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Tuan Anh L, Ngoc Hoang T, Thibaut Y, Chatzipapas K, Sakata D, Incerti S, Villagrasa C, Perrot Y. "dsbandrepair" - An updated Geant4-DNA simulation tool for evaluating the radiation-induced DNA damage and its repair. Phys Med 2024; 124:103422. [PMID: 38981169 DOI: 10.1016/j.ejmp.2024.103422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/07/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024] Open
Abstract
PURPOSE Interdisciplinary scientific communities have shown large interest to achieve a mechanistic description of radiation-induced biological damage, aiming to predict biological results produced by different radiation quality exposures. Monte Carlo track-structure simulations are suitable and reliable for the study of early DNA damage induction used as input for assessing DNA damage. This study presents the most recent improvements of a Geant4-DNA simulation tool named "dsbandrepair". METHODS "dsbandrepair" is a Monte Carlo simulation tool based on a previous code (FullSim) that estimates the induction of early DNA single-strand breaks (SSBs) and double-strand breaks (DSBs). It uses DNA geometries generated by the DNAFabric computational tool for simulating the induction of early single-strand breaks (SSBs) and double-strand breaks (DSBs). Moreover, the new tool includes some published radiobiological models for survival fraction and un-rejoined DSB. Its application for a human fibroblast cell and human umbilical vein endothelial cell containing both heterochromatin and euchromatin was conducted. In addition, this new version offers the possibility of using the new IRT-syn method for computing the chemical stage. RESULTS The direct and indirect strand breaks, SSBs, DSBs, and damage complexity obtained in this work are equivalent to those obtained with the previously published simulation tool when using the same configuration in the physical and chemical stages. Simulation results on survival fraction and un-rejoined DSB are in reasonable agreement with experimental data. CONCLUSIONS "dsbandrepair" is a tool for simulating DNA damage and repair, benchmarked against experimental data. It has been released as an advanced example in Geant4.11.2.
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Affiliation(s)
- Le Tuan Anh
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | - Tran Ngoc Hoang
- CNRS/IN2P3, CENBG, UMR 5797, Bordeaux University, 33170 Gradignan, France
| | - Yann Thibaut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | | | | | - Sébastien Incerti
- CNRS/IN2P3, CENBG, UMR 5797, Bordeaux University, 33170 Gradignan, France
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
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2
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Bergis-Ser C, Reji M, Latrasse D, Bergounioux C, Benhamed M, Raynaud C. Chromatin dynamics and RNA metabolism are double-edged swords for the maintenance of plant genome integrity. NATURE PLANTS 2024; 10:857-873. [PMID: 38658791 DOI: 10.1038/s41477-024-01678-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
Maintenance of genome integrity is an essential process in all organisms. Mechanisms avoiding the formation of DNA lesions or mutations are well described in animals because of their relevance to human health and cancer. In plants, they are of growing interest because DNA damage accumulation is increasingly recognized as one of the consequences of stress. Although the cellular response to DNA damage is mostly studied in response to genotoxic treatments, the main source of DNA lesions is cellular activity itself. This can occur through the production of reactive oxygen species as well as DNA processing mechanisms such as DNA replication or transcription and chromatin dynamics. In addition, how lesions are formed and repaired is greatly influenced by chromatin features and dynamics and by DNA and RNA metabolism. Notably, actively transcribed regions or replicating DNA, because they are less condensed and are sites of DNA processing, are more exposed to DNA damage. However, at the same time, a wealth of cellular mechanisms cooperate to favour DNA repair at these genomic loci. These intricate relationships that shape the distribution of mutations along the genome have been studied extensively in animals but much less in plants. In this Review, we summarize how chromatin dynamics influence lesion formation and DNA repair in plants, providing a comprehensive view of current knowledge and highlighting open questions with regard to what is known in other organisms.
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Affiliation(s)
- Clara Bergis-Ser
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Meega Reji
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
- Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, India
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
- Université Paris Cité, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
- Institut Universitaire de France, Orsay, France
| | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France.
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3
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Walker FM, Sobral LM, Danis E, Sanford B, Donthula S, Balakrishnan I, Wang D, Pierce A, Karam SD, Kargar S, Serkova NJ, Foreman NK, Venkataraman S, Dowell R, Vibhakar R, Dahl NA. Rapid P-TEFb-dependent transcriptional reorganization underpins the glioma adaptive response to radiotherapy. Nat Commun 2024; 15:4616. [PMID: 38816355 PMCID: PMC11139976 DOI: 10.1038/s41467-024-48214-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Dynamic regulation of gene expression is fundamental for cellular adaptation to exogenous stressors. P-TEFb-mediated pause-release of RNA polymerase II (Pol II) is a conserved regulatory mechanism for synchronous transcriptional induction in response to heat shock, but this pro-survival role has not been examined in the applied context of cancer therapy. Using model systems of pediatric high-grade glioma, we show that rapid genome-wide reorganization of active chromatin facilitates P-TEFb-mediated nascent transcriptional induction within hours of exposure to therapeutic ionizing radiation. Concurrent inhibition of P-TEFb disrupts this chromatin reorganization and blunts transcriptional induction, abrogating key adaptive programs such as DNA damage repair and cell cycle regulation. This combination demonstrates a potent, synergistic therapeutic potential agnostic of glioma subtype, leading to a marked induction of tumor cell apoptosis and prolongation of xenograft survival. These studies reveal a central role for P-TEFb underpinning the early adaptive response to radiotherapy, opening avenues for combinatorial treatment in these lethal malignancies.
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Affiliation(s)
- Faye M Walker
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Lays Martin Sobral
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Etienne Danis
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- University of Colorado Cancer Center, University of Colorado School of Medicine, Aurora, CO, USA
| | - Bridget Sanford
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sahiti Donthula
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ilango Balakrishnan
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dong Wang
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Angela Pierce
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sana D Karam
- Department of Radiation Oncology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Soudabeh Kargar
- University of Colorado Cancer Center, University of Colorado School of Medicine, Aurora, CO, USA
| | - Natalie J Serkova
- Department of Radiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA
- Department of Neurosurgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sujatha Venkataraman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Robin Dowell
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Rajeev Vibhakar
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA
- Department of Neurosurgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nathan A Dahl
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA.
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA.
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4
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Seane EN, Nair S, Vandevoorde C, Joubert A. Mechanistic Sequence of Histone Deacetylase Inhibitors and Radiation Treatment: An Overview. Pharmaceuticals (Basel) 2024; 17:602. [PMID: 38794172 PMCID: PMC11124271 DOI: 10.3390/ph17050602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases inhibitors (HDACis) have shown promising therapeutic outcomes in haematological malignancies such as leukaemia, multiple myeloma, and lymphoma, with disappointing results in solid tumours when used as monotherapy. As a result, combination therapies either with radiation or other deoxyribonucleic acid (DNA) damaging agents have been suggested as ideal strategy to improve their efficacy in solid tumours. Numerous in vitro and in vivo studies have demonstrated that HDACis can sensitise malignant cells to both electromagnetic and particle types of radiation by inhibiting DNA damage repair. Although the radiosensitising ability of HDACis has been reported as early as the 1990s, the mechanisms of radiosensitisation are yet to be fully understood. This review brings forth the various protocols used to sequence the administration of radiation and HDACi treatments in the different studies. The possible contribution of these various protocols to the ambiguity that surrounds the mechanisms of radiosensitisation is also highlighted.
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Affiliation(s)
- Elsie Neo Seane
- Department of Radiography, School of Health Care Sciences, Faculty of Health Sciences, University of Pretoria, Pretoria 0028, South Africa
- Department of Medical Imaging and Therapeutic Sciences, Faculty of Health and Wellness, Cape Peninsula University of Technology, Cape Town 7530, South Africa
- Radiation Biophysics Division, Separate Sector Cyclotron (SSC) Laboratory, iThemba LABS, Cape Town 7131, South Africa;
| | - Shankari Nair
- Radiation Biophysics Division, Separate Sector Cyclotron (SSC) Laboratory, iThemba LABS, Cape Town 7131, South Africa;
| | - Charlot Vandevoorde
- GSI Helmholtz Centre for Heavy Ion Research, Department of Biophysics, 64291 Darmstadt, Germany;
| | - Anna Joubert
- Department of Physiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria 0028, South Africa;
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5
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Oikeh E, Ziebarth J, Dinar MAM, Kirchhoff D, Aronova A, Dziubla TD, Wang Y, DeRouchey JE. DNA Packaging and Polycation Length Determine DNA Susceptibility to Free Radical Damage in Condensed DNA. J Phys Chem B 2024; 128:3329-3339. [PMID: 38557033 DOI: 10.1021/acs.jpcb.3c06116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In nature, DNA exists primarily in a highly compacted form. The compaction of DNA in vivo is mediated by cationic proteins: histones in somatic nuclei and protamines in sperm chromatin. The extreme, nearly crystalline packaging of DNA by protamines in spermatozoa is thought to be essential for both efficient genetic delivery as well as DNA protection against damage by mutagens and oxidative species. The protective role of protamines is required in sperm, as they are sensitive to ROS damage due to the progressive loss of DNA repair mechanisms during maturation. The degree to which DNA packaging directly relates to DNA protection in the condensed state, however, is poorly understood. Here, we utilized different polycation condensing agents to achieve varying DNA packaging densities and quantify DNA damage by free radical oxidation within the condensates. Although we see that tighter DNA packaging generally leads to better protection, the length of the polycation also plays a significant role. Molecular dynamics simulations suggest that longer polyarginine chains offer increased protection by occupying more space on the DNA surface and forming more stable interactions. Taken together, our results suggest a complex interplay among polycation properties, DNA packaging density, and DNA protection against free radical damage within condensed states.
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Affiliation(s)
- Ehigbai Oikeh
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Jesse Ziebarth
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Md Abu Monsur Dinar
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Daniel Kirchhoff
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Anastasiia Aronova
- Chemical and Materials Engineering Department, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Thomas D Dziubla
- Chemical and Materials Engineering Department, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yongmei Wang
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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6
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Li H, Playter C, Das P, McCord RP. Chromosome compartmentalization: causes, changes, consequences, and conundrums. Trends Cell Biol 2024:S0962-8924(24)00021-7. [PMID: 38395734 DOI: 10.1016/j.tcb.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
The spatial segregation of the genome into compartments is a major feature of 3D genome organization. New data on mammalian chromosome organization across different conditions reveal important information about how and why these compartments form and change. A combination of epigenetic state, nuclear body tethering, physical forces, gene expression, and replication timing (RT) can all influence the establishment and alteration of chromosome compartments. We review the causes and implications of genomic regions undergoing a 'compartment switch' that changes their physical associations and spatial location in the nucleus. About 20-30% of genomic regions change compartment during cell differentiation or cancer progression, whereas alterations in response to a stimulus within a cell type are usually much more limited. However, even a change in 1-2% of genomic bins may have biologically relevant implications. Finally, we review the effects of compartment changes on gene regulation, DNA damage repair, replication, and the physical state of the cell.
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Affiliation(s)
- Heng Li
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Christopher Playter
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Priyojit Das
- University of Tennessee-Oak Ridge National Laboratory (UT-ORNL) Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Rachel Patton McCord
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.
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7
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Paine PT, Rechsteiner C, Morandini F, Desdín-Micó G, Mrabti C, Parras A, Haghani A, Brooke R, Horvath S, Seluanov A, Gorbunova V, Ocampo A. Initiation phase cellular reprogramming ameliorates DNA damage in the ERCC1 mouse model of premature aging. FRONTIERS IN AGING 2024; 4:1323194. [PMID: 38322248 PMCID: PMC10844398 DOI: 10.3389/fragi.2023.1323194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024]
Abstract
Unlike aged somatic cells, which exhibit a decline in molecular fidelity and eventually reach a state of replicative senescence, pluripotent stem cells can indefinitely replenish themselves while retaining full homeostatic capacity. The conferment of beneficial-pluripotency related traits via in vivo partial cellular reprogramming in vivo partial reprogramming significantly extends lifespan and restores aging phenotypes in mouse models. Although the phases of cellular reprogramming are well characterized, details of the rejuvenation processes are poorly defined. To understand whether cellular reprogramming can ameliorate DNA damage, we created a reprogrammable accelerated aging mouse model with an ERCC1 mutation. Importantly, using enhanced partial reprogramming by combining small molecules with the Yamanaka factors, we observed potent reversion of DNA damage, significant upregulation of multiple DNA damage repair processes, and restoration of the epigenetic clock. In addition, we present evidence that pharmacological inhibition of ALK5 and ALK2 receptors in the TGFb pathway are able to phenocopy some benefits including epigenetic clock restoration suggesting a role in the mechanism of rejuvenation by partial reprogramming.
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Affiliation(s)
- Patrick Treat Paine
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Center for Virology and Vaccine Research, Harvard Medical School, Boston, MA, United States
| | | | - Francesco Morandini
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Gabriela Desdín-Micó
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Calida Mrabti
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alberto Parras
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- EPITERNA SA, Vaud, Switzerland
| | | | - Robert Brooke
- Epigenetic Clock Development Foundation, Torrance, CA, United States
| | - Steve Horvath
- Altos Labs, San Diego, CA, United States
- Epigenetic Clock Development Foundation, Torrance, CA, United States
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, United States
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, United States
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Alejandro Ocampo
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- EPITERNA SA, Vaud, Switzerland
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8
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Maeshima K, Iida S, Shimazoe MA, Tamura S, Ide S. Is euchromatin really open in the cell? Trends Cell Biol 2024; 34:7-17. [PMID: 37385880 DOI: 10.1016/j.tcb.2023.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 07/01/2023]
Abstract
Genomic DNA is wrapped around a core histone octamer and forms a nucleosome. In higher eukaryotic cells, strings of nucleosomes are irregularly folded as chromatin domains that act as functional genome units. According to a typical textbook model, chromatin can be categorized into two types, euchromatin and heterochromatin, based on its degree of compaction. Euchromatin is open, while heterochromatin is closed and condensed. However, is euchromatin really open in the cell? New evidence from genomics and advanced imaging studies has revealed that euchromatin consists of condensed liquid-like domains. Condensed chromatin seems to be the default chromatin state in higher eukaryotic cells. We discuss this novel view of euchromatin in the cell and how the revealed organization is relevant to genome functions.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Masa A Shimazoe
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
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9
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Li Q, Qin K, Tian Y, Chen B, Zhao G, Xu S, Wu L. Inhibition of demethylase by IOX1 modulates chromatin accessibility to enhance NSCLC radiation sensitivity through attenuated PIF1. Cell Death Dis 2023; 14:817. [PMID: 38086789 PMCID: PMC10716120 DOI: 10.1038/s41419-023-06346-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]
Abstract
Chromatin accessibility is a critical determinant of gene transcriptional expression and regulated by histones modification. However, the potential for manipulating chromatin accessibility to regulate radiation sensitivity remains unclear. Our findings demonstrated that the histone demethylase inhibitor, 5-carboxy-8-hydroxyquinoline (IOX1), could enhance the radiosensitivity of non-small cell lung cancer (NSCLC) in vitro and in vivo. Mechanistically, IOX1 treatment reduced chromatin accessibility in the promoter region of DNA damage repair genes, leading to decreased DNA repair efficiency and elevated DNA damage induced by γ irradiation. Notably, IOX1 treatment significantly reduced both chromatin accessibility and the transcription of phytochrome interacting factor 1 (PIF1), a key player in telomere maintenance. Inhibition of PIF1 delayed radiation-induced DNA and telomeric DNA damage repair, as well as increased radiosensitivity of NSCLC in vitro and in vivo. Further study indicated that the above process was regulated by a reduction of transcription factor myc-associated zinc finger protein (MAZ) binding to the distal intergenic region of the PIF1. Taken together, IOX1-mediated demethylase inactivation reduced chromatin accessibility, leading to elevated telomere damage which is partly due to PIF1 inhibition, thereby enhancing NSCLC radiosensitivity.
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Affiliation(s)
- Qian Li
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Kexin Qin
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Yushan Tian
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, Henan, 450001, PR China
| | - Biao Chen
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Guoping Zhao
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Shengmin Xu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China.
| | - Lijun Wu
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China.
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China.
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10
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Dahl H, Ballangby J, Tengs T, Wojewodzic MW, Eide DM, Brede DA, Graupner A, Duale N, Olsen AK. Dose rate dependent reduction in chromatin accessibility at transcriptional start sites long time after exposure to gamma radiation. Epigenetics 2023; 18:2193936. [PMID: 36972203 PMCID: PMC10054331 DOI: 10.1080/15592294.2023.2193936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Ionizing radiation (IR) impact cellular and molecular processes that require chromatin remodelling relevant for cellular integrity. However, the cellular implications of ionizing radiation (IR) delivered per time unit (dose rate) are still debated. This study investigates whether the dose rate is relevant for inflicting changes to the epigenome, represented by chromatin accessibility, or whether it is the total dose that is decisive. CBA/CaOlaHsd mice were whole-body exposed to either chronic low dose rate (2.5 mGy/h for 54 d) or the higher dose rates (10 mGy/h for 14 d and 100 mGy/h for 30 h) of gamma radiation (60Co, total dose: 3 Gy). Chromatin accessibility was analysed in liver tissue samples using Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-Seq), both one day after and over three months post-radiation (>100 d). The results show that the dose rate contributes to radiation-induced epigenomic changes in the liver at both sampling timepoints. Interestingly, chronic low dose rate exposure to a high total dose (3 Gy) did not inflict long-term changes to the epigenome. In contrast to the acute high dose rate given to the same total dose, reduced accessibility at transcriptional start sites (TSS) was identified in genes relevant for the DNA damage response and transcriptional activity. Our findings link dose rate to essential biological mechanisms that could be relevant for understanding long-term changes after ionizing radiation exposure. However, future studies are needed to comprehend the biological consequence of these findings.
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Affiliation(s)
- Hildegunn Dahl
- Division of Climate and Environmental Health, Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Environmental Radiation (CERAD), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jarle Ballangby
- Division of Climate and Environmental Health, Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Environmental Radiation (CERAD), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Torstein Tengs
- Division of Climate and Environmental Health, Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Environmental Radiation (CERAD), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Division for Aquaculture, Department of breeding and genetics, Nofima, Ås, Norway
| | - Marcin W Wojewodzic
- Division of Climate and Environmental Health, Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Environmental Radiation (CERAD), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Department of Research, Section Molecular Epidemiology and Infections, Cancer Registry of Norway, Oslo, Norway
| | - Dag M Eide
- Division of Climate and Environmental Health, Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Environmental Radiation (CERAD), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Dag Anders Brede
- Centre for Environmental Radiation (CERAD), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Anne Graupner
- Division of Climate and Environmental Health, Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Environmental Radiation (CERAD), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Nur Duale
- Division of Climate and Environmental Health, Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Environmental Radiation (CERAD), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ann-Karin Olsen
- Division of Climate and Environmental Health, Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Environmental Radiation (CERAD), Norwegian University of Life Sciences (NMBU), Ås, Norway
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11
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Chen Y, Ai L, Zhang Y, Li X, Xu S, Yang W, Jin J, Ma Y, Hu Z, Zhang Y, Rong Y, Zhang S. The EZH2-H3K27me3 axis modulates aberrant transcription and apoptosis in cyclophosphamide-induced ovarian granulosa cell injury. Cell Death Discov 2023; 9:413. [PMID: 37963880 PMCID: PMC10646043 DOI: 10.1038/s41420-023-01705-6] [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: 07/11/2023] [Revised: 10/21/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023] Open
Abstract
Chemotherapy-induced ovarian damage and infertility are significant concerns for women of childbearing age with cancer; however, the underlying mechanisms are still not fully understood. Our study has revealed a close association between epigenetic regulation and cyclophosphamide (CTX)-induced ovarian damage. Specifically, CTX and its active metabolite 4-hydroperoxy cyclophosphamide (4-HC) were found to increase the apoptosis of granulosa cells (GCs) by reducing EZH2 and H3K27me3 levels, both in vivo and in vitro. Furthermore, RNA-seq and CUT&Tag analyses revealed that the loss of H3K27me3 peaks on promoters led to the overactivation of genes associated with transcriptional regulation and apoptosis, indicating that stable H3K27me3 status could help to provide a safeguard against CTX-induced ovarian damage. Administration of the H3K27me3-demethylase inhibitor, GSK-J4, prior to CTX treatment could partially mitigate GC apoptosis by reversing the reduction of H3K27me3 and the aberrant upregulation of specific genes involved in transcriptional regulation and apoptosis. GSK-J4 could thus potentially be a protective agent for female fertility when undergoing chemotherapy. The results provide new insights into the mechanisms for chemotherapy injury and future clinical interventions for fertility preservation.
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Affiliation(s)
- Yingyan Chen
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Leilei Ai
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Yingyi Zhang
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Xiang Li
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Shiqian Xu
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Weijie Yang
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Jiamin Jin
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Yerong Ma
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Zhanhong Hu
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Yinli Zhang
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Yan Rong
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China.
| | - Songying Zhang
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China.
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12
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Mamontova EM, Clément MJ, Sukhanova MV, Joshi V, Bouhss A, Rengifo-Gonzalez JC, Desforges B, Hamon L, Lavrik OI, Pastré D. FUS RRM regulates poly(ADP-ribose) levels after transcriptional arrest and PARP-1 activation on DNA damage. Cell Rep 2023; 42:113199. [PMID: 37804508 DOI: 10.1016/j.celrep.2023.113199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/08/2023] [Accepted: 09/15/2023] [Indexed: 10/09/2023] Open
Abstract
PARP-1 activation at DNA damage sites leads to the synthesis of long poly(ADP-ribose) (PAR) chains, which serve as a signal for DNA repair. Here we show that FUS, an RNA-binding protein, is specifically directed to PAR through its RNA recognition motif (RRM) to increase PAR synthesis by PARP-1 in HeLa cells after genotoxic stress. Using a structural approach, we also identify specific residues located in the FUS RRM, which can be PARylated by PARP-1 to control the level of PAR synthesis. Based on the results of this work, we propose a model in which, following a transcriptional arrest that releases FUS from nascent mRNA, FUS can be recruited by PARP-1 activated by DNA damage to stimulate PAR synthesis. We anticipate that this model offers new perspectives to understand the role of FET proteins in cancers and in certain neurodegenerative diseases such as amyotrophic lateral sclerosis.
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Affiliation(s)
- Evgeniya M Mamontova
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France; Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Av. 8, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Street, Novosibirsk 630090, Russia
| | - Marie-Jeanne Clément
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Av. 8, Novosibirsk 630090, Russia
| | - Vandana Joshi
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Ahmed Bouhss
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | | | - Bénédicte Desforges
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Loic Hamon
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Av. 8, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Street, Novosibirsk 630090, Russia.
| | - David Pastré
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France.
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13
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Akuwudike P, López-Riego M, Ginter J, Cheng L, Wieczorek A, Życieńska K, Łysek-Gładysińska M, Wojcik A, Brzozowska B, Lundholm L. Mechanistic insights from high resolution DNA damage analysis to understand mixed radiation exposure. DNA Repair (Amst) 2023; 130:103554. [PMID: 37595330 DOI: 10.1016/j.dnarep.2023.103554] [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: 04/20/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 08/20/2023]
Abstract
Cells exposed to densely ionising high and scattered low linear energy transfer (LET) radiation (50 % dose of each) react more strongly than to the same dose of each separately. The relationship between DNA double strand break location inside the nucleus and chromatin structure was evaluated, using high-resolution transmission electron microscopy (TEM) in breast cancer MDA-MB-231 cells at 30 min post 5 Gy. Additionally, response to high and/or low LET radiation was assessed using single (1 ×1.5 Gy) versus fractionated dose delivery (5 ×0.3 Gy). By TEM analysis, the highest total number of γH2AX nanobeads were found in cells irradiated with alpha radiation just prior to gamma radiation (called mixed beam), followed by alpha, then gamma radiation. γH2AX foci induced by mixed beam radiation tended to be surrounded by open chromatin (lighter TEM regions), yet foci containing the highest number of beads, i.e. larger foci representing complex damage, remained in the heterochromatic areas. The γH2AX large focus area was also greater in mixed beam-treated cells when analysed by immunofluorescence. Fractionated mixed beams given daily induced the strongest reduction in cell viability and colony formation in MDA-MB-231 and osteosarcoma U2OS cells compared to the other radiation qualities, as well as versus acute exposure. This may partially be explained by recurring low LET oxidative DNA damage by every fraction together with a delay in recompaction of chromatin after high LET, demonstrated by low levels of heterochromatin marker H3K9me3 at 2 h after the last mixed beam fraction in MDA-MB-231. In conclusion, early differences in response to complex DNA damage may lead to a stronger cell kill induced by fractionated exposure, which suggest a therapeutic potential of combined high and low LET irradiation.
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Affiliation(s)
- Pamela Akuwudike
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Milagrosa López-Riego
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Józef Ginter
- Biomedical Physics Division, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Lei Cheng
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Anna Wieczorek
- Division of Medical Biology, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
| | - Katarzyna Życieńska
- Biomedical Physics Division, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | | | - Andrzej Wojcik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Beata Brzozowska
- Biomedical Physics Division, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Lovisa Lundholm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden.
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14
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Buglewicz DJ, Su C, Banks AB, Stenger-Smith J, Elmegerhi S, Hirakawa H, Fujimori A, Kato TA. Metal Ions Modify In Vitro DNA Damage Yields with High-LET Radiation. TOXICS 2023; 11:773. [PMID: 37755783 PMCID: PMC10537317 DOI: 10.3390/toxics11090773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023]
Abstract
Cu2+ and Co2+ are metals known to increase DNA damage in the presence of hydrogen peroxide through a Fenton-type reaction. We hypothesized that these metals could increase DNA damage following irradiations of increasing LET values as hydrogen peroxide is a product of the radiolysis of water. The reaction mixtures contain either double- or single-stranded DNA in solution with Cu2+ or Co2+ and were irradiated either with X-ray, carbon-ion or iron-ion beams, or they were treated with hydrogen peroxide or bleomycin at increasing radiation dosages or chemical concentrations. DNA damage was then assessed via gel electrophoresis followed with a band intensity analysis. DNA damage was the greatest when DNA in the solution with either metal was treated with only hydrogen peroxide followed by the DNA damage of DNA in the solution with either metal post irradiation of low-LET (X-Ray) or high-LET (carbon-ion and iron-ion), respectively, and demonstrated the least damage after treatment with bleomycin. Cu2+ portrayed greater DNA damage than Co2+ following all experimental conditions. The metals' effect caused more DNA damage and was observed to be LET-dependent for single-strand break formation but inversely dependent for double-strand break formation. These results suggest that Cu2+ is more efficient than Co2+ at inducing both DNA single-strand and double-strand breaks following all irradiations and chemical treatments.
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Affiliation(s)
- Dylan J. Buglewicz
- National Institute of Radiological Sciences, National Institutes of Quantum Science and Technology, Chiba 263-8555, Japan; (D.J.B.); (H.H.); (A.F.)
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA; (C.S.); (A.B.B.); (J.S.-S.); (S.E.)
| | - Cathy Su
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA; (C.S.); (A.B.B.); (J.S.-S.); (S.E.)
| | - Austin B. Banks
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA; (C.S.); (A.B.B.); (J.S.-S.); (S.E.)
| | - Jazmine Stenger-Smith
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA; (C.S.); (A.B.B.); (J.S.-S.); (S.E.)
| | - Suad Elmegerhi
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA; (C.S.); (A.B.B.); (J.S.-S.); (S.E.)
| | - Hirokazu Hirakawa
- National Institute of Radiological Sciences, National Institutes of Quantum Science and Technology, Chiba 263-8555, Japan; (D.J.B.); (H.H.); (A.F.)
| | - Akira Fujimori
- National Institute of Radiological Sciences, National Institutes of Quantum Science and Technology, Chiba 263-8555, Japan; (D.J.B.); (H.H.); (A.F.)
| | - Takamitsu A. Kato
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA; (C.S.); (A.B.B.); (J.S.-S.); (S.E.)
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15
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Liang Y, Wu J, Ding Z, Liu C, Fu Q. Evaluation of the Yield of DNA Double-Strand Breaks for Carbon Ions Using Monte Carlo Simulation and DNA Fragment Distribution. Int J Radiat Oncol Biol Phys 2023; 117:252-261. [PMID: 36966847 DOI: 10.1016/j.ijrobp.2023.03.049] [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: 11/29/2022] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 04/07/2023]
Abstract
PURPOSE The aim of this work was to provide a method to evaluate the yield of DNA double-strand breaks (DSBs) for carbon ions, overcoming the bias in existing methods due to the nonrandom distribution of DSBs. METHODS AND MATERIALS A previously established biophysical program based on the radiation track structure and a multilevel chromosome model was used to simulate DNA damage induced by x-rays and carbon ions. The fraction of activity retained (FAR) as a function of absorbed dose or particle fluence was obtained by counting the fraction of DNA fragments larger than 6 Mbp. Simulated FAR curves for the 250 kV x-rays and carbon ions at various energies were compared with measurements using constant-field gel electrophoresis. The doses or fluences at the FAR of 0.7 based on linear interpolation were used to estimate the simulation error for the production of DSBs. RESULTS The relative difference of doses at the FAR of 0.7 between simulation and experiment was -8.5% for the 250 kV x-rays. The relative differences of fluences at the FAR of 0.7 between simulations and experiments were -17.5%, -42.2%, -18.2%, -3.1%, 10.8%, and -14.5% for the 34, 65, 130, 217, 2232, and 3132 MeV carbon ions, respectively. In comparison, the measurement uncertainty was about 20%. Carbon ions produced remarkably more DSBs and DSB clusters per unit dose than x-rays. The yield of DSBs for carbon ions, ranging from 10 to 16 Gbp-1Gy-1, increased with linear energy transfer (LET) but plateaued in the high-LET end. The yield of DSB clusters first increased and then decreased with LET. This pattern was similar to the relative biological effectiveness for cell survival for heavy ions. CONCLUSIONS The estimated yields of DSBs for carbon ions increased from 10 Gbp-1Gy-1 in the low-LET end to 16 Gbp-1Gy-1 in the high-LET end with 20% uncertainty.
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Affiliation(s)
- Ying Liang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.
| | - Jianan Wu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Zhen Ding
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Chenbin Liu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Qibin Fu
- Sino-French Institute of Nuclear Engineering and Technology, Sun Yat-sen University, Zhuhai, China
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16
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Aguilar R, Khan L, Arslanovic N, Birmingham K, Kasliwal K, Posnikoff S, Chakraborty U, Hickman AR, Watson R, Ezell RJ, Willis HE, Cowles MW, Garner R, Shim A, Gutierrez I, Marunde MR, Keogh MC, Tyler JK. Multivalent binding of the tardigrade Dsup protein to chromatin promotes yeast survival and longevity upon exposure to oxidative damage. RESEARCH SQUARE 2023:rs.3.rs-3182883. [PMID: 37546815 PMCID: PMC10402244 DOI: 10.21203/rs.3.rs-3182883/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Tardigrades are remarkable in their ability to survive extreme environments. The damage suppressor (Dsup) protein is thought responsible for their extreme resistance to reactive oxygen species (ROS) generated by irradiation. Here we show that expression of Ramazzottius varieornatus Dsup in Saccharomyces cerevisiae reduces oxidative DNA damage and extends the lifespan of budding yeast exposed to chronic oxidative genotoxicity. This protection from ROS requires either the Dsup HMGN-like domain or sequences C-terminal to same. Dsup associates with no apparent bias across the yeast genome, using multiple modes of nucleosome binding; the HMGN-like region interacts with both the H2A/H2B acidic patch and H3/H4 histone tails, while the C-terminal region binds DNA. These findings give precedent for engineering an organism by physically shielding its genome to promote survival and longevity in the face of oxidative damage.
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Affiliation(s)
- Rhiannon Aguilar
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | | | - Nina Arslanovic
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Kaylah Birmingham
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Pharmacology Graduate Program, New York, NY 10065 United States
| | - Kritika Kasliwal
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Biochemistry, Cellular, and Molecular Biology Graduate Program, New York, NY 10065, USA
| | - Spike Posnikoff
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Ujani Chakraborty
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | | | | | | | | | | | - Richard Garner
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Biochemistry, Cellular, and Molecular Biology Graduate Program, New York, NY 10065, USA
| | - Abraham Shim
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Biochemistry, Cellular, and Molecular Biology Graduate Program, New York, NY 10065, USA
| | - Ignacio Gutierrez
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | | | | | - Jessica K. Tyler
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
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17
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Nozaki T, Shinkai S, Ide S, Higashi K, Tamura S, Shimazoe MA, Nakagawa M, Suzuki Y, Okada Y, Sasai M, Onami S, Kurokawa K, Iida S, Maeshima K. Condensed but liquid-like domain organization of active chromatin regions in living human cells. SCIENCE ADVANCES 2023; 9:eadf1488. [PMID: 37018405 PMCID: PMC10075990 DOI: 10.1126/sciadv.adf1488] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/07/2023] [Indexed: 05/31/2023]
Abstract
In eukaryotes, higher-order chromatin organization is spatiotemporally regulated as domains, for various cellular functions. However, their physical nature in living cells remains unclear (e.g., condensed domains or extended fiber loops; liquid-like or solid-like). Using novel approaches combining genomics, single-nucleosome imaging, and computational modeling, we investigated the physical organization and behavior of early DNA replicated regions in human cells, which correspond to Hi-C contact domains with active chromatin marks. Motion correlation analysis of two neighbor nucleosomes shows that nucleosomes form physically condensed domains with ~150-nm diameters, even in active chromatin regions. The mean-square displacement analysis between two neighbor nucleosomes demonstrates that nucleosomes behave like a liquid in the condensed domain on the ~150 nm/~0.5 s spatiotemporal scale, which facilitates chromatin accessibility. Beyond the micrometers/minutes scale, chromatin seems solid-like, which may contribute to maintaining genome integrity. Our study reveals the viscoelastic principle of the chromatin polymer; chromatin is locally dynamic and reactive but globally stable.
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Affiliation(s)
- Tadasu Nozaki
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Soya Shinkai
- Laboratory for Developmental Dynamics, Center for Biosystems Dynamics Research (BDR), RIKEN, Kobe, Hyogo 650-0047, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Koichi Higashi
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masa A. Shimazoe
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Masaki Nakagawa
- Department of Computer Science and Engineering, Fukuoka Institute of Technology, Fukuoka, Fukuoka 811-0295, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, University of Tokyo, 5-1-5 Kashiwanoha Kashiwa, Chiba 277-8562, Japan
| | - Yasushi Okada
- Laboratory for Cell Polarity Regulation, Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka 565-0874, Japan
| | - Masaki Sasai
- Department of Complex Systems Science, Nagoya University, Nagoya 464-8601, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Shuichi Onami
- Laboratory for Developmental Dynamics, Center for Biosystems Dynamics Research (BDR), RIKEN, Kobe, Hyogo 650-0047, Japan
| | - Ken Kurokawa
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
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18
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Al-Wahaibi ASM, Upstill-Goddard RC, Burgess JG. Isolation and Staining Reveal the Presence of Extracellular DNA in Marine Gel Particles. Gels 2023; 9:gels9030251. [PMID: 36975700 PMCID: PMC10048003 DOI: 10.3390/gels9030251] [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: 02/22/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Marine gel particles (MGP) are amorphous hydrogel exudates from bacteria and microalgae that are ubiquitous in the oceans, but their biochemical composition and function are poorly understood. While dynamic ecological interactions between marine microorganisms and MGPs may result in the secretion and mixing of bacterial extracellular polymeric substances (EPS) such as nucleic acids, compositional studies currently are limited to the identification of acidic polysaccharides and proteins in transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP). Previous studies targeted MGPs isolated by filtration. We developed a new way of isolating MGPs from seawater in liquid suspension and applied it to identify extracellular DNA (eDNA) in North Sea surface seawater. Seawater was filtered onto polycarbonate (PC) filters with gentle vacuum filtration, and then the filtered particles were gently resuspended in a smaller volume of sterile seawater. The resulting MGPs ranged in size from 0.4 to 100 µm in diameter. eDNA was detected by fluorescent microscopy using YOYO-1 (for eDNA), with Nile red (targeting cell membranes) as a counterstain. TOTO-3 was also used to stain eDNA, with ConA to localise glycoproteins and SYTO-9 for the live/dead staining of cells. Confocal laser scanning microscopy (CLSM) revealed the presence of proteins and polysaccharides. We found eDNA to be universally associated with MGPs. To further elucidate the role of eDNA, we established a model experimental MGP system using bacterial EPS from Pseudoalteromonas atlantica that also contained eDNA. Our results clearly demonstrate the occurrence of eDNA in MGPs, and should aid furthering our understanding of the micro-scale dynamics and fate of MGPs that underly the large-scale processes of carbon cycling and sedimentation in the ocean.
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Affiliation(s)
- Aisha S M Al-Wahaibi
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Muscat 123, Oman
| | - Robert C Upstill-Goddard
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - J Grant Burgess
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Walker FM, Sobral LM, Danis E, Sanford B, Balakrishnan I, Wang D, Pierce A, Karam SD, Serkova NJ, Foreman NK, Venkataraman S, Dowell R, Vibhakar R, Dahl NA. Rapid PTEFb-dependent transcriptional reorganization underpins the glioma adaptive response to radiotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525424. [PMID: 36747867 PMCID: PMC9900817 DOI: 10.1101/2023.01.24.525424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Dynamic regulation of gene expression is fundamental for cellular adaptation to exogenous stressors. PTEFb-mediated pause-release of RNA polymerase II (Pol II) is a conserved regulatory mechanism for synchronous transcriptional induction in response to heat shock, but this pro-survival role has not been examined in the applied context of cancer therapy. Using model systems of pediatric high-grade glioma, we show that rapid genome-wide reorganization of active chromatin facilitates PTEFb-mediated nascent transcriptional induction within hours of exposure to therapeutic ionizing radiation. Concurrent inhibition of PTEFb disrupts this chromatin reorganization and blunts transcriptional induction, abrogating key adaptive programs such as DNA damage repair and cell cycle regulation. This combination demonstrates a potent, synergistic therapeutic potential agnostic of glioma subtype, leading to a marked induction of tumor cell apoptosis and prolongation of xenograft survival. These studies reveal a central role for PTEFb underpinning the early adaptive response to radiotherapy, opening new avenues for combinatorial treatment in these lethal malignancies.
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20
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Kwok ACM, Li C, Lam WT, Wong JTY. Responses of dinoflagellate cells to ultraviolet-C irradiation. Environ Microbiol 2022; 24:5936-5950. [PMID: 35837869 DOI: 10.1111/1462-2920.16135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 01/12/2023]
Abstract
Dinoflagellates are important aquatic microbes and major harmful algal bloom (HAB) agents that form invasive species through ship ballast transfer. UV-C installations are recommended for ballast treatments and HAB controls, but there is a lack of knowledge in dinoflagellate responses to UV-C. We report here dose-dependent cell cycle delay and viability loss of dinoflagellate cells irradiated with UV-C, with significant proliferative reduction at 800 Jm-2 doses or higher, but immediate LD50 was in the range of 2400-3200 Jm-2 . At higher dosages, some dinoflagellate cells surprisingly survived after days of recovery incubation, and continued viability loss, with samples exhibiting DNA fragmentations per proliferative resumption. Sequential cell cycle postponements, suggesting DNA damages were repaired over one cell cycle, were revealed with flow cytometric analysis and transcriptomic analysis. Over a sustained level of other DNA damage repair pathways, transcript elevation was observed only for several components of base pair repair and mismatch repair. Cumulatively, our findings demonstrated special DNA damage responses in dinoflagellate cells, which we discussed in relation to their unique chromo-genomic characters, as well as indicating resilience of dinoflagellate cells to UV-C.
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Affiliation(s)
- Alvin Chun Man Kwok
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Chongping Li
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Wing Tai Lam
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Joseph Tin Yum Wong
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
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21
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Lacombe J, Zenhausern F. Effect of mechanical forces on cellular response to radiation. Radiother Oncol 2022; 176:187-198. [PMID: 36228760 DOI: 10.1016/j.radonc.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/08/2022] [Accepted: 10/05/2022] [Indexed: 12/14/2022]
Abstract
While the cellular interactions and biochemical signaling has been investigated for long and showed to play a major role in the cell's fate, it is now also evident that mechanical forces continuously applied to the cells in their microenvironment are as important for tissue homeostasis. Mechanical cues are emerging as key regulators of cellular drug response and we aimed to demonstrate in this review that such effects should also be considered vital for the cellular response to radiation. In order to explore the mechanobiology of the radiation response, we reviewed the main mechanoreceptors and transducers, including integrin-mediated adhesion, YAP/TAZ pathways, Wnt/β-catenin signaling, ion channels and G protein-coupled receptors and showed their implication in the modulation of cellular radiosensitivity. We then discussed the current studies that investigated a direct effect of mechanical stress, including extracellular matrix stiffness, shear stress and mechanical strain, on radiation response of cancer and normal cells and showed through preliminary results that such stress effectively can alter cell response after irradiation. However, we also highlighted the limitations of these studies and emphasized some of the contradictory data, demonstrating that the effect of mechanical cues could involve complex interactions and potential crosstalk with numerous cellular processes also affected by irradiation. Overall, mechanical forces alter radiation response and although additional studies are required to deeply understand the underlying mechanisms, these effects should not be neglected in radiation research as they could reveal new fundamental knowledge for predicting radiosensitivity or understanding resistance to radiotherapy.
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Affiliation(s)
- Jerome Lacombe
- Center for Applied NanoBioscience and Medicine, College of Medicine Phoenix, University of Arizona, 475 North 5th Street, Phoenix, AZ 85004, USA; Department of Basic Medical Sciences, College of Medicine Phoenix, University of Arizona, 425 N 5th St, Phoenix, AZ 85004, USA.
| | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine, College of Medicine Phoenix, University of Arizona, 475 North 5th Street, Phoenix, AZ 85004, USA; Department of Basic Medical Sciences, College of Medicine Phoenix, University of Arizona, 425 N 5th St, Phoenix, AZ 85004, USA; Department of Biomedical Engineering, College of Engineering, University of Arizona, 1127 E. James E. Rogers Way, Tucson, AZ 85721, USA.
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Yoshikawa K. Quantitative evaluation of DNA double-strand breaks (DSBs) through single-molecule observation. Enzymes 2022; 51:7-27. [PMID: 36336410 DOI: 10.1016/bs.enz.2022.08.002] [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] [Indexed: 06/16/2023]
Abstract
By adapting the method of single molecular observation for individual DNAs, it will be shown that reliable analysis of double-strand breaks, DSBs, becomes possible for various kinds of damage sources. Single DNA above the size of several-tens kilo base-pairs exhibits the length scale above several μm, indicating that their whole conformation is visible with fluorescence microscopy by adding suitable fluoresce dye to the solution. Various examples of the quantitative evaluation on DSBs are described, together with the evaluation of the protective effects of anti-oxidants.
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Affiliation(s)
- Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan; Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, Japan.
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23
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Naumenko NV, Petruseva IO, Lavrik OI. Bulky Adducts in Clustered DNA Lesions: Causes of Resistance to the NER System. Acta Naturae 2022; 14:38-49. [PMID: 36694906 PMCID: PMC9844087 DOI: 10.32607/actanaturae.11741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/18/2022] [Indexed: 01/22/2023] Open
Abstract
The nucleotide excision repair (NER) system removes a wide range of bulky DNA lesions that cause significant distortions of the regular double helix structure. These lesions, mainly bulky covalent DNA adducts, are induced by ultraviolet and ionizing radiation or the interaction between exogenous/endogenous chemically active substances and nitrogenous DNA bases. As the number of DNA lesions increases, e.g., due to intensive chemotherapy and combination therapy of various diseases or DNA repair impairment, clustered lesions containing bulky adducts may occur. Clustered lesions are two or more lesions located within one or two turns of the DNA helix. Despite the fact that repair of single DNA lesions by the NER system in eukaryotic cells has been studied quite thoroughly, the repair mechanism of these lesions in clusters remains obscure. Identification of the structural features of the DNA regions containing irreparable clustered lesions is of considerable interest, in particular due to a relationship between the efficiency of some antitumor drugs and the activity of cellular repair systems. In this review, we analyzed data on the induction of clustered lesions containing bulky adducts, the potential biological significance of these lesions, and methods for quantification of DNA lesions and considered the causes for the inhibition of NER-catalyzed excision of clustered bulky lesions.
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Affiliation(s)
- N. V. Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - I. O. Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - O. I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
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Abstract
Genomic DNA is organized three-dimensionally in the nucleus as chromatin. Recent accumulating evidence has demonstrated that chromatin organizes into numerous dynamic domains in higher eukaryotic cells, which act as functional units of the genome. These compacted domains facilitate DNA replication and gene regulation. Undamaged chromatin is critical for healthy cells to function and divide. However, the cellular genome is constantly threatened by many sources of DNA damage (e.g., radiation). How do cells maintain their genome integrity when subjected to DNA damage? This chapter describes how the compact state of chromatin safeguards the genome from radiation damage and chemical attacks. Together with recent genomics data, our finding suggests that DNA compaction, such as chromatin domain formation, plays a critical role in maintaining genome integrity. But does the formation of such domains limit DNA accessibility inside the domain and hinder the recruitment of repair machinery to the damaged site(s) during DNA repair? To approach this issue, we first describe a sensitive imaging method to detect changes in chromatin states in living cells (single-nucleosome imaging/tracking). We then use this method to explain how cells can overcome potential recruiting difficulties; cells can decompact chromatin domains following DNA damage and temporarily increase chromatin motion (∼DNA accessibility) to perform efficient DNA repair. We also speculate on how chromatin compaction affects DNA damage-resistance in the clinical setting.
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Affiliation(s)
- Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan; Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan; Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan; Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan.
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25
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Kalukula Y, Stephens AD, Lammerding J, Gabriele S. Mechanics and functional consequences of nuclear deformations. Nat Rev Mol Cell Biol 2022; 23:583-602. [PMID: 35513718 PMCID: PMC9902167 DOI: 10.1038/s41580-022-00480-z] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2022] [Indexed: 02/08/2023]
Abstract
As the home of cellular genetic information, the nucleus has a critical role in determining cell fate and function in response to various signals and stimuli. In addition to biochemical inputs, the nucleus is constantly exposed to intrinsic and extrinsic mechanical forces that trigger dynamic changes in nuclear structure and morphology. Emerging data suggest that the physical deformation of the nucleus modulates many cellular and nuclear functions. These functions have long been considered to be downstream of cytoplasmic signalling pathways and dictated by gene expression. In this Review, we discuss an emerging perspective on the mechanoregulation of the nucleus that considers the physical connections from chromatin to nuclear lamina and cytoskeletal filaments as a single mechanical unit. We describe key mechanisms of nuclear deformations in time and space and provide a critical review of the structural and functional adaptive responses of the nucleus to deformations. We then consider the contribution of nuclear deformations to the regulation of important cellular functions, including muscle contraction, cell migration and human disease pathogenesis. Collectively, these emerging insights shed new light on the dynamics of nuclear deformations and their roles in cellular mechanobiology.
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Affiliation(s)
- Yohalie Kalukula
- University of Mons, Soft Matter and Biomaterials group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, CIRMAP, Place du Parc, 20 B-7000 Mons, Belgium
| | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA,Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Sylvain Gabriele
- University of Mons, Soft Matter and Biomaterials group, Interfaces and Complex Fluids Laboratory, Research Institute for Biosciences, CIRMAP, Place du Parc, 20 B-7000 Mons, Belgium
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26
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Danforth JM, Provencher L, Goodarzi AA. Chromatin and the Cellular Response to Particle Radiation-Induced Oxidative and Clustered DNA Damage. Front Cell Dev Biol 2022; 10:910440. [PMID: 35912116 PMCID: PMC9326100 DOI: 10.3389/fcell.2022.910440] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Exposure to environmental ionizing radiation is prevalent, with greatest lifetime doses typically from high Linear Energy Transfer (high-LET) alpha particles via the radioactive decay of radon gas in indoor air. Particle radiation is highly genotoxic, inducing DNA damage including oxidative base lesions and DNA double strand breaks. Due to the ionization density of high-LET radiation, the consequent damage is highly clustered wherein ≥2 distinct DNA lesions occur within 1–2 helical turns of one another. These multiply-damaged sites are difficult for eukaryotic cells to resolve either quickly or accurately, resulting in the persistence of DNA damage and/or the accumulation of mutations at a greater rate per absorbed dose, relative to lower LET radiation types. The proximity of the same and different types of DNA lesions to one another is challenging for DNA repair processes, with diverse pathways often confounding or interplaying with one another in complex ways. In this context, understanding the state of the higher order chromatin compaction and arrangements is essential, as it influences the density of damage produced by high-LET radiation and regulates the recruitment and activity of DNA repair factors. This review will summarize the latest research exploring the processes by which clustered DNA damage sites are induced, detected, and repaired in the context of chromatin.
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27
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Kolobynina KG, Rapp A, Cardoso MC. Chromatin Ubiquitination Guides DNA Double Strand Break Signaling and Repair. Front Cell Dev Biol 2022; 10:928113. [PMID: 35865631 PMCID: PMC9294282 DOI: 10.3389/fcell.2022.928113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin is the context for all DNA-based molecular processes taking place in the cell nucleus. The initial chromatin structure at the site of the DNA damage determines both, lesion generation and subsequent activation of the DNA damage response (DDR) pathway. In turn, proceeding DDR changes the chromatin at the damaged site and across large fractions of the genome. Ubiquitination, besides phosphorylation and methylation, was characterized as an important chromatin post-translational modification (PTM) occurring at the DNA damage site and persisting during the duration of the DDR. Ubiquitination appears to function as a highly versatile “signal-response” network involving several types of players performing various functions. Here we discuss how ubiquitin modifiers fine-tune the DNA damage recognition and response and how the interaction with other chromatin modifications ensures cell survival.
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28
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Liu Q, Liu P, Ji T, Zheng L, Shen C, Ran S, Liu J, Zhao Y, Niu Y, Wang T, Dong J. The histone methyltransferase SUVR2 promotes DSB repair via chromatin remodeling and liquid-liquid phase separation. MOLECULAR PLANT 2022; 15:1157-1175. [PMID: 35610973 DOI: 10.1016/j.molp.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Maintaining genomic integrity and stability is particularly important for stem cells, which are at the top of the cell lineage origin. Here, we discovered that the plant-specific histone methyltransferase SUVR2 maintains the genome integrity of the root tip stem cells through chromatin remodeling and liquid-liquid phase separation (LLPS) when facing DNA double-strand breaks (DSBs). The histone methyltransferase SUVR2 (MtSUVR2) has histone methyltransferase activity and catalyzes the conversion of histone H3 lysine 9 monomethylation (H3K9me1) to H3K9me2/3 in vitro and in Medicago truncatula. Under DNA damage, the proportion of heterochromatin decreased and the level of DSB damage marker γ-H2AX increased in suvr2 mutants, indicating that MtSUVR2 promotes the compaction of the chromatin structure through H3K9 methylation modification to protect DNA from damage. Interestingly, MtSUVR2 was induced by DSBs to phase separate and form droplets to localize at the damage sites, and this was confirmed by immunofluorescence and fluorescence recovery after photobleaching experiments. The IDR1 and low-complexity domain regions of MtSUVR2 determined its phase separation in the nucleus, whereas the IDR2 region determined the interaction with the homologous recombinase MtRAD51. Furthermore, we found that MtSUVR2 drove the phase separation of MtRAD51 to form "DNA repair bodies," which could enhance the stability of MtRAD51 proteins to facilitate error-free homologous recombination repair of stem cells. Taken together, our study reveals that chromatin remodeling-associated proteins participate in DNA repair through LLPS.
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Affiliation(s)
- Qianwen Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Peng Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tuo Ji
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lihua Zheng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Chen Shen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shasha Ran
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jinling Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yafei Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiding Niu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Tchurikov NA, Alembekov IR, Klushevskaya ES, Kretova AN, Keremet AM, Sidorova AE, Meilakh PB, Chechetkin VR, Kravatskaya GI, Kravatsky YV. Genes Possessing the Most Frequent DNA DSBs Are Highly Associated with Development and Cancers, and Essentially Overlap with the rDNA-Contacting Genes. Int J Mol Sci 2022; 23:ijms23137201. [PMID: 35806206 PMCID: PMC9266645 DOI: 10.3390/ijms23137201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
Double-strand DNA breakes (DSBs) are the most deleterious and widespread examples of DNA damage. They inevitably originate from endogenous mechanisms in the course of transcription, replication, and recombination, as well as from different exogenous factors. If not properly repaired, DSBs result in cell death or diseases. Genome-wide analysis of DSBs has revealed the numerous endogenous DSBs in human chromosomes. However, until now, it has not been clear what kind of genes are preferentially subjected to breakage. We performed a genetic and epigenetic analysis of the most frequent DSBs in HEK293T cells. Here, we show that they predominantly occur in the active genes controlling differentiation, development, and morphogenesis. These genes are highly associated with cancers and other diseases. About one-third of the genes possessing frequent DSBs correspond to rDNA-contacting genes. Our data suggest that a specific set of active genes controlling morphogenesis are the main targets of DNA breakage in human cells, although there is a specific set of silent genes controlling metabolism that also are enriched in DSBs. We detected this enrichment by different activators and repressors of transcription at DSB target sites, as well breakage at promoters. We propose that both active transcription and silencing of genes give a propensity for DNA breakage. These results have implications for medicine and gene therapy.
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Affiliation(s)
- Nickolai A. Tchurikov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
- Correspondence:
| | - Ildar R. Alembekov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Elena S. Klushevskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Antonina N. Kretova
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Ann M. Keremet
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Anastasia E. Sidorova
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Polina B. Meilakh
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Vladimir R. Chechetkin
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Galina I. Kravatskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Yuri V. Kravatsky
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
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30
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Gianella M, Doria E, Dondi D, Milanese C, Gallotti L, Börner A, Zannino L, Macovei A, Pagano A, Guzzon F, Biggiogera M, Balestrazzi A. Physiological and molecular aspects of seed longevity: exploring intra-species variation in eight Pisum sativum L. accessions. PHYSIOLOGIA PLANTARUM 2022; 174:e13698. [PMID: 35526223 PMCID: PMC9321030 DOI: 10.1111/ppl.13698] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/20/2022] [Accepted: 05/02/2022] [Indexed: 05/12/2023]
Abstract
Conservation of plant genetic diversity is fundamental for crop improvement, increasing agricultural production and sustainability, especially in the face of climatic changes. Although seed longevity is essential for the management of seed banks, few studies have, so far, addressed differences in this trait among the accessions of a single species. Eight Pisum sativum L. (pea) accessions were investigated to study the impact of long-term (approximately 20 years) storage, aiming to reveal contrasting seed longevity and clarify the causes for these differences. The outstanding seed longevity observed in the G4 accession provided a unique experimental system. To characterize the biochemical and physical status of stored seeds, reactive oxygen species, lipid peroxidation, tocopherols, free proline and reducing sugars were measured. Thermoanalytical measurements (thermogravimetry and differential scanning calorimetry) and transmission electron microscopy combined with immunohistochemical analysis were performed. The long-lived G4 seeds neither consumed tocopherols during storage nor showed free proline accumulation, as a deterioration hallmark, whereas reducing sugars were not affected. Thermal decomposition suggested a biomass composition compatible with the presence of low molecular weight molecules. Expansion of heterochromatic areas and reduced occurrence of γH2AX foci were highlighted in the nucleus of G4 seeds. The longevity of G4 seeds correlates with the occurrence of a reducing cellular environment and a nuclear ultrastructure favourable to genome stability. This work brings novelty to the study of within-species variations in seed longevity, underlining the relevance of multidisciplinary approaches in seed longevity research.
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Affiliation(s)
- Maraeva Gianella
- Department of Biology and Biotechnology ‘L. Spallanzani’University of PaviaPaviaItaly
- Royal Botanic Gardens, Kew, Wakehurst, ArdinglyHaywards HeathWest SussexUK
| | - Enrico Doria
- Department of Biology and Biotechnology ‘L. Spallanzani’University of PaviaPaviaItaly
| | - Daniele Dondi
- C.S.G.I. & Department of ChemistryUniversity of PaviaPaviaItaly
| | - Chiara Milanese
- C.S.G.I. & Department of ChemistryUniversity of PaviaPaviaItaly
| | - Lucia Gallotti
- C.S.G.I. & Department of ChemistryUniversity of PaviaPaviaItaly
| | - Andreas Börner
- Genebank DepartmentLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) CorrensstrSeelandGermany
| | - Lorena Zannino
- Department of Biology and Biotechnology ‘L. Spallanzani’University of PaviaPaviaItaly
| | - Anca Macovei
- Department of Biology and Biotechnology ‘L. Spallanzani’University of PaviaPaviaItaly
| | - Andrea Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani’University of PaviaPaviaItaly
| | - Filippo Guzzon
- International Maize and Wheat Improvement Center (CIMMYT)Carretera México‐VeracruzTexcocoMexico StateMexico
- Centre for Pacific Crops and Trees (CePaCT), Land Resource Division (LRD)Pacific Community (SPC)SuvaFiji
| | - Marco Biggiogera
- Department of Biology and Biotechnology ‘L. Spallanzani’University of PaviaPaviaItaly
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘L. Spallanzani’University of PaviaPaviaItaly
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Adhikari S, Bhattacharya A, Adhikary S, Singh V, Gadad S, Roy S, Das C. The paradigm of drug resistance in cancer: an epigenetic perspective. Biosci Rep 2022; 42:BSR20211812. [PMID: 35438143 PMCID: PMC9069444 DOI: 10.1042/bsr20211812] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 12/12/2022] Open
Abstract
Innate and acquired resistance towards the conventional therapeutic regimen imposes a significant challenge for the successful management of cancer for decades. In patients with advanced carcinomas, acquisition of drug resistance often leads to tumor recurrence and poor prognosis after the first therapeutic cycle. In this context, cancer stem cells (CSCs) are considered as the prime drivers of therapy resistance in cancer due to their 'non-targetable' nature. Drug resistance in cancer is immensely influenced by different properties of CSCs such as epithelial-to-mesenchymal transition (EMT), a profound expression of drug efflux pump genes, detoxification genes, quiescence, and evasion of apoptosis, has been highlighted in this review article. The crucial epigenetic alterations that are intricately associated with regulating different mechanisms of drug resistance, have been discussed thoroughly. Additionally, special attention is drawn towards the epigenetic mechanisms behind the interaction between the cancer cells and their microenvironment which assists in tumor progression and therapy resistance. Finally, we have provided a cumulative overview of the alternative treatment strategies and epigenome-modifying therapies that show the potential of sensitizing the resistant cells towards the conventional treatment strategies. Thus, this review summarizes the epigenetic and molecular background behind therapy resistance, the prime hindrance of present day anti-cancer therapies, and provides an account of the novel complementary epi-drug-based therapeutic strategies to combat drug resistance.
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Affiliation(s)
- Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhaba National Institute, Mumbai 400094, India
| | - Apoorva Bhattacharya
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Vipin Singh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhaba National Institute, Mumbai 400094, India
| | - Shrikanth S. Gadad
- Department of Molecular and Translational Medicine, Center of Emphasis in Cancer, Texas Tech University Health Sciences Center El Paso, El Paso, TX, U.S.A
- Mays Cancer Center, UT Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229, U.S.A
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhaba National Institute, Mumbai 400094, India
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32
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Okada Y. Sperm chromatin structure: Insights from in vitro to in situ experiments. Curr Opin Cell Biol 2022; 75:102075. [PMID: 35344802 DOI: 10.1016/j.ceb.2022.102075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/14/2022] [Accepted: 02/20/2022] [Indexed: 11/25/2022]
Abstract
The sperm genome is tightly packed into a minimal volume of sperm nuclei. Sperm chromatin is highly condensed by protamines (PRMs) after histone-protamine replacement, and the majority of the sperm genome forms a nucleo-protamine structure, namely, the PRM-DNA complex. The outline of sperm chromatin structure was proposed 30 years ago, and the details have been explored by approaches from several independent research fields including male reproduction and infertility, DNA biopolymer, and most recently, genome-wide sequence-based approaches. In this review, the history of research on sperm chromatin structure is briefly described, and the progress of recent related studies is summarized to obtain a more integrated view for the sperm chromatin, an extremely compacted "black box."
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Affiliation(s)
- Yuki Okada
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
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33
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Sanders JT, Golloshi R, Das P, Xu Y, Terry PH, Nash DG, Dekker J, McCord RP. Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling. Sci Rep 2022; 12:4721. [PMID: 35304523 PMCID: PMC8933507 DOI: 10.1038/s41598-022-08602-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/09/2022] [Indexed: 11/09/2022] Open
Abstract
Layers of genome organization are becoming increasingly better characterized, but less is known about how these structures respond to perturbation or shape changes. Low-salt swelling of isolated chromatin fibers or nuclei has been used for decades to investigate the structural properties of chromatin. But, visible changes in chromatin appearance have not been linked to known building blocks of genome structure or features along the genome sequence. We combine low-salt swelling of isolated nuclei with genome-wide chromosome conformation capture (Hi-C) and imaging approaches to probe the effects of chromatin extension genome-wide. Photoconverted patterns on nuclei during expansion and contraction indicate that global genome structure is preserved after dramatic nuclear volume swelling, suggesting a highly elastic chromosome topology. Hi-C experiments before, during, and after nuclear swelling show changes in average contact probabilities at short length scales, reflecting the extension of the local chromatin fiber. But, surprisingly, during this large increase in nuclear volume, there is a striking maintenance of loops, TADs, active and inactive compartments, and chromosome territories. Subtle differences after expansion are observed, suggesting that the local chromatin state, protein interactions, and location in the nucleus can affect how strongly a given structure is maintained under stress. From these observations, we propose that genome topology is robust to extension of the chromatin fiber and isotropic shape change, and that this elasticity may be beneficial in physiological circumstances of changes in nuclear size and volume.
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Affiliation(s)
- Jacob T Sanders
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Rosela Golloshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Priyojit Das
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Yang Xu
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Peyton H Terry
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Darrian G Nash
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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Xin Y, Wang J, Wu Y, Li Q, Dong M, Liu C, He Q, Wang R, Wang D, Jiang S, Xiao W, Tian Y, Zhang W. Identification of Nanog as a novel inhibitor of Rad51. Cell Death Dis 2022; 13:193. [PMID: 35220392 PMCID: PMC8882189 DOI: 10.1038/s41419-022-04644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/12/2022] [Accepted: 02/01/2022] [Indexed: 11/09/2022]
Abstract
AbstractTo develop inhibitors targeting DNA damage repair pathways is important to improve the effectiveness of chemo- and radiotherapy for cancer patients. Rad51 mediates homologous recombination (HR) repair of DNA damages. It is widely overexpressed in human cancers and overwhelms chemo- and radiotherapy-generated DNA damages through enhancing HR repair signaling, preventing damage-caused cancer cell death. Therefore, to identify inhibitors of Rad51 is important to achieve effective treatment of cancers. Transcription factor Nanog is a core regulator of embryonic stem (ES) cells for its indispensable role in stemness maintenance. In this study, we identified Nanog as a novel inhibitor of Rad51. It interacts with Rad51 and inhibits Rad51-mediated HR repair of DNA damage through its C/CD2 domain. Moreover, Rad51 inhibition can be achieved by nanoscale material- or cell-penetrating peptide (CPP)-mediated direct delivery of Nanog-C/CD2 peptides into somatic cancer cells. Furthermore, we revealed that Nanog suppresses the binding of Rad51 to single-stranded DNAs to stall the HR repair signaling. This study provides explanation for the high γH2AX level in unperturbed ES cells and early embryos, and suggests Nanog-C/CD2 as a promising drug candidate applied to Rad51-related basic research and therapeutic application studies.
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Tartour K, Padmanabhan K. The Clock Takes Shape-24 h Dynamics in Genome Topology. Front Cell Dev Biol 2022; 9:799971. [PMID: 35047508 PMCID: PMC8762244 DOI: 10.3389/fcell.2021.799971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/14/2021] [Indexed: 11/20/2022] Open
Abstract
Circadian rhythms orchestrate organismal physiology and behavior in order to anticipate daily changes in the environment. Virtually all cells have an internal rhythm that is synchronized every day by Zeitgebers (environmental cues). The synchrony between clocks within the animal enables the fitness and the health of organisms. Conversely, disruption of rhythms is linked to a variety of disorders: aging, cancer, metabolic diseases, and psychological disorders among others. At the cellular level, mammalian circadian rhythms are built on several layers of complexity. The transcriptional-translational feedback loop (TTFL) was the first to be described in the 90s. Thereafter oscillations in epigenetic marks highlighted the role of chromatin state in organizing the TTFL. More recently, studies on the 3D organization of the genome suggest that genome topology could be yet another layer of control on cellular circadian rhythms. The dynamic nature of genome topology over a solar day implies that the 3D mammalian genome has to be considered in the fourth dimension-in time. Whether oscillations in genome topology are a consequence of 24 h gene-expression or a driver of transcriptional cycles remains an open question. All said and done, circadian clock-gated phenomena such as gene expression, DNA damage response, cell metabolism and animal behavior-go hand in hand with 24 h rhythms in genome topology.
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Affiliation(s)
- Kévin Tartour
- Institut de Genomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard, Lyon, France
| | - Kiran Padmanabhan
- Institut de Genomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard, Lyon, France
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D-Kondo N, Moreno-Barbosa E, Štěphán V, Stefanová K, Perrot Y, Villagrasa C, Incerti S, De Celis Alonso B, Schuemann J, Faddegon B, Ramos-Méndez J. DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions. Phys Med Biol 2021; 66. [PMID: 34787099 DOI: 10.1088/1361-6560/ac3a22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022]
Abstract
The chemical stage of the Monte Carlo track-structure (MCTS) code Geant4-DNA was extended for its use in DNA strand break (SB) simulations and compared against published experimental data. Geant4-DNA simulations were performed using pUC19 plasmids (2686 base pairs) in a buffered solution of DMSO irradiated by60Co or137Csγ-rays. A comprehensive evaluation of SSB yields was performed considering DMSO, DNA concentration, dose and plasmid supercoiling. The latter was measured using the super helix density value used in a Brownian dynamics plasmid generation algorithm. The Geant4-DNA implementation of the independent reaction times method (IRT), developed to simulate the reaction kinetics of radiochemical species, allowed to score the fraction of supercoiled, relaxed and linearized plasmid fractions as a function of the absorbed dose. The percentage of the number of SB after •OH + DNA and H• + DNA reactions, referred as SSB efficiency, obtained using MCTS were 13.77% and 0.74% respectively. This is in reasonable agreement with published values of 12% and 0.8%. The SSB yields as a function of DMSO concentration, DNA concentration and super helix density recreated the expected published experimental behaviors within 5%, one standard deviation. The dose response of SSB and DSB yields agreed with published measurements within 5%, one standard deviation. We demonstrated that the developed extension of IRT in Geant4-DNA, facilitated the reproduction of experimental conditions. Furthermore, its calculations were strongly in agreement with experimental data. These two facts will facilitate the use of this extension in future radiobiological applications, aiding the study of DNA damage mechanisms with a high level of detail.
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Affiliation(s)
- N D-Kondo
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - E Moreno-Barbosa
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - V Štěphán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - K Stefanová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - Y Perrot
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - C Villagrasa
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - S Incerti
- Univ. Bordeaux, CNRS/IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - B De Celis Alonso
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - J Schuemann
- Department of Radiation Oncology, Massachusets General Hospital and Hardvard Medical School, Boston, MA, United States of America
| | - B Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America
| | - J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America
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Porazzi P, Petruk S, Pagliaroli L, De Dominici M, Deming D, Puccetti MV, Kushinsky S, Kumar G, Minieri V, Barbieri E, Deliard S, Grande A, Trizzino M, Gardini A, Canaani E, Palmisiano N, Porcu P, Ertel A, Fortina PM, Eischen CM, Mazo A, Calabretta B. Targeting chemotherapy to de-condensed H3K27me3-marked chromatin of AML cells enhances leukemia suppression. Cancer Res 2021; 82:458-471. [PMID: 34903608 DOI: 10.1158/0008-5472.can-21-1297] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 09/15/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022]
Abstract
Despite treatment with intensive chemotherapy, acute myeloid leukemia (AML) remains an aggressive malignancy with a dismal outcome in most patients. We found that AML cells exhibit an unusually rapid accumulation of the repressive histone mark H3K27me3 on nascent DNA. In cell lines, primary cells and xenograft mouse models, inhibition of the H3K27 histone methyltransferase EZH2 to de-condense the H3K27me3-marked chromatin of AML cells enhanced chromatin accessibility and chemotherapy-induced DNA damage, apoptosis, and leukemia suppression. These effects were further promoted when chromatin de-condensation of AML cells was induced upon S-phase entry after release from a transient G1 arrest mediated by CDK4/6 inhibition. In the p53-null KG-1 and THP-1 AML cell lines, EZH2 inhibitor and doxorubicin co-treatment induced transcriptional reprogramming that was, in part, dependent on de-repression of H3K27me3-marked gene promoters and led to increased expression of cell death-promoting and growth-inhibitory genes. In conclusion, decondensing H3K27me3-marked chromatin by EZH2 inhibition represents a promising approach to improve the efficacy of DNA-damaging cytotoxic agents in AML patients. This strategy might allow for a lowering of chemotherapy doses with a consequent reduction of treatment-related side effects in elderly AML patients or those with significant comorbidities.
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Affiliation(s)
- Patrizia Porazzi
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | - Luca Pagliaroli
- Department of Biochemistry and Molecular Biology and Sidney Kimmel Cancer Center,, Thomas Jefferson University
| | | | - David Deming
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | - Matthew V Puccetti
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Saul Kushinsky
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Gaurav Kumar
- Department of Cancer Biology, Thomas Jefferson University
| | - Valentina Minieri
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Elisa Barbieri
- Gene Expression and Regulation Program, The Wistar Institute
| | - Sandra Deliard
- Gene Expression and Regulation Program, The Wistar Institute
| | - Alexis Grande
- Department of Life Sciences, University of Modena and Reggio Emilia
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | | | - Eli Canaani
- The Department of Molecular Cell Biology, Weizmann Institute of Science
| | | | | | - Adam Ertel
- Department of Cancer Biology, Thomas Jefferson University
| | | | | | - Alexander Mazo
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | - Bruno Calabretta
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
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38
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Ikuta T, Koike A, Koike M. Detection of double-stranded DNA breaks and apoptosis induced by bleomycin in mouse intestine. J Toxicol Sci 2021; 46:611-618. [PMID: 34853246 DOI: 10.2131/jts.46.611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The gastrointestinal tract is exposed to a myriad of mutagens, making the DNA damage response (DDR) essential to maintain intestinal homeostasis. In vivo models to study DDRs are necessary to understand the mechanisms of disease development caused by genetic disorders such as colorectal cancer. A double-stranded break (DSB) in DNA is the most toxic type of DNA damage; it can be induced by either X-rays or chemicals, including anticancer agents. If DSBs in DNA cannot be repaired, cells can die by apoptosis to be removed from tissues. Here, we show that the DDRs observed as the phosphorylation of H2AX (γH2AX) and caspase-3-dependent apoptosis-induction are under critical control in the intestine of C57BL mice that were injected intraperitoneally with bleomycin, a natural glycopeptide used clinically as an antitumor agent. We found a significant increase in γH2AX expression 2-6 hr post-treatment in mouse ileum, cecum, and colon tissues by Western blotting and immunostaining. Apoptotic cells were observed after 6-24 hr by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay and immunofluorescence of active caspase-3. We observed that γH2AX expression and apoptotic cells were distributed in the lower part of the crypt. The experimental protocol described here is a simple procedure that can be used generally as an in vivo intestinal toxicity assay. Our experimental approach provides a useful method for examining the effects of various bioactive compounds on the DDR, which is essential for understanding intestinal homeostasis.
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Affiliation(s)
- Togo Ikuta
- Research Institute for Clinical Oncology, Saitama Cancer Center
| | - Aki Koike
- Institute for Quantum Medical Science, National Institutes for Quantum and Radiological Science and Technology
| | - Manabu Koike
- Institute for Quantum Medical Science, National Institutes for Quantum and Radiological Science and Technology
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Sarwar M, Sykes PH, Chitcholtan K, Evans JJ. Collagen I dysregulation is pivotal for ovarian cancer progression. Tissue Cell 2021; 74:101704. [PMID: 34871826 DOI: 10.1016/j.tice.2021.101704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022]
Abstract
As a principal matrisomal protein, collagen is involved in the regulation of the structural framework of extracellular matrix (ECM) and therefore is potentially crucial in determining the biophysical character of the ECM. It has been suggested that collagen architecture plays a role in ovarian cancer development, progression and therapeutic responses which led us to examine the collagen morphology in normal and cancerous ovarian tissue. Also, the behaviour of ovarian cancer cells cultured in four qualitatively different collagen gels was investigated. The results here provide evidence that collagen I morphology in the cancerous ovary is distinct from that in the normal ovary. Tumour-associated collagen I showed streams or channels of thick elongated collagen I fibrils. Moreover, fibril alignment was significantly more prevalent in endometrioid and clear cell cancers than other ovarian cancer subtypes. In this work, for the first-time collagen I architecture profiling (CAP) was introduced using histochemical staining, which distinguished between the collagen I morphologies of ovarian cancer subtypes. Immunohistochemical examination of ovarian normal and cancerous tissues also supported the notion that focal adhesion and Rho signalling are upregulated in ovarian cancers, especially in the high-grade serous tumours, as indicated by higher expression of p-FAK and p190RhoGEF. The results also support the concept that collagen I architecture, which might be collagen I concentration-dependent, influences proliferation in ovarian cancer cells. The study provides evidence that modification of collagen I architecture integrity is associated with ovarian cancer development and therapeutic responses.
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Affiliation(s)
- Makhdoom Sarwar
- Department of Obstetrics and Gynaecology, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch, 8011, New Zealand.
| | - Peter H Sykes
- Department of Obstetrics and Gynaecology, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch, 8011, New Zealand
| | - Kenny Chitcholtan
- Department of Obstetrics and Gynaecology, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch, 8011, New Zealand
| | - John J Evans
- Department of Obstetrics and Gynaecology, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch, 8011, New Zealand; MacDiarmid Institute of Advanced Materials and Nanotechnology, Christchurch, New Zealand
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Carlos-Reyes A, Muñiz-Lino MA, Romero-Garcia S, López-Camarillo C, Hernández-de la Cruz ON. Biological Adaptations of Tumor Cells to Radiation Therapy. Front Oncol 2021; 11:718636. [PMID: 34900673 PMCID: PMC8652287 DOI: 10.3389/fonc.2021.718636] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Radiation therapy has been used worldwide for many decades as a therapeutic regimen for the treatment of different types of cancer. Just over 50% of cancer patients are treated with radiotherapy alone or with other types of antitumor therapy. Radiation can induce different types of cell damage: directly, it can induce DNA single- and double-strand breaks; indirectly, it can induce the formation of free radicals, which can interact with different components of cells, including the genome, promoting structural alterations. During treatment, radiosensitive tumor cells decrease their rate of cell proliferation through cell cycle arrest stimulated by DNA damage. Then, DNA repair mechanisms are turned on to alleviate the damage, but cell death mechanisms are activated if damage persists and cannot be repaired. Interestingly, some cells can evade apoptosis because genome damage triggers the cellular overactivation of some DNA repair pathways. Additionally, some surviving cells exposed to radiation may have alterations in the expression of tumor suppressor genes and oncogenes, enhancing different hallmarks of cancer, such as migration, invasion, and metastasis. The activation of these genetic pathways and other epigenetic and structural cellular changes in the irradiated cells and extracellular factors, such as the tumor microenvironment, is crucial in developing tumor radioresistance. The tumor microenvironment is largely responsible for the poor efficacy of antitumor therapy, tumor relapse, and poor prognosis observed in some patients. In this review, we describe strategies that tumor cells use to respond to radiation stress, adapt, and proliferate after radiotherapy, promoting the appearance of tumor radioresistance. Also, we discuss the clinical impact of radioresistance in patient outcomes. Knowledge of such cellular strategies could help the development of new clinical interventions, increasing the radiosensitization of tumor cells, improving the effectiveness of these therapies, and increasing the survival of patients.
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Affiliation(s)
- Angeles Carlos-Reyes
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases “Ismael Cosío Villegas”, Mexico City, Mexico
| | - Marcos A. Muñiz-Lino
- Laboratorio de Patología y Medicina Bucal, Universidad Autónoma Metropolitana Unidad Xochimilco, Mexico City, Mexico
| | - Susana Romero-Garcia
- Department of Chronic-Degenerative Diseases, National Institute of Respiratory Diseases “Ismael Cosío Villegas”, Mexico City, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico, Mexico City
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Shikata M, Toyooka T, Komaki Y, Ibuki Y. 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone-Induced Histone Acetylation via α7nAChR-Mediated PI3K/Akt Activation and Its Impact on γ-H2AX Generation. Chem Res Toxicol 2021; 34:2512-2521. [PMID: 34784199 DOI: 10.1021/acs.chemrestox.1c00287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A typical tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is known as a strong carcinogen. We previously reported that metabolized NNK induced histone H2AX phosphorylation (γ-H2AX), a DNA damage-induced histone modification. In this study, we found that NNK globally acetylated histone H3, which affected γ-H2AX generation. Human lung adenocarcinoma A549 was treated with several doses of NNK. NNK induced dose-dependent global histone H3 acetylation (Ac-H3), at 2 to 12 h after the treatment, independent of the cell cycle. The Ac-H3 pattern was not affected by CYP2A13 overexpression unlike γ-H2AX, indicating no requirement of NNK metabolism to induce Ac-H3. Immunofluorescence staining of Ac-H3 was uniform throughout the nucleus, whereas γ-H2AX was formed as foci and did not coincide with Ac-H3. Nicotinic receptor antagonist methyllycaconitine inhibited Ac-H3 and also γ-H2AX. Phosphoinositide-3-kinase (PI3K)/Akt inhibitors, LY294002, wortmannin, and GSK690693, also suppressed both Ac-H3 and γ-H2AX, whereas KU-55933, an inhibitor of ataxia telangiectasia mutated (ATM) upstream of γ-H2AX, inhibited γ-H2AX but not Ac-H3. These results suggested that binding of NNK to the nicotinic acetylcholine receptor (α7nAChR) activated the PI3K/Akt pathway, resulting in Ac-H3. The activated pathway leading to Ac-H3 enhanced γ-H2AX, suggesting that NNK-induced DNA damage is impacted by the α7nAChR-mediated signal transduction pathway.
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Affiliation(s)
- Mariko Shikata
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka 422-8526, Japan
| | - Tatsushi Toyooka
- National Institute of Occupational Safety and Health, 6-21-1 Nagao, Tama-ku, Kawasaki 214-8585, Japan
| | - Yukako Komaki
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yuko Ibuki
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Yada 52-1, Suruga-ku, Shizuoka 422-8526, Japan
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42
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Disruption of Chromatin Dynamics by Hypotonic Stress Suppresses HR and Shifts DSB Processing to Error-Prone SSA. Int J Mol Sci 2021; 22:ijms222010957. [PMID: 34681628 PMCID: PMC8535785 DOI: 10.3390/ijms222010957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/17/2022] Open
Abstract
The processing of DNA double-strand breaks (DSBs) depends on the dynamic characteristics of chromatin. To investigate how abrupt changes in chromatin compaction alter these dynamics and affect DSB processing and repair, we exposed irradiated cells to hypotonic stress (HypoS). Densitometric and chromosome-length analyses show that HypoS transiently decompacts chromatin without inducing histone modifications known from regulated local chromatin decondensation, or changes in Micrococcal Nuclease (MNase) sensitivity. HypoS leaves undisturbed initial stages of DNA-damage-response (DDR), such as radiation-induced ATM activation and H2AX-phosphorylation. However, detection of ATM-pS1981, γ-H2AX and 53BP1 foci is reduced in a protein, cell cycle phase and cell line dependent manner; likely secondary to chromatin decompaction that disrupts the focal organization of DDR proteins. While HypoS only exerts small effects on classical nonhomologous end-joining (c-NHEJ) and alternative end-joining (alt-EJ), it markedly suppresses homologous recombination (HR) without affecting DNA end-resection at DSBs, and clearly enhances single-strand annealing (SSA). These shifts in pathway engagement are accompanied by decreases in HR-dependent chromatid-break repair in the G2-phase, and by increases in alt-EJ and SSA-dependent chromosomal translocations. Consequently, HypoS sensitizes cells to ionizing radiation (IR)-induced killing. We conclude that HypoS-induced global chromatin decompaction compromises regulated chromatin dynamics and genomic stability by suppressing DSB-processing by HR, and allowing error-prone processing by alt-EJ and SSA.
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43
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Likhatcheva M, Gieling RG, Brown JAL, Demonacos C, Williams KJ. A Novel Mechanism of Ataxia Telangiectasia Mutated Mediated Regulation of Chromatin Remodeling in Hypoxic Conditions. Front Cell Dev Biol 2021; 9:720194. [PMID: 34621741 PMCID: PMC8491615 DOI: 10.3389/fcell.2021.720194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/31/2021] [Indexed: 12/27/2022] Open
Abstract
The effects of genotoxic stress can be mediated by activation of the Ataxia Telangiectasia Mutated (ATM) kinase, under both DNA damage-dependent (including ionizing radiation), and independent (including hypoxic stress) conditions. ATM activation is complex, and primarily mediated by the lysine acetyltransferase Tip60. Epigenetic changes can regulate this Tip60-dependent activation of ATM, requiring the interaction of Tip60 with tri-methylated histone 3 lysine 9 (H3K9me3). Under hypoxic stress, the role of Tip60 in DNA damage-independent ATM activation is unknown. However, epigenetic changes dependent on the methyltransferase Suv39H1, which generates H3K9me3, have been implicated. Our results demonstrate severe hypoxic stress (0.1% oxygen) caused ATM auto-phosphorylation and activation (pS1981), H3K9me3, and elevated both Suv39H1 and Tip60 protein levels in FTC133 and HCT116 cell lines. Exploring the mechanism of ATM activation under these hypoxic conditions, siRNA-mediated Suv39H1 depletion prevented H3K9me3 induction, and Tip60 inhibition (by TH1834) blocked ATM auto-phosphorylation. While MDM2 (Mouse double minute 2) can target Suv39H1 for degradation, it can be blocked by sirtuin-1 (Sirt1). Under severe hypoxia MDM2 protein levels were unchanged, and Sirt1 levels depleted. SiRNA-mediated depletion of MDM2 revealed MDM2 dependent regulation of Suv39H1 protein stability under these conditions. We describe a novel molecular circuit regulating the heterochromatic state (H3K9me3 positive) under severe hypoxic conditions, showing that severe hypoxia-induced ATM activation maintains H3K9me3 levels by downregulating MDM2 and preventing MDM2-mediated degradation of Suv39H1. This novel mechanism is a potential anti-cancer therapeutic opportunity, which if exploited could target the hypoxic tumor cells known to drive both tumor progression and treatment resistance.
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Affiliation(s)
- Maria Likhatcheva
- Division of Pharmacy and Optometry, Faculty of Biology Medicine and Health, School of Health Science, University of Manchester, Manchester, United Kingdom
| | - Roben G Gieling
- Division of Pharmacy and Optometry, Faculty of Biology Medicine and Health, School of Health Science, University of Manchester, Manchester, United Kingdom.,Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - James A L Brown
- Department of Biological Science, University of Limerick, Limerick, Ireland.,Discipline of Biochemistry, Centre for Chromosome Biology, School of Science, National University of Ireland Galway, Galway, Ireland.,Health Research Institute, University of Limerick, Limerick, Ireland
| | - Constantinos Demonacos
- Division of Pharmacy and Optometry, Faculty of Biology Medicine and Health, School of Health Science, University of Manchester, Manchester, United Kingdom
| | - Kaye J Williams
- Division of Pharmacy and Optometry, Faculty of Biology Medicine and Health, School of Health Science, University of Manchester, Manchester, United Kingdom
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44
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Stanic M, Mekhail K. Integration of DNA damage responses with dynamic spatial genome organization. Trends Genet 2021; 38:290-304. [PMID: 34598804 DOI: 10.1016/j.tig.2021.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022]
Abstract
The maintenance of genome stability and cellular homeostasis depends on the temporal and spatial coordination of successive events constituting the classical DNA damage response (DDR). Recent findings suggest close integration and coordination of DDR signaling with specific cellular processes. The mechanisms underlying such coordination remain unclear. We review emerging crosstalk between DNA repair factors, chromatin remodeling, replication, transcription, spatial genome organization, cytoskeletal forces, and liquid-liquid phase separation (LLPS) in mediating DNA repair. We present an overarching DNA repair framework within which these dynamic processes intersect in nuclear space over time. Collectively, this interplay ensures the efficient assembly of DNA repair proteins onto shifting genome structures to preserve genome stability and cell survival.
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Affiliation(s)
- Mia Stanic
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON M5G 1M1, Canada; Canada Research Chairs Program, Temerty Faculty of Medicine, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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45
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Takatsuka H, Shibata A, Umeda M. Genome Maintenance Mechanisms at the Chromatin Level. Int J Mol Sci 2021; 22:ijms221910384. [PMID: 34638727 PMCID: PMC8508675 DOI: 10.3390/ijms221910384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
Genome integrity is constantly threatened by internal and external stressors, in both animals and plants. As plants are sessile, a variety of environment stressors can damage their DNA. In the nucleus, DNA twines around histone proteins to form the higher-order structure “chromatin”. Unraveling how chromatin transforms on sensing genotoxic stress is, thus, key to understanding plant strategies to cope with fluctuating environments. In recent years, accumulating evidence in plant research has suggested that chromatin plays a crucial role in protecting DNA from genotoxic stress in three ways: (1) changes in chromatin modifications around damaged sites enhance DNA repair by providing a scaffold and/or easy access to DNA repair machinery; (2) DNA damage triggers genome-wide alterations in chromatin modifications, globally modulating gene expression required for DNA damage response, such as stem cell death, cell-cycle arrest, and an early onset of endoreplication; and (3) condensed chromatin functions as a physical barrier against genotoxic stressors to protect DNA. In this review, we highlight the chromatin-level control of genome stability and compare the regulatory systems in plants and animals to find out unique mechanisms maintaining genome integrity under genotoxic stress.
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Affiliation(s)
- Hirotomo Takatsuka
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-Machi, Kanazawa 920-1192, Japan;
| | - Atsushi Shibata
- Signal Transduction Program, Gunma University Initiative for Advanced Research (GIAR), 3-39-22, Showa-Machi, Maebashi 371-8511, Japan;
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
- Correspondence:
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46
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Borg AM, Baker JE. Contemporary biomedical engineering perspective on volitional evolution for human radiotolerance enhancement beyond low-earth orbit. Synth Biol (Oxf) 2021; 6:ysab023. [PMID: 34522784 PMCID: PMC8434797 DOI: 10.1093/synbio/ysab023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/15/2021] [Accepted: 09/01/2021] [Indexed: 11/14/2022] Open
Abstract
A primary objective of the National Aeronautics and Space Administration (NASA) is expansion of humankind's presence outside low-Earth orbit, culminating in permanent interplanetary travel and habitation. Having no inherent means of physiological detection or protection against ionizing radiation, humans incur capricious risk when journeying beyond low-Earth orbit for long periods. NASA has made large investments to analyze pathologies from space radiation exposure, emphasizing the importance of characterizing radiation's physiological effects. Because natural evolution would require many generations to confer resistance against space radiation, immediately pragmatic approaches should be considered. Volitional evolution, defined as humans steering their own heredity, may inevitably retrofit the genome to mitigate resultant pathologies from space radiation exposure. Recently, uniquely radioprotective genes have been identified, conferring local or systemic radiotolerance when overexpressed in vitro and in vivo. Aiding in this process, the CRISPR/Cas9 technique is an inexpensive and reproducible instrument capable of making limited additions and deletions to the genome. Although cohorts can be identified and engineered to protect against radiation, alternative and supplemental strategies should be seriously considered. Advanced propulsion and mild synthetic torpor are perhaps the most likely to be integrated. Interfacing artificial intelligence with genetic engineering using predefined boundary conditions may enable the computational modeling of otherwise overly complex biological networks. The ethical context and boundaries of introducing genetically pioneered humans are considered.
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Affiliation(s)
- Alexander M Borg
- Departments of Biomedical Engineering and Radiation Oncology, Wake Forest University, Winston-Salem, NC, USA
| | - John E Baker
- Radiation Biosciences Laboratory, Medical College of Wisconsin, Milwaukee, WI, USA
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47
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Swift ML, Beishline K, Azizkhan-Clifford J. Sp1-dependent recruitment of the histone acetylase p300 to DSBs facilitates chromatin remodeling and recruitment of the NHEJ repair factor Ku70. DNA Repair (Amst) 2021; 105:103171. [PMID: 34252870 DOI: 10.1016/j.dnarep.2021.103171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/18/2021] [Accepted: 07/04/2021] [Indexed: 11/18/2022]
Abstract
In response to DNA damage, most factors involved in damage recognition and repair are tightly regulated to ensure proper repair pathway choice. Histone acetylation at DNA double strand breaks (DSBs) by p300 histone acetyltransferase (HAT) is critical for the recruitment of DSB repair proteins to chromatin. Here, we show that phosphorylation of Sp1 by ATM increases its interaction with p300 and that Sp1-dependent recruitment of p300 to DSBs is necessary to modify the histones associated with p300 activity and NHEJ repair factor recruitment and repair. p300 is known to acetylate multiple residues on histones H3 and H4 necessary for NHEJ. Acetylation of H3K18 by p300 is associated with the recruitment of the SWI/SNF chromatin remodeling complex and Ku70 to DSBs for NHEJ repair. Depletion of Sp1 results in decreased acetylation of lysines on histones H3 and H4. Specifically, cells depleted of Sp1 display defects in the acetylation of H3K18, resulting in defective SWI/SNF and Ku70 recruitment to DSBs. These results shed light on mechanisms by which chromatin remodelers are regulated to ensure activation of the appropriate DSB repair pathway.
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Affiliation(s)
- Michelle L Swift
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Kate Beishline
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jane Azizkhan-Clifford
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA.
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48
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Zhang J, Bellani MA, Huang J, James RC, Pokharel D, Gichimu J, Gali H, Stewart G, Seidman MM. Replication of the Mammalian Genome by Replisomes Specific for Euchromatin and Heterochromatin. Front Cell Dev Biol 2021; 9:729265. [PMID: 34532320 PMCID: PMC8438199 DOI: 10.3389/fcell.2021.729265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/10/2021] [Indexed: 11/26/2022] Open
Abstract
Replisomes follow a schedule in which replication of DNA in euchromatin is early in S phase while sequences in heterochromatin replicate late. Impediments to DNA replication, referred to as replication stress, can stall replication forks triggering activation of the ATR kinase and downstream pathways. While there is substantial literature on the local consequences of replisome stalling-double strand breaks, reversed forks, or genomic rearrangements-there is limited understanding of the determinants of replisome stalling vs. continued progression. Although many proteins are recruited to stalled replisomes, current models assume a single species of "stressed" replisome, independent of genomic location. Here we describe our approach to visualizing replication fork encounters with the potent block imposed by a DNA interstrand crosslink (ICL) and our discovery of an unexpected pathway of replication restart (traverse) past an intact ICL. Additionally, we found two biochemically distinct replisomes distinguished by activity in different stages of S phase and chromatin environment. Each contains different proteins that contribute to ICL traverse.
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Affiliation(s)
- Jing Zhang
- Department of Neurosurgery, Institute for Advanced Study, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Marina A. Bellani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Jing Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, China
| | - Ryan C. James
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Durga Pokharel
- Horizon Discovery Group plc, Lafayette, CO, United States
| | - Julia Gichimu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Himabindu Gali
- Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Grant Stewart
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, United Kingdom
| | - Michael M. Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
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49
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Itoh Y, Woods EJ, Minami K, Maeshima K, Collepardo-Guevara R. Liquid-like chromatin in the cell: What can we learn from imaging and computational modeling? Curr Opin Struct Biol 2021; 71:123-135. [PMID: 34303931 DOI: 10.1016/j.sbi.2021.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022]
Abstract
Chromatin in eukaryotic cells is a negatively charged long polymer consisting of DNA, histones, and various associated proteins. With its highly charged and heterogeneous nature, chromatin structure varies greatly depending on various factors (e.g. chemical modifications and protein enrichment) and the surrounding environment (e.g. cations): from a 10-nm fiber, a folded 30-nm fiber, to chromatin condensates/droplets. Recent advanced imaging has observed that chromatin exhibits a dynamic liquid-like behavior and undergoes structural variations within the cell. Current computational modeling has made it possible to reconstruct the liquid-like chromatin in the cell by dealing with a number of nucleosomes on multiscale levels and has become a powerful technique to inspect the molecular mechanisms giving rise to the observed behavior, which imaging methods cannot do on their own. Based on new findings from both imaging and modeling studies, we discuss the dynamic aspect of chromatin in living cells and its functional relevance.
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Affiliation(s)
- Yuji Itoh
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Esmae J Woods
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan.
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK; Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
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50
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Ma Y, Ishihara K, Yoshida K, Akiyama I, Yoshikawa K. Double-strand breaks in genome-sized DNA caused by megahertz ultrasound. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2021; 150:241. [PMID: 34340483 DOI: 10.1121/10.0005539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Double-strand breaks (DSBs) of giant DNA molecules after exposure to 1.0 MHz pulsed-wave ultrasound were quantitatively evaluated by single-molecule observation of giant DNA (T4 GT7 DNA; 166 kbp) through fluorescence microscopy. Aqueous solutions of DNA were exposed to ultrasonic waves with different sound pressures, repetition periods (1, 2, 5 ms), and pulse durations (5, 10, 50 μs). Below a threshold value of sound pressure, almost no double-strand breaks were generated, and above the threshold, the degree of damage increased in an accelerated manner as the pressure increased. DNA damage was much more severe for exposure to ultrasound with a shorter pulse duration. In addition, a longer pulse repetition period caused worse damage in DNA molecules. The effect of microbubbles on the damage induced by exposure to ultrasound had also been studied. While a result showed that a very small amount of microbubbles increased DSBs of DNA, this effect of microbubbles only weakly depended on their concentrations.
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Affiliation(s)
- Yue Ma
- Faculty of Life and Medical Science, Doshisha University, Kyotanabe, 6100394, Japan
| | - Kazuya Ishihara
- Faculty of Science and Engineering, Doshisha University, Kyotanabe, 6100394, Japan
| | - Kenji Yoshida
- Center for Frontier Medical Engineering, Chiba University, Chiba, 2638522, Japan
| | - Iwaki Akiyama
- Faculty of Life and Medical Science, Doshisha University, Kyotanabe, 6100394, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Science, Doshisha University, Kyotanabe, 6100394, Japan
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