chromatin architecture is regulated remains unclear. Here, we show that the GATAD2B-NuRD complex associates with DSBs in a transcription- and DNA:RNA hybrid-dependent manner, to promote histone deacetylation and chromatin condensation. This activity establishes a spatio-temporal boundary between open and closed chromatin, which is necessary for the correct termination of DNA end resection. The lack of the GATAD2B-NuRD complex leads to chromatin hyperrelaxation and extended DNA end resection, resulting in homologous recombination (HR) repair failure. Our results suggest that the GATAD2B-NuRD complex is a key coordinator of the dynamic interplay between transcription and the chromatin landscape, underscoring its biological significance in the RNA-dependent DNA damage response.
Collapse
Affiliation(s)
- Zhichao Liu
- Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, United Kingdom
| | - Kamal Ajit
- Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, United Kingdom
| | - Yupei Wu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, 518055, Shenzhen, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, 518055, Shenzhen, China
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, United Kingdom.
| |
Collapse
|
6
|
Yang L, Guttman L, Dawson VL, Dawson TM. Parthanatos: Mechanisms, modulation, and therapeutic prospects in neurodegenerative disease and stroke. Biochem Pharmacol 2024:116174. [PMID: 38552851 DOI: 10.1016/j.bcp.2024.116174] [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: 01/21/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
Parthanatos is a cell death signaling pathway that has emerged as a compelling target for pharmaceutical intervention. It plays a pivotal role in the neuron loss and neuroinflammation that occurs in Parkinson's Disease (PD), Alzheimer's Disease (AD), Huntington's Disease (HD), Amyotrophic Lateral Sclerosis (ALS), and stroke. There are currently no treatments available to humans to prevent cell death in any of these diseases. This review provides an in-depth examination of the current understanding of the Parthanatos mechanism, with a particular focus on its implications in neuroinflammation and various diseases discussed herein. Furthermore, we thoroughly review potential intervention targets within the Parthanatos pathway. We dissect recent progress in inhibitory strategies, complimented by a detailed structural analysis of key Parthanatos executioners, PARP-1, AIF, and MIF, along with an assessment of their established inhibitors. We hope to introduce a new perspective on the feasibility of targeting components within the Parthanatos pathway, emphasizing its potential to bring about transformative outcomes in therapeutic interventions. By delineating therapeutic opportunities and known targets, we seek to emphasize the imperative of blocking Parthanatos as a precursor to developing disease-modifying treatments. This comprehensive exploration aims to catalyze a paradigm shift in our understanding of potential neurodegenerative disease therapeutics, advocating for the pursuit of effective interventions centered around Parthanatos inhibition.
Collapse
Affiliation(s)
- Liu Yang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lauren Guttman
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
7
|
Pinto Jurado E, Smith R, Bigot N, Chapuis C, Timinszky G, Huet S. The recruitment of ACF1 and SMARCA5 to DNA lesions relies on ADP-ribosylation dependent chromatin unfolding. Mol Biol Cell 2024; 35:br7. [PMID: 38170578 PMCID: PMC10916859 DOI: 10.1091/mbc.e23-07-0281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
ADP-ribosylation signaling orchestrates the recruitment of various repair actors and chromatin remodeling processes promoting access to lesions during the early stages of the DNA damage response. The chromatin remodeler complex ACF, composed of the ATPase subunit SMARCA5/SNF2H and the cofactor ACF1/BAZ1A, is among the factors that accumulate at DNA lesions in an ADP-ribosylation dependent manner. In this work, we show that each subunit of the ACF complex accumulates to DNA breaks independently from its partner. Furthermore, we demonstrate that the recruitment of SMARCA5 and ACF1 to sites of damage is not due to direct binding to the ADP-ribose moieties but due to facilitated DNA binding at relaxed ADP-ribosylated chromatin. Therefore, our work provides new insights regarding the mechanisms underlying the timely accumulation of ACF1 and SMARCA5 to DNA lesions, where they contribute to efficient DNA damage resolution.
Collapse
Affiliation(s)
- Eva Pinto Jurado
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes), F-35000 Rennes, France
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, 6720 Szeged, Hungary
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes), F-35000 Rennes, France
| | - Nicolas Bigot
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes), F-35000 Rennes, France
| | - Catherine Chapuis
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes), F-35000 Rennes, France
| | - Gyula Timinszky
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes), F-35000 Rennes, France
- Institut Universitaire de France, F-75000 Paris, France
| |
Collapse
|
8
|
Nosella ML, Kim TH, Huang SK, Harkness RW, Goncalves M, Pan A, Tereshchenko M, Vahidi S, Rubinstein JL, Lee HO, Forman-Kay JD, Kay LE. Poly(ADP-ribosyl)ation enhances nucleosome dynamics and organizes DNA damage repair components within biomolecular condensates. Mol Cell 2024; 84:429-446.e17. [PMID: 38215753 DOI: 10.1016/j.molcel.2023.12.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Nucleosomes, the basic structural units of chromatin, hinder recruitment and activity of various DNA repair proteins, necessitating modifications that enhance DNA accessibility. Poly(ADP-ribosyl)ation (PARylation) of proteins near damage sites is an essential initiation step in several DNA-repair pathways; however, its effects on nucleosome structural dynamics and organization are unclear. Using NMR, cryoelectron microscopy (cryo-EM), and biochemical assays, we show that PARylation enhances motions of the histone H3 tail and DNA, leaving the configuration of the core intact while also stimulating nuclease digestion and ligation of nicked nucleosomal DNA by LIG3. PARylation disrupted interactions between nucleosomes, preventing self-association. Addition of LIG3 and XRCC1 to PARylated nucleosomes generated condensates that selectively partition DNA repair-associated proteins in a PAR- and phosphorylation-dependent manner in vitro. Our results establish that PARylation influences nucleosomes across different length scales, extending from the atom-level motions of histone tails to the mesoscale formation of condensates with selective compositions.
Collapse
Affiliation(s)
- Michael L Nosella
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Tae Hun Kim
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuya Kate Huang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert W Harkness
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Monica Goncalves
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alisia Pan
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Maria Tereshchenko
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Julie D Forman-Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Lewis E Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
9
|
Robeska E, Lalanne K, Vianna F, Sutcu HH, Khobta A, Busso D, Radicella JP, Campalans A, Baldeyron C. Targeted nuclear irradiation with a proton microbeam induces oxidative DNA base damage and triggers the recruitment of DNA glycosylases OGG1 and NTH1. DNA Repair (Amst) 2024; 133:103610. [PMID: 38101146 DOI: 10.1016/j.dnarep.2023.103610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/10/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
DNA is the major target of radiation therapy of malignant tumors. Ionizing radiation (IR) induces a variety of DNA lesions, including chemically modified bases and strand breaks. The use of proton beam therapy for cancer treatment is ramping up, as it is expected to reduce normal tissue damage. Thus, it is important to understand the molecular mechanisms of recognition, signaling, and repair of DNA damage induced by protons in the perspective of assessing not only the risk associated with human exposure to IR but also the possibility to improve the efficacy of therapy. Here, we used targeted irradiation of nuclear regions of living cells with controlled number of protons at a high spatio-temporal resolution to detect the induced base lesions and characterize the recruitment kinetics of the specific DNA glycosylases to DNA damage sites. We show that localized irradiation with 4 MeV protons induces, in addition to DNA double strand breaks (DSBs), the oxidized bases 7,8-dihydro-8-oxoguanine (8-oxoG) and thymine glycol (TG) at the site of irradiation. Consistently, the DNA glycosylases OGG1 and NTH1, capable of excising 8-oxoG and TG, respectively, and initiating the base excision repair (BER) pathway, are recruited to the site of damage. To our knowledge, this is the first direct evidence indicating that proton microbeams induce oxidative base damage, and thus implicating BER in the repair of DNA lesions induced by protons.
Collapse
Affiliation(s)
- Elena Robeska
- Université Paris-Saclay, iRCM/IBFJ, CEA, Genetic Stability, Stem Cells and Radiation, F-92260 Fontenay-aux-Roses, France; Université Paris Cité, iRCM/IBFJ, CEA, Genetic Stability, Stem Cells and Radiation, F-92260 Fontenay-aux-Roses, France
| | - Kévin Lalanne
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LMDN, Cadarache, F-13115 Saint-Paul-Lez-Durance, France
| | - François Vianna
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LMDN, Cadarache, F-13115 Saint-Paul-Lez-Durance, France
| | - Haser Hasan Sutcu
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRAcc, F-92262 Fontenay aux Roses, France
| | - Andriy Khobta
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Didier Busso
- Université Paris Cité et Université Paris-Saclay, INSERM, CEA, iRCM/IBFJ, Genetic Stability, Stem Cells and Radiation, F-92260 Fontenay-aux-Roses, France
| | - J Pablo Radicella
- Université Paris-Saclay, iRCM/IBFJ, CEA, Genetic Stability, Stem Cells and Radiation, F-92260 Fontenay-aux-Roses, France; Université Paris Cité, iRCM/IBFJ, CEA, Genetic Stability, Stem Cells and Radiation, F-92260 Fontenay-aux-Roses, France
| | - Anna Campalans
- Université Paris-Saclay, iRCM/IBFJ, CEA, Genetic Stability, Stem Cells and Radiation, F-92260 Fontenay-aux-Roses, France; Université Paris Cité, iRCM/IBFJ, CEA, Genetic Stability, Stem Cells and Radiation, F-92260 Fontenay-aux-Roses, France.
| | - Céline Baldeyron
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRAcc, F-92262 Fontenay aux Roses, France.
| |
Collapse
|
10
|
Rouleau-Turcotte É, Pascal JM. ADP-ribose contributions to genome stability and PARP enzyme trapping on sites of DNA damage; paradigm shifts for a coming-of-age modification. J Biol Chem 2023; 299:105397. [PMID: 37898399 PMCID: PMC10722394 DOI: 10.1016/j.jbc.2023.105397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023] Open
Abstract
ADP-ribose is a versatile modification that plays a critical role in diverse cellular processes. The addition of this modification is catalyzed by ADP-ribosyltransferases, among which notable poly(ADP-ribose) polymerase (PARP) enzymes are intimately involved in the maintenance of genome integrity. The role of ADP-ribose modifications during DNA damage repair is of significant interest for the proper development of PARP inhibitors targeted toward the treatment of diseases caused by genomic instability. More specifically, inhibitors promoting PARP persistence on DNA lesions, termed PARP "trapping," is considered a desirable characteristic. In this review, we discuss key classes of proteins involved in ADP-ribose signaling (writers, readers, and erasers) with a focus on those involved in the maintenance of genome integrity. An overview of factors that modulate PARP1 and PARP2 persistence at sites of DNA lesions is also discussed. Finally, we clarify aspects of the PARP trapping model in light of recent studies that characterize the kinetics of PARP1 and PARP2 recruitment at sites of lesions. These findings suggest that PARP trapping could be considered as the continuous recruitment of PARP molecules to sites of lesions, rather than the physical stalling of molecules. Recent studies and novel research tools have elevated the level of understanding of ADP-ribosylation, marking a coming-of-age for this interesting modification.
Collapse
Affiliation(s)
- Élise Rouleau-Turcotte
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada.
| |
Collapse
|
11
|
García Fernández F, Huet S, Miné-Hattab J. Multi-Scale Imaging of the Dynamic Organization of Chromatin. Int J Mol Sci 2023; 24:15975. [PMID: 37958958 PMCID: PMC10649806 DOI: 10.3390/ijms242115975] [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: 09/19/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Chromatin is now regarded as a heterogeneous and dynamic structure occupying a non-random position within the cell nucleus, where it plays a key role in regulating various functions of the genome. This current view of chromatin has emerged thanks to high spatiotemporal resolution imaging, among other new technologies developed in the last decade. In addition to challenging early assumptions of chromatin being regular and static, high spatiotemporal resolution imaging made it possible to visualize and characterize different chromatin structures such as clutches, domains and compartments. More specifically, super-resolution microscopy facilitates the study of different cellular processes at a nucleosome scale, providing a multi-scale view of chromatin behavior within the nucleus in different environments. In this review, we describe recent imaging techniques to study the dynamic organization of chromatin at high spatiotemporal resolution. We also discuss recent findings, elucidated by these techniques, on the chromatin landscape during different cellular processes, with an emphasis on the DNA damage response.
Collapse
Affiliation(s)
- Fabiola García Fernández
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, 75005 Paris, France;
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, 35000 Rennes, France;
- Institut Universitaire de France, 75231 Paris, France
| | - Judith Miné-Hattab
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, 75005 Paris, France;
| |
Collapse
|
12
|
Hu ML, Pan YR, Yong YY, Liu Y, Yu L, Qin DL, Qiao G, Law BYK, Wu JM, Zhou XG, Wu AG. Poly (ADP-ribose) polymerase 1 and neurodegenerative diseases: Past, present, and future. Ageing Res Rev 2023; 91:102078. [PMID: 37758006 DOI: 10.1016/j.arr.2023.102078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/30/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) is a first responder that recognizes DNA damage and facilitates its repair. Neurodegenerative diseases, characterized by progressive neuron loss driven by various risk factors, including DNA damage, have increasingly shed light on the pivotal involvement of PARP1. During the early phases of neurodegenerative diseases, PARP1 experiences controlled activation to swiftly address mild DNA damage, thereby contributing to maintain brain homeostasis. However, in late stages, exacerbated PARP1 activation precipitated by severe DNA damage exacerbates the disease condition. Consequently, inhibition of PARP1 overactivation emerges as a promising therapeutic approach for neurodegenerative diseases. In this review, we comprehensively synthesize and explore the multifaceted role of PARP1 in neurodegenerative diseases, with a particular emphasis on its over-activation in the aggregation of misfolded proteins, dysfunction of the autophagy-lysosome pathway, mitochondrial dysfunction, neuroinflammation, and blood-brain barrier (BBB) injury. Additionally, we encapsulate the therapeutic applications and limitations intrinsic of PARP1 inhibitors, mainly including limited specificity, intricate pathway dynamics, constrained clinical translation, and the heterogeneity of patient cohorts. We also explore and discuss the potential synergistic implementation of these inhibitors alongside other agents targeting DNA damage cascades within neurodegenerative diseases. Simultaneously, we propose several recommendations for the utilization of PARP1 inhibitors within the realm of neurodegenerative disorders, encompassing factors like the disease-specific roles of PARP1, combinatorial therapeutic strategies, and personalized medical interventions. Lastly, the encompassing review presents a forward-looking perspective along with strategic recommendations that could guide future research endeavors in this field.
Collapse
Affiliation(s)
- Meng-Ling Hu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yi-Ru Pan
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yuan-Yuan Yong
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yi Liu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Lu Yu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Da-Lian Qin
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Gan Qiao
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Betty Yuen-Kwan Law
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Jian-Ming Wu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China.
| | - Xiao-Gang Zhou
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China.
| | - An-Guo Wu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China.
| |
Collapse
|
13
|
Suskiewicz MJ, Prokhorova E, Rack JGM, Ahel I. ADP-ribosylation from molecular mechanisms to therapeutic implications. Cell 2023; 186:4475-4495. [PMID: 37832523 PMCID: PMC10789625 DOI: 10.1016/j.cell.2023.08.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 10/15/2023]
Abstract
ADP-ribosylation is a ubiquitous modification of biomolecules, including proteins and nucleic acids, that regulates various cellular functions in all kingdoms of life. The recent emergence of new technologies to study ADP-ribosylation has reshaped our understanding of the molecular mechanisms that govern the establishment, removal, and recognition of this modification, as well as its impact on cellular and organismal function. These advances have also revealed the intricate involvement of ADP-ribosylation in human physiology and pathology and the enormous potential that their manipulation holds for therapy. In this review, we present the state-of-the-art findings covering the work in structural biology, biochemistry, cell biology, and clinical aspects of ADP-ribosylation.
Collapse
Affiliation(s)
| | | | - Johannes G M Rack
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; MRC Centre of Medical Mycology, University of Exeter, Exeter, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| |
Collapse
|
14
|
Li Z, Luo A, Xie B. The Complex Network of ADP-Ribosylation and DNA Repair: Emerging Insights and Implications for Cancer Therapy. Int J Mol Sci 2023; 24:15028. [PMID: 37834477 PMCID: PMC10573881 DOI: 10.3390/ijms241915028] [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: 08/21/2023] [Revised: 09/23/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
ADP-ribosylation is a post-translational modification of proteins that plays a key role in various cellular processes, including DNA repair. Recently, significant progress has been made in understanding the mechanism and function of ADP-ribosylation in DNA repair. ADP-ribosylation can regulate the recruitment and activity of DNA repair proteins by facilitating protein-protein interactions and regulating protein conformations. Moreover, ADP-ribosylation can influence additional post-translational modifications (PTMs) of proteins involved in DNA repair, such as ubiquitination, methylation, acetylation, phosphorylation, and SUMOylation. The interaction between ADP-ribosylation and these additional PTMs can fine-tune the activity of DNA repair proteins and ensure the proper execution of the DNA repair process. In addition, PARP inhibitors have been developed as a promising cancer therapeutic strategy by exploiting the dependence of certain cancer types on the PARP-mediated DNA repair pathway. In this paper, we review the progress of ADP-ribosylation in DNA repair, discuss the crosstalk of ADP-ribosylation with additional PTMs in DNA repair, and summarize the progress of PARP inhibitors in cancer therapy.
Collapse
Affiliation(s)
| | - Aiqin Luo
- Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment (Ministry of Industry and Information Technology), School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Bingteng Xie
- Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment (Ministry of Industry and Information Technology), School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| |
Collapse
|
15
|
Groslambert J, Prokhorova E, Wondisford AR, Tromans-Coia C, Giansanti C, Jansen J, Timinszky G, Dobbelstein M, Ahel D, O'Sullivan RJ, Ahel I. The interplay of TARG1 and PARG protects against genomic instability. Cell Rep 2023; 42:113113. [PMID: 37676774 PMCID: PMC10933786 DOI: 10.1016/j.celrep.2023.113113] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/20/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
The timely removal of ADP-ribosylation is crucial for efficient DNA repair. However, much remains to be discovered about ADP-ribosylhydrolases. Here, we characterize the physiological role of TARG1, an ADP-ribosylhydrolase that removes aspartate/glutamate-linked ADP-ribosylation. We reveal its function in the DNA damage response and show that the loss of TARG1 sensitizes cells to inhibitors of topoisomerase II, ATR, and PARP. Furthermore, we find a PARP1-mediated synthetic lethal interaction between TARG1 and PARG, driven by the toxic accumulation of ADP-ribosylation, that induces replication stress and genomic instability. Finally, we show that histone PARylation factor 1 (HPF1) deficiency exacerbates the toxicity and genomic instability induced by excessive ADP-ribosylation, suggesting a close crosstalk between components of the serine- and aspartate/glutamate-linked ADP-ribosylation pathways. Altogether, our data identify TARG1 as a potential biomarker for the response of cancer cells to PARP and PARG inhibition and establish that the interplay of TARG1 and PARG protects cells against genomic instability.
Collapse
Affiliation(s)
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer, University of Pittsburgh, Pittsburgh, PA, USA
| | - Callum Tromans-Coia
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Celeste Giansanti
- Department of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Jennifer Jansen
- Department of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Gyula Timinszky
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), 6276 Szeged, Hungary
| | - Matthias Dobbelstein
- Department of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
| |
Collapse
|
16
|
Ferrand J, Dabin J, Chevallier O, Kupai A, Rothbart SB, Polo SE. Mitotic chromatin marking governs asymmetric segregation of DNA damage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.04.556166. [PMID: 37732208 PMCID: PMC10508772 DOI: 10.1101/2023.09.04.556166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The faithful segregation of intact genetic material and the perpetuation of chromatin states through mitotic cell divisions are pivotal for maintaining cell function and identity across cell generations. However, most exogenous mutagens generate long-lasting DNA lesions that are segregated during mitosis. How this segregation is controlled is unknown. Here, we uncover a mitotic chromatin-marking pathway that governs the segregation of UV-induced damage in human cells. Our mechanistic analyses reveal two layers of control: histone ADP-ribosylation, and the incorporation of newly synthesized histones at UV damage sites, that both prevent local mitotic phosphorylations on histone H3 serines. Functionally, this chromatin-marking pathway drives the asymmetric segregation of UV damage in the cell progeny with potential consequences on daughter cell fate. We propose that this mechanism may help preserve the integrity of stem cell compartments during asymmetric cell divisions.
Collapse
Affiliation(s)
- Juliette Ferrand
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, Paris, France
| | - Juliette Dabin
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, Paris, France
| | - Odile Chevallier
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, Paris, France
| | - Ariana Kupai
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Scott B. Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Sophie E. Polo
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université Paris Cité, Paris, France
| |
Collapse
|
17
|
Cintori L, Di Guilmi AM, Canitrot Y, Huet S, Campalans A. Spatio-temporal dynamics of the DNA glycosylase OGG1 in finding and processing 8-oxoguanine. DNA Repair (Amst) 2023; 129:103550. [PMID: 37542751 DOI: 10.1016/j.dnarep.2023.103550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023]
Abstract
OGG1 is the DNA glycosylase responsible for the removal of the oxidative lesion 8-oxoguanine (8-oxoG) from DNA. The recognition of this lesion by OGG1 is a complex process that involves scanning the DNA for the presence of 8-oxoG, followed by recognition and lesion removal. Structural data have shown that OGG1 evolves through different stages of conformation onto the DNA, corresponding to elementary steps of the 8-oxoG recognition and extrusion from the double helix. Single-molecule studies of OGG1 on naked DNA have shown that OGG1 slides in persistent contact with the DNA, displaying different binding states probably corresponding to the different conformation stages. However, in cells, the DNA is not naked and OGG1 has to navigate into a complex and highly crowded environment within the nucleus. To ensure rapid detection of 8-oxoG, OGG1 alternates between 3D diffusion and sliding along the DNA. This process is regulated by the local chromatin state but also by protein co-factors that could facilitate the detection of oxidized lesions. We will review here the different methods that have been used over the last years to better understand how OGG1 detects and process 8-oxoG lesions.
Collapse
Affiliation(s)
- Luana Cintori
- Molecular, Cellular and Developmental Biology unit, Centre de Biologie Integrative, University of Toulouse, CNRS, F-31062 Toulouse, France
| | - Anne-Marie Di Guilmi
- Université de Paris-Cite, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France; Université Paris-Saclay, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France
| | - Yvan Canitrot
- Molecular, Cellular and Developmental Biology unit, Centre de Biologie Integrative, University of Toulouse, CNRS, F-31062 Toulouse, France
| | - Sebastien Huet
- Université Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, BIOSIT (Biologie, ´ Sante, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France; Institut Universitaire de France, Paris, France
| | - Anna Campalans
- Université de Paris-Cite, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France; Université Paris-Saclay, CEA /IBFJ/IRCM. UMR Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France.
| |
Collapse
|
18
|
Beneyton A, Nonfoux L, Gagné JP, Rodrigue A, Kothari C, Atalay N, Hendzel M, Poirier G, Masson JY. The dynamic process of covalent and non-covalent PARylation in the maintenance of genome integrity: a focus on PARP inhibitors. NAR Cancer 2023; 5:zcad043. [PMID: 37609662 PMCID: PMC10440794 DOI: 10.1093/narcan/zcad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023] Open
Abstract
Poly(ADP-ribosylation) (PARylation) by poly(ADP-ribose) polymerases (PARPs) is a highly regulated process that consists of the covalent addition of polymers of ADP-ribose (PAR) through post-translational modifications of substrate proteins or non-covalent interactions with PAR via PAR binding domains and motifs, thereby reprogramming their functions. This modification is particularly known for its central role in the maintenance of genomic stability. However, how genomic integrity is controlled by an intricate interplay of covalent PARylation and non-covalent PAR binding remains largely unknown. Of importance, PARylation has caught recent attention for providing a mechanistic basis of synthetic lethality involving PARP inhibitors (PARPi), most notably in homologous recombination (HR)-deficient breast and ovarian tumors. The molecular mechanisms responsible for the anti-cancer effect of PARPi are thought to implicate both catalytic inhibition and trapping of PARP enzymes on DNA. However, the relative contribution of each on tumor-specific cytotoxicity is still unclear. It is paramount to understand these PAR-dependent mechanisms, given that resistance to PARPi is a challenge in the clinic. Deciphering the complex interplay between covalent PARylation and non-covalent PAR binding and defining how PARP trapping and non-trapping events contribute to PARPi anti-tumour activity is essential for developing improved therapeutic strategies. With this perspective, we review the current understanding of PARylation biology in the context of the DNA damage response (DDR) and the mechanisms underlying PARPi activity and resistance.
Collapse
Affiliation(s)
- Adèle Beneyton
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Louis Nonfoux
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Jean-Philippe Gagné
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Amélie Rodrigue
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Charu Kothari
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Nurgul Atalay
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AlbertaT6G 1Z2, Canada
| | - Guy G Poirier
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| |
Collapse
|
19
|
Duma L, Ahel I. The function and regulation of ADP-ribosylation in the DNA damage response. Biochem Soc Trans 2023; 51:995-1008. [PMID: 37171085 PMCID: PMC10317172 DOI: 10.1042/bst20220749] [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: 03/13/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
ADP-ribosylation is a post-translational modification involved in DNA damage response (DDR). In higher organisms it is synthesised by PARP 1-3, DNA strand break sensors. Recent advances have identified serine residues as the most common targets for ADP-ribosylation during DDR. To ADP-ribosylate serine, PARPs require an accessory factor, HPF1 which completes the catalytic domain. Through ADP-ribosylation, PARPs recruit a variety of factors to the break site and control their activities. However, the timely removal of ADP-ribosylation is also key for genome stability and is mostly performed by two hydrolases: PARG and ARH3. Here, we describe the key writers, readers and erasers of ADP-ribosylation and their contribution to the mounting of the DDR. We also discuss the use of PARP inhibitors in cancer therapy and the ways to tackle PARPi treatment resistance.
Collapse
Affiliation(s)
- Lena Duma
- Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K
| |
Collapse
|
20
|
Raja SJ, Van Houten B. UV-DDB as a General Sensor of DNA Damage in Chromatin: Multifaceted Approaches to Assess Its Direct Role in Base Excision Repair. Int J Mol Sci 2023; 24:10168. [PMID: 37373320 PMCID: PMC10298998 DOI: 10.3390/ijms241210168] [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: 05/26/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Base excision repair (BER) is a cellular process that removes damaged bases arising from exogenous and endogenous sources including reactive oxygen species, alkylation agents, and ionizing radiation. BER is mediated by the actions of multiple proteins which work in a highly concerted manner to resolve DNA damage efficiently to prevent toxic repair intermediates. During the initiation of BER, the damaged base is removed by one of 11 mammalian DNA glycosylases, resulting in abasic sites. Many DNA glycosylases are product-inhibited by binding to the abasic site more avidly than the damaged base. Traditionally, apurinic/apyrimidinic endonuclease 1, APE1, was believed to help turn over the glycosylases to undergo multiple rounds of damaged base removal. However, in a series of papers from our laboratory, we have demonstrated that UV-damaged DNA binding protein (UV-DDB) stimulates the glycosylase activities of human 8-oxoguanine glycosylase (OGG1), MUTY DNA glycosylase (MUTYH), alkyladenine glycosylase/N-methylpurine DNA glycosylase (AAG/MPG), and single-strand selective monofunctional glycosylase (SMUG1), between three- and five-fold. Moreover, we have shown that UV-DDB can assist chromatin decompaction, facilitating access of OGG1 to 8-oxoguanine damage in telomeres. This review summarizes the biochemistry, single-molecule, and cell biology approaches that our group used to directly demonstrate the essential role of UV-DDB in BER.
Collapse
Affiliation(s)
- Sripriya J. Raja
- Molecular Pharmacology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA;
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Bennett Van Houten
- Molecular Pharmacology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA;
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| |
Collapse
|
21
|
Fontana P, Buch-Larsen SC, Suyari O, Smith R, Suskiewicz MJ, Schützenhofer K, Ariza A, Rack JGM, Nielsen ML, Ahel I. Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling. Nat Commun 2023; 14:3200. [PMID: 37268618 PMCID: PMC10238386 DOI: 10.1038/s41467-023-38793-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
In the mammalian DNA damage response, ADP-ribosylation signalling is of crucial importance to mark sites of DNA damage as well as recruit and regulate repairs factors. Specifically, the PARP1:HPF1 complex recognises damaged DNA and catalyses the formation of serine-linked ADP-ribosylation marks (mono-Ser-ADPr), which are extended into ADP-ribose polymers (poly-Ser-ADPr) by PARP1 alone. Poly-Ser-ADPr is reversed by PARG, while the terminal mono-Ser-ADPr is removed by ARH3. Despite its significance and apparent evolutionary conservation, little is known about ADP-ribosylation signalling in non-mammalian Animalia. The presence of HPF1, but absence of ARH3, in some insect genomes, including Drosophila species, raises questions regarding the existence and reversal of serine-ADP-ribosylation in these species. Here we show by quantitative proteomics that Ser-ADPr is the major form of ADP-ribosylation in the DNA damage response of Drosophila melanogaster and is dependent on the dParp1:dHpf1 complex. Moreover, our structural and biochemical investigations uncover the mechanism of mono-Ser-ADPr removal by Drosophila Parg. Collectively, our data reveal PARP:HPF1-mediated Ser-ADPr as a defining feature of the DDR in Animalia. The striking conservation within this kingdom suggests that organisms that carry only a core set of ADP-ribosyl metabolising enzymes, such as Drosophila, are valuable model organisms to study the physiological role of Ser-ADPr signalling.
Collapse
Affiliation(s)
- Pietro Fontana
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Sara C Buch-Larsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Osamu Suyari
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Rebecca Smith
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Marcin J Suskiewicz
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071, Orléans, France
| | - Kira Schützenhofer
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Johannes Gregor Matthias Rack
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
- MRC Centre for Medical Mycology, School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - 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.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
| |
Collapse
|
22
|
Dasovich M, Leung AK. Molecular tools unveil distinct waves of ADP-ribosylation during DNA repair. CELL REPORTS METHODS 2023; 3:100484. [PMID: 37323576 PMCID: PMC10261921 DOI: 10.1016/j.crmeth.2023.100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
ADP-ribosylation is a complex post-translation modification involved in DNA repair. In a recent Molecular Cell publication, Longarini and colleagues measured ADP-ribosylation dynamics with unprecedented specificity, revealing how the monomeric and polymeric forms of ADP-ribosylation regulate the timing of DNA repair events following strand breaks.
Collapse
Affiliation(s)
- Morgan Dasovich
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anthony K.L. Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Department of Oncology, and Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| |
Collapse
|
23
|
Rudolph J, Luger K. PARP1 and HPF1 team up to flag down DNA-repair machinery. Nat Struct Mol Biol 2023; 30:568-569. [PMID: 37161004 DOI: 10.1038/s41594-023-00987-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
|