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Johann To Berens P, Peter J, Koechler S, Bruggeman M, Staerck S, Molinier J. The histone demethylase JMJ27 acts during the UV-induced modulation of H3K9me2 landscape and facilitates photodamage repair. NATURE PLANTS 2024:10.1038/s41477-024-01814-9. [PMID: 39367258 DOI: 10.1038/s41477-024-01814-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 09/11/2024] [Indexed: 10/06/2024]
Abstract
Plants have evolved sophisticated DNA repair mechanisms to cope with the deleterious effects of ultraviolet (UV)-induced DNA damage. Indeed, DNA repair pathways cooperate with epigenetic-related processes to efficiently maintain genome integrity. However, it remains to be deciphered how photodamages are recognized within different chromatin landscapes, especially in compacted genomic regions such as constitutive heterochromatin. Here we combined cytogenetics and epigenomics to identify that UV-C irradiation induces modulation of the main epigenetic mark found in constitutive heterochromatin, H3K9me2. We demonstrated that the histone demethylase, Jumonji27 (JMJ27), contributes to the UV-induced reduction of H3K9me2 content at chromocentres. In addition, we identified that JMJ27 forms a complex with the photodamage recognition factor, DNA Damage Binding protein 2 (DDB2), and that the fine-tuning of H3K9me2 contents orchestrates DDB2 dynamics on chromatin in response to UV-C exposure. Hence, this study uncovers the unexpected existence of an interplay between photodamage repair and H3K9me2 homeostasis.
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Affiliation(s)
| | - Jackson Peter
- Institut de biologie moléculaire des plantes du CNRS, Strasbourg, France
| | - Sandrine Koechler
- Institut de biologie moléculaire des plantes du CNRS, Strasbourg, France
| | - Mathieu Bruggeman
- Institut de biologie moléculaire des plantes du CNRS, Strasbourg, France
| | - Sébastien Staerck
- Institut de biologie moléculaire des plantes du CNRS, Strasbourg, France
| | - Jean Molinier
- Institut de biologie moléculaire des plantes du CNRS, Strasbourg, France.
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Mancarella D, Ellinghaus H, Sigismondo G, Veselinov O, Kühn A, Goyal A, Hartmann M, Fellenberg J, Krijgsveld J, Plass C, Popanda O, Schmezer P, Bakr A. Deposition of onco-histone H3.3-G34W leads to DNA repair deficiency and activates cGAS/STING-mediated immune responses. Int J Cancer 2024; 154:2106-2120. [PMID: 38353495 DOI: 10.1002/ijc.34883] [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: 11/23/2023] [Revised: 01/08/2024] [Accepted: 01/24/2024] [Indexed: 04/14/2024]
Abstract
Mutations in histone H3.3-encoding genes causing mutant histone tails are associated with specific cancers such as pediatric glioblastomas (H3.3-G34R/V) and giant cell tumor of the bone (H3.3-G34W). The mechanisms by which these mutations promote malignancy are not completely understood. Here we show that cells expressing H3.3-G34W exhibit DNA double-strand breaks (DSBs) repair defects and increased cellular sensitivity to ionizing radiation (IR). Mechanistically, H3.3-G34W can be deposited to damaged chromatin, but in contrast to wild-type H3.3, does not interact with non-homologous end-joining (NHEJ) key effectors KU70/80 and XRCC4 leading to NHEJ deficiency. Together with defective cell cycle checkpoints reported previously, this DNA repair deficiency in H3.3-G34W cells led to accumulation of micronuclei and cytosolic DNA following IR, which subsequently led to activation of the cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) pathway, thereby inducing release of immune-stimulatory cytokines. These findings suggest a potential for radiotherapy for tumors expressing H3.3-G34W, which can be further improved by combination with STING agonists to induce immune-mediated therapeutic efficacy.
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Affiliation(s)
- Daniela Mancarella
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Henrik Ellinghaus
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and Heidelberg University Medical Faculty, Heidelberg, Germany
| | - Olivera Veselinov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander Kühn
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Ashish Goyal
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mark Hartmann
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg Fellenberg
- Department of Experimental Orthopaedics, Orthopaedic University Hospital Heidelberg, Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and Heidelberg University Medical Faculty, Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Odilia Popanda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Schmezer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ali Bakr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Pachva MC, Kisselev AF, Matkarimov BT, Saparbaev M, Groisman R. DNA-Histone Cross-Links: Formation and Repair. Front Cell Dev Biol 2021; 8:607045. [PMID: 33409281 PMCID: PMC7779557 DOI: 10.3389/fcell.2020.607045] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/30/2020] [Indexed: 12/25/2022] Open
Abstract
The nucleosome is a stretch of DNA wrapped around a histone octamer. Electrostatic interactions and hydrogen bonds between histones and DNA are vital for the stable organization of nucleosome core particles, and for the folding of chromatin into more compact structures, which regulate gene expression via controlled access to DNA. As a drawback of tight association, under genotoxic stress, DNA can accidentally cross-link to histone in a covalent manner, generating a highly toxic DNA-histone cross-link (DHC). DHC is a bulky lesion that can impede DNA transcription, replication, and repair, often with lethal consequences. The chemotherapeutic agent cisplatin, as well as ionizing and ultraviolet irradiations and endogenously occurring reactive aldehydes, generate DHCs by forming either stable or transient covalent bonds between DNA and side-chain amino groups of histone lysine residues. The mechanisms of DHC repair start to unravel, and certain common principles of DNA-protein cross-link (DPC) repair mechanisms that participate in the removal of cross-linked histones from DNA have been described. In general, DPC is removed via a two-step repair mechanism. First, cross-linked proteins are degraded by specific DPC proteases or by the proteasome, relieving steric hindrance. Second, the remaining DNA-peptide cross-links are eliminated in various DNA repair pathways. Delineating the molecular mechanisms of DHC repair would help target specific DNA repair proteins for therapeutic intervention to combat tumor resistance to chemotherapy and radiotherapy.
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Affiliation(s)
- Manideep C Pachva
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Alexei F Kisselev
- Department Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, United States
| | | | - Murat Saparbaev
- Groupe "Mechanisms of DNA Repair and Carcinogenesis", Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Regina Groisman
- Groupe "Mechanisms of DNA Repair and Carcinogenesis", Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
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Rohde K, Rønningen T, la Cour Poulsen L, Keller M, Blüher M, Böttcher Y. Role of the DNA repair genes H2AX and HMGB1 in human fat distribution and lipid profiles. BMJ Open Diabetes Res Care 2020; 8:8/1/e000831. [PMID: 32114485 PMCID: PMC7050360 DOI: 10.1136/bmjdrc-2019-000831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/25/2019] [Accepted: 01/15/2020] [Indexed: 11/05/2022] Open
Abstract
INTRODUCTION Regional fat distribution strongly relates to metabolic comorbidities. We identified the DNA repair genes H2AX and HMGB1 to be differentially expressed between human subcutaneous (SAT) and omental visceral adipose tissue (OVAT) depots. As increased DNA damage is linked to metabolic disease, we here sought to analyze whether depot-specific H2AX and HMGB1 expression is related to anthropometric and metabolic profiles of obesity. We further tested for different H2AX mRNA regulatory mechanisms by analyzing promoter DNA methylation and genotyped rs7350 in the H2AX locus. RESEARCH DESIGN AND METHODS Gene expression (OVAT n=48; SAT n=55) and DNA promoter methylation data (OVAT and SAT n=77) were extracted from an existing dataset as described elsewhere. Genotype data for the 3'untranslated region (3'UTR) H2AX variant rs7350 were generated by using the TaqMan genotyping system in 243 subjects of the same cohort. Statistical analyses were done using SPSS statistics software 24 and GraphPad Prism 6. RESULTS We identified H2AX being higher (p=0.002) and HMGB1 being less expressed (p=0.0001) in OVAT compared with SAT. Further, we observed positive interdepot correlations of OVAT and SAT for both HMGB1 (p=1×10-6) and H2AX mRNA levels (p=0.024). Depot-specific associations were observed for both genes' methylation levels with either high density lipoprotein cholesterol, low density lipoprotein cholesterol, triglycerides and/or with OVAT/SAT-ratio (all p<0.05). A significantly lower level of total cholesterol in minor A-Allele carriers of rs7350 compared with AG and GG carriers (p=0.001) was observed. Additionally, subjects carrying the A-allele showed lower SAT HMGB1 expression level (p=0.030). CONCLUSION Our results suggest a fat depot-specific regulation of H2AX and HMGB1 potentially mediated by both DNA methylation and genetic variation. Rs7350, DNA methylation and/or mRNA levels of H2AX and HMGB1 are related to lipid parameters. Further studies are warranted to evaluate the functional role of the DNA repair genes H2AX and HMGB1 in obesity and fat distribution.
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Affiliation(s)
- Kerstin Rohde
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Torunn Rønningen
- Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Lars la Cour Poulsen
- Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Maria Keller
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Matthias Blüher
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Medical Department, University of Leipzig, Leipzig, Germany
| | - Yvonne Böttcher
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
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Scott DD, Oeffinger M. Nucleolin and nucleophosmin: nucleolar proteins with multiple functions in DNA repair. Biochem Cell Biol 2016; 94:419-432. [PMID: 27673355 DOI: 10.1139/bcb-2016-0068] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The nucleolus represents a highly multifunctional intranuclear organelle in which, in addition to the canonical ribosome assembly, numerous processes such as transcription, DNA repair and replication, the cell cycle, and apoptosis are coordinated. The nucleolus is further a key hub in the sensing of cellular stress and undergoes major structural and compositional changes in response to cellular perturbations. Numerous nucleolar proteins have been identified that, upon sensing nucleolar stress, deploy additional, non-ribosomal roles in the regulation of varied cell processes including cell cycle arrest, arrest of DNA replication, induction of DNA repair, and apoptosis, among others. The highly abundant proteins nucleophosmin (NPM1) and nucleolin (NCL) are two such factors that transit to the nucleoplasm in response to stress, and participate directly in the repair of numerous different DNA damages. This review discusses the contributions made by NCL and (or) NPM1 to the different DNA repair pathways employed by mammalian cells to repair DNA insults, and examines the implications of such activities for the regulation, pathogenesis, and therapeutic targeting of NPM1 and NCL.
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Affiliation(s)
- Daniel D Scott
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
| | - Marlene Oeffinger
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
- c Département de biochimie et médecine moléculaire, Faculté de Médecine, Université de Montréal, QC H3T 1J4, Canada
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Donà M, Mittelsten Scheid O. DNA Damage Repair in the Context of Plant Chromatin. PLANT PHYSIOLOGY 2015; 168:1206-18. [PMID: 26089404 PMCID: PMC4528755 DOI: 10.1104/pp.15.00538] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/17/2015] [Indexed: 05/03/2023]
Abstract
The integrity of DNA molecules is constantly challenged. All organisms have developed mechanisms to detect and repair multiple types of DNA lesions. The basic principles of DNA damage repair (DDR) in prokaryotes and unicellular and multicellular eukaryotes are similar, but the association of DNA with nucleosomes in eukaryotic chromatin requires mechanisms that allow access of repair enzymes to the lesions. This is achieved by chromatin-remodeling factors, and their necessity for efficient DDR has recently been demonstrated for several organisms and repair pathways. Plants share many features of chromatin organization and DNA repair with fungi and animals, but they differ in other, important details, which are both interesting and relevant for our understanding of genome stability and genetic diversity. In this Update, we compare the knowledge of the role of chromatin and chromatin-modifying factors during DDR in plants with equivalent systems in yeast and humans. We emphasize plant-specific elements and discuss possible implications.
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Affiliation(s)
- Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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Lou Y, Li R, Zhang Y, Zhong R, Pei J, Xiong L, Zhang X, Han B. XPA gene rs1800975 single nucleotide polymorphism and lung cancer risk: a meta-analysis. Tumour Biol 2014; 35:6607-17. [PMID: 24696258 DOI: 10.1007/s13277-014-1824-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 03/05/2014] [Indexed: 12/26/2022] Open
Abstract
No clear consensus has been reached on the XPA gene rs1800975 polymorphism and lung cancer risk. We performed a meta-analysis in an effort to systematically explore the possible association. We conducted a computer retrieval of PubMed, Embase, Wanfang, China National Knowledge Infrastructure Platform, and VIP databases prior to November 2013. References of retrieved articles were also screened. The fixed- and the random-effects model were applied for dichotomous outcomes to combine the results of the individual studies. According to the inclusion criteria, 10 articles (11 studies) were finally included. In overall, statistical association could be found between rs1800975 polymorphism and lung cancer in recessive genetic model [AA vs. (AG + GG): P = 0.02, OR = 1.16, 95% CI 1.02-1.31, P heterogeneity = 0.14, fixed-effects model]. In the East Asians, significant association was found in allele comparison model (A vs. G: P = 0.03, OR = 1.13, 95% CI 1.01-1.26, P heterogeneity = 0.39, fixed-effects model), in recessive genetic model [AA vs. (AG + GG): P = 0.005, OR = 1.30, 95% CI 1.08-1.56, P heterogeneity = 0.58, fixed-effects model] and in the homozygote comparison (AA vs. GG: P = 0.02, OR = 1.30, 95% CI 1.04-1.63, P heterogeneity = 0.39, fixed-effects model). No evidence suggested that rs1800975 polymorphism might associate with lung cancer in other ethnicities. Stratification analysis performed by histologic types indicated that AA genotype might represent a risk factor for squamous cell carcinoma [AA vs. (AG + GG): P = 0.01, OR = 1.42, 95% CI 1.08-1.86, P heterogeneity = 0.27, fixed-effects model; AA vs. GG: P = 0.03, OR = 1.43, 95% CI 1.04-1.96, P heterogeneity = 0.21, fixed-effects model]. No association was observed in adenocarcinoma subgroup. Our study suggested that XPA rs1800975 polymorphism might associate with lung cancer risk in overall and in East Asians. This polymorphism might also associate with squamous cell carcinoma.
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Affiliation(s)
- Yuqing Lou
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiaotong University, 241 West Huaihai Road, Shanghai, 200030, People's Republic of China
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