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McLaughlin E, Zavala Martinez MG, Dujeancourt-Henry A, Chaze T, Gianetto QG, Matondo M, Urbaniak MD, Glover L. Phosphoproteomic analysis of the response to DNA damage in Trypanosoma brucei. J Biol Chem 2024; 300:107657. [PMID: 39128729 PMCID: PMC11408851 DOI: 10.1016/j.jbc.2024.107657] [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: 07/02/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024] Open
Abstract
Damage to the genetic material of the cell poses a universal threat to all forms of life. The DNA damage response is a coordinated cellular response to a DNA break, key to which is the phosphorylation signaling cascade. Identifying which proteins are phosphorylated is therefore crucial to understanding the mechanisms that underlie it. We have used stable isotopic labeling of amino acids in cell culture-based quantitative phosphoproteomics to profile changes in phosphorylation site abundance following double stranded DNA breaks, at two distinct loci in the genome of the single cell eukaryote Trypanosoma brucei. Here, we report on the T. brucei phosphoproteome following a single double-strand break at either a chromosome internal or subtelomeric locus, specifically the bloodstream form expression site. We detected >6500 phosphorylation sites, of which 211 form a core set of double-strand break responsive phosphorylation sites. Along with phosphorylation of canonical DNA damage factors, we have identified two novel phosphorylation events on histone H2A and found that in response to a chromosome internal break, proteins are predominantly phosphorylated, while a greater proportion of proteins dephosphorylated following a DNA break at a subtelomeric bloodstream form expression site. Our data represent the first DNA damage phosphoproteome and provides novel insights into repair at distinct chromosomal contexts in T. brucei.
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Affiliation(s)
- Emilia McLaughlin
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France; Sorbonne Université, Collège doctoral, Paris, France
| | - Monica Gabriela Zavala Martinez
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
| | - Annick Dujeancourt-Henry
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France
| | - Thibault Chaze
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, Centre National de la Recherche Scientifique, UAR 2024, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, Centre National de la Recherche Scientifique, UAR 2024, Paris, France; Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, Centre National de la Recherche Scientifique, UAR 2024, Paris, France
| | - Michael D Urbaniak
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| | - Lucy Glover
- Institut Pasteur, Université Paris Cité, Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Paris, France.
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2
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Özdemir C, Purkey LR, Sanchez A, Miller KM. PARticular MARks: Histone ADP-ribosylation and the DNA damage response. DNA Repair (Amst) 2024; 140:103711. [PMID: 38924925 DOI: 10.1016/j.dnarep.2024.103711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/04/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
Cellular and molecular responses to DNA damage are highly orchestrated and dynamic, acting to preserve the maintenance and integrity of the genome. Histone proteins bind DNA and organize the genome into chromatin. Post-translational modifications of histones have been shown to play an essential role in orchestrating the chromatin response to DNA damage by regulating the DNA damage response pathway. Among the histone modifications that contribute to this intricate network, histone ADP-ribosylation (ADPr) is emerging as a pivotal component of chromatin-based DNA damage response (DDR) pathways. In this review, we survey how histone ADPr is regulated to promote the DDR and how it impacts chromatin and other histone marks. Recent advancements have revealed histone ADPr effects on chromatin structure and the regulation of DNA repair factor recruitment to DNA lesions. Additionally, we highlight advancements in technology that have enabled the identification and functional validation of histone ADPr in cells and in response to DNA damage. Given the involvement of DNA damage and epigenetic regulation in human diseases including cancer, these findings have clinical implications for histone ADPr, which are also discussed. Overall, this review covers the involvement of histone ADPr in the DDR and highlights potential future investigations aimed at identifying mechanisms governed by histone ADPr that participate in the DDR, human diseases, and their treatments.
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Affiliation(s)
- Cem Özdemir
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Laura R Purkey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
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3
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Ren XG, Li W, Li WX, Yu WQ. Mechanism of Histone Arginine Methylation Dynamic Change in Cellular Stress. Int J Mol Sci 2024; 25:7562. [PMID: 39062806 PMCID: PMC11277302 DOI: 10.3390/ijms25147562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/03/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024] Open
Abstract
Histone arginine residue methylation is crucial for individual development and gene regulation. However, the dynamics of histone arginine methylation in response to cellular stress remains largely unexplored. In addition, the interplay and regulatory mechanisms between this and other histone modifications are important scientific questions that require further investigation. This study aimed to investigate the changes in histone arginine methylation in response to DNA damage. We report a global decrease in histone H3R26 symmetric dimethylation (H3R26me2s) and hypoacetylation at the H3K27 site in response to DNA damage. Notably, H3R26me2s exhibits a distribution pattern similar to that of H3K27ac across the genome, both of which are antagonistic to H3K27me3. Additionally, histone deacetylase 1 (HDAC1) may be recruited to the H3R26me2s demethylation region to mediate H3K27 deacetylation. These findings suggest crosstalk between H3R26me2s and H3K27ac in regulating gene expression.
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Affiliation(s)
| | | | | | - Wen-Qiang Yu
- Department of RNA Epigenetics, Faculty of Institute of Biomedical Sciences, Campus of Shanghai Medical College, Fudan University, Shanghai 200032, China; (X.-G.R.); (W.L.); (W.-X.L.)
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4
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Ni S, Takada Y, Ando T, Yu S, Yamashita Y, Takahashi Y, Sawada M, Oba M, Itoh Y, Suzuki T. Identification of a novel histone H2A mono-ubiquitination-inhibiting cell-active small molecule. Bioorg Med Chem Lett 2024; 105:129759. [PMID: 38636717 DOI: 10.1016/j.bmcl.2024.129759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Histone H2A mono-ubiquitination plays important roles in epigenetic gene expression and is also involved in tumorigenesis. Small molecules controlling H2A ubiquitination are of interest as potential chemical tools and anticancer drugs. To identify novel small molecule inhibitors of H2A ubiquitination, we synthesized and evaluated several compounds designed based on PRT4165 (1), which is a reported histone ubiquitin ligase RING1A inhibitor. We found that compound 11b strongly inhibited the viability and reduced histone H2A mono-ubiquitination in human osteosarcoma U2OS cells. Therefore, compound 11b is a promising lead compound for the development of H2A histone ubiquitination-inhibiting small molecules.
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Affiliation(s)
- Siyao Ni
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yuri Takada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takaaki Ando
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Shengwang Yu
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | | | - Yukari Takahashi
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Miho Sawada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Makoto Oba
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yukihiro Itoh
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Takayoshi Suzuki
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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5
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Affandi T, Haas A, Ohm AM, Wright GM, Black JC, Reyland ME. PKCδ Regulates Chromatin Remodeling and DNA Repair through SIRT6. Mol Cancer Res 2024; 22:181-196. [PMID: 37889141 PMCID: PMC10872792 DOI: 10.1158/1541-7786.mcr-23-0493] [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: 06/26/2023] [Revised: 09/07/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023]
Abstract
Irradiation (IR) is a highly effective cancer therapy; however, IR damage to tumor-adjacent healthy tissues can result in significant comorbidities and potentially limit the course of therapy. We have previously shown that protein kinase C delta (PKCδ) is required for IR-induced apoptosis and that inhibition of PKCδ activity provides radioprotection in vivo. Here we show that PKCδ regulates histone modification, chromatin accessibility, and double-stranded break (DSB) repair through a mechanism that requires Sirtuin 6 (SIRT6). Overexpression of PKCδ promotes genomic instability and increases DNA damage and apoptosis. Conversely, depletion of PKCδ increases DNA repair via nonhomologous end joining (NHEJ) and homologous recombination (HR) as evidenced by increased formation of DNA damage foci, increased expression of DNA repair proteins, and increased repair of NHEJ and HR fluorescent reporter constructs. Nuclease sensitivity indicates that PKCδ depletion is associated with more open chromatin, while overexpression of PKCδ reduces chromatin accessibility. Epiproteome analysis reveals increased chromatin associated H3K36me2 in PKCδ-depleted cells which is accompanied by chromatin disassociation of KDM2A. We identify SIRT6 as a downstream mediator of PKCδ. PKCδ-depleted cells have increased SIRT6 expression, and depletion of SIRT6 reverses changes in chromatin accessibility, histone modification and DSB repair in PKCδ-depleted cells. Furthermore, depletion of SIRT6 reverses radioprotection in PKCδ-depleted cells. Our studies describe a novel pathway whereby PKCδ orchestrates SIRT6-dependent changes in chromatin accessibility to regulate DNA repair, and define a mechanism for regulation of radiation-induced apoptosis by PKCδ. IMPLICATIONS PKCδ controls sensitivity to irradiation by regulating DNA repair.
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Affiliation(s)
- Trisiani Affandi
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ami Haas
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Angela M. Ohm
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Gregory M. Wright
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joshua C. Black
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mary E. Reyland
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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6
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Kawaguchi K, Kazama M, Hata T, Matsuo M, Obokata J, Satoh S. Inducible Expression of the Restriction Enzyme Uncovered Genome-Wide Distribution and Dynamic Behavior of Histones H4K16ac and H2A.Z at DNA Double-Strand Breaks in Arabidopsis. PLANT & CELL PHYSIOLOGY 2024; 65:142-155. [PMID: 37930797 DOI: 10.1093/pcp/pcad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
DNA double-strand breaks (DSBs) are among the most serious types of DNA damage, causing mutations and chromosomal rearrangements. In eukaryotes, DSBs are immediately repaired in coordination with chromatin remodeling for the deposition of DSB-related histone modifications and variants. To elucidate the details of DSB-dependent chromatin remodeling throughout the genome, artificial DSBs need to be reproducibly induced at various genomic loci. Recently, a comprehensive method for elucidating chromatin remodeling at multiple DSB loci via chemically induced expression of a restriction enzyme was developed in mammals. However, this DSB induction system is unsuitable for investigating chromatin remodeling during and after DSB repair, and such an approach has not been performed in plants. Here, we established a transgenic Arabidopsis plant harboring a restriction enzyme gene Sbf I driven by a heat-inducible promoter. Using this transgenic line, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of histones H4K16ac and H2A.Z and investigated the dynamics of these histone marks around the endogenous 623 Sbf I recognition sites. We also precisely quantified DSB efficiency at all cleavage sites using the DNA resequencing data obtained by the ChIP-seq procedure. From the results, Sbf I-induced DSBs were detected at 360 loci, which induced the transient deposition of H4K16ac and H2A.Z around these regions. Interestingly, we also observed the co-localization of H4K16ac and H2A.Z at some DSB loci. Overall, DSB-dependent chromatin remodeling was found to be highly conserved between plants and animals. These findings provide new insights into chromatin remodeling that occurs in response to DSBs in Arabidopsis.
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Affiliation(s)
- Kohei Kawaguchi
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Mei Kazama
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Takayuki Hata
- Graduate School of Medicine, Hirosaki University, Hirosaki, Aomori 036-8560, Japan
| | - Mitsuhiro Matsuo
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Junichi Obokata
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
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7
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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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/08/2023] [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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8
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Rungratanawanich W, Ballway JW, Wang X, Won KJ, Hardwick JP, Song BJ. Post-translational modifications of histone and non-histone proteins in epigenetic regulation and translational applications in alcohol-associated liver disease: Challenges and research opportunities. Pharmacol Ther 2023; 251:108547. [PMID: 37838219 DOI: 10.1016/j.pharmthera.2023.108547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/30/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Epigenetic regulation is a process that takes place through adaptive cellular pathways influenced by environmental factors and metabolic changes to modulate gene activity with heritable phenotypic variations without altering the DNA sequences of many target genes. Epigenetic regulation can be facilitated by diverse mechanisms: many different types of post-translational modifications (PTMs) of histone and non-histone nuclear proteins, DNA methylation, altered levels of noncoding RNAs, incorporation of histone variants, nucleosomal positioning, chromatin remodeling, etc. These factors modulate chromatin structure and stability with or without the involvement of metabolic products, depending on the cellular context of target cells or environmental stimuli, such as intake of alcohol (ethanol) or Western-style high-fat diets. Alterations of epigenetics have been actively studied, since they are frequently associated with multiple disease states. Consequently, explorations of epigenetic regulation have recently shed light on the pathogenesis and progression of alcohol-associated disorders. In this review, we highlight the roles of various types of PTMs, including less-characterized modifications of nuclear histone and non-histone proteins, in the epigenetic regulation of alcohol-associated liver disease (ALD) and other disorders. We also describe challenges in characterizing specific PTMs and suggest future opportunities for basic and translational research to prevent or treat ALD and many other disease states.
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Affiliation(s)
- Wiramon Rungratanawanich
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Jacob W Ballway
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Xin Wang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kyoung-Jae Won
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, 90069, USA
| | - James P Hardwick
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA.
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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9
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Previtali V, Myers SH, Poppi L, Wynne K, Casamassima I, Girotto S, Di Stefano G, Farabegoli F, Roberti M, Oliviero G, Cavalli A. Preomic profile of BxPC-3 cells after treatment with BRC4. J Proteomics 2023; 288:104983. [PMID: 37536521 DOI: 10.1016/j.jprot.2023.104983] [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: 04/11/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
BRCA2 and RAD51 are two proteins that play a central role in homologous recombination (HR) and DNA double strand break (DSB) repair. BRCA2 assists RAD51 fibrillation and defibrillation through binding with its eight BRC repeats, with BRC4 being one of the most efficient and best characterized. RAD51 inactivation by small molecules has been proposed as a strategy to impair BRCA2/RAD51 binding and, ultimately, the HR pathway, with the aim of making cancer cells more sensitive to PARP inhibitors (PARPi). This strategy, which mimics a synthetic lethality (SL) approach, has been successfully performed in vitro by using the myristoylated derivative of BRC4 (myr-BRC4), designed for a more efficient cell entry. The present study applies a method to obtain a proteomic fingerprint after cellular treatment with the myr-BRC4 peptide using a mass spectroscopy (MS) proteomic approach. (Data are available via ProteomeXchange with identifier PXD042696.) We performed a comparative proteomic profiling of the myr-BRC4 treated vs. untreated BxPC-3 pancreatic cancer cells and evaluated the differential expression of proteins. Among the identified proteins, we focused our attention on proteins shared by both the RAD51 and the BRCA2 interactomes, and on those whose reduction showed high statistical significance. Three downregulated proteins were identified (FANCI, FANCD2, and RPA3), and protein downregulation was confirmed through immunoblotting analysis, validating the MS approach. Our results suggest that, being a direct consequence of myr-BRC4 treatment, the detection of FANCD2, FANCI, and RPA3 downregulation could be used as an indicator for monitoring HR impairment. SIGNIFICANCE: RAD51's inhibition has gained increasing attention because of its possible implications in personalized medicine through the SL approach. Chemical disruption of protein-protein interactions (PPIs) between RAD51 and BRCA2, or some of its partner proteins, could potentiate PARPi DNA damage-induced cell death. This could have application for difficult to treat cancers, such as BRCA-competent and olaparib (PARPi) resistant pancreatic adenocarcinoma. Despite RAD51 being a widely studied target, researchers still lack detailed mechanistic information. This has stifled progress in the field with only a few RAD51 inhibitors having been identified, none of which have gained regulatory approval. Nevertheless, the peptide BRC4 is one of the most specific and best characterized RAD51 binder and inhibitor reported to date. Our study is the first to report the proteomic fingerprint consequent to cellular treatment of myr-BRC4, to offer a reference for the discovery of specific protein/pathway alterations within DNA damage repair. Our results suggest that, being a direct consequence of myr-BRC4 treatment, and ultimately ofBRCA2/RAD51 disruption, the detection of FANCD2, FANCI, and RPA3 downregulation could be used as an indicator for monitoring DNA damage repair impairment and therefore be used to potentiate the development of new effective therapeutic strategies.
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Affiliation(s)
- Viola Previtali
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Samuel H Myers
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Laura Poppi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Irene Casamassima
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Stefania Girotto
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy; Structural Biophysics and Translational Pharmacology Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Giuseppina Di Stefano
- Department of Surgical and Medical Sciences, University of Bologna, 40126 Bologna, Italy
| | - Fulvia Farabegoli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Giorgio Oliviero
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
| | - Andrea Cavalli
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy; Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
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10
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Guo B, Huang X, Chen Y, Broxmeyer HE. Ex Vivo Expansion and Homing of Human Cord Blood Hematopoietic Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:85-104. [PMID: 38228960 DOI: 10.1007/978-981-99-7471-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Cord blood (CB) has been proven to be an alternative source of haematopoietic stem cells (HSCs) for clinical transplantation and has multiple advantages, including but not limited to greater HLA compatibility, lower incidence of graft-versus-host disease (GvHD), higher survival rates and lower relapse rates among patients with minimal residual disease. However, the limited number of HSCs in a single CB unit limits the wider use of CB in clinical treatment. Many efforts have been made to enhance the efficacy of CB HSC transplantation, particularly by ex vivo expansion or enhancing the homing efficiency of HSCs. In this chapter, we will document the major advances regarding human HSC ex vivo expansion and homing and will also discuss the possibility of clinical translation of such laboratory work.
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Affiliation(s)
- Bin Guo
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Xinxin Huang
- Xuhui Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Yandan Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hal E Broxmeyer
- Department of Microbiology and Immunology, School of Medicine, Indiana University, Indianapolis, IN, USA.
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11
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Post-Translational Modifications by Lipid Metabolites during the DNA Damage Response and Their Role in Cancer. Biomolecules 2022; 12:biom12111655. [DOI: 10.3390/biom12111655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Genomic DNA damage occurs as an inevitable consequence of exposure to harmful exogenous and endogenous agents. Therefore, the effective sensing and repair of DNA damage are essential for maintaining genomic stability and cellular homeostasis. Inappropriate responses to DNA damage can lead to genomic instability and, ultimately, cancer. Protein post-translational modifications (PTMs) are a key regulator of the DNA damage response (DDR), and recent progress in mass spectrometry analysis methods has revealed that a wide range of metabolites can serve as donors for PTMs. In this review, we will summarize how the DDR is regulated by lipid metabolite-associated PTMs, including acetylation, S-succinylation, N-myristoylation, palmitoylation, and crotonylation, and the implications for tumorigenesis. We will also discuss potential novel targets for anti-cancer drug development.
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12
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Aricthota S, Rana PP, Haldar D. Histone acetylation dynamics in repair of DNA double-strand breaks. Front Genet 2022; 13:926577. [PMID: 36159966 PMCID: PMC9503837 DOI: 10.3389/fgene.2022.926577] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022] Open
Abstract
Packaging of eukaryotic genome into chromatin is a major obstacle to cells encountering DNA damage caused by external or internal agents. For maintaining genomic integrity, the double-strand breaks (DSB) must be efficiently repaired, as these are the most deleterious type of DNA damage. The DNA breaks have to be detected in chromatin context, the DNA damage response (DDR) pathways have to be activated to repair breaks either by non‐ homologous end joining and homologous recombination repair. It is becoming clearer now that chromatin is not a mere hindrance to DDR, it plays active role in sensing, detection and repair of DNA damage. The repair of DSB is governed by the reorganization of the pre-existing chromatin, leading to recruitment of specific machineries, chromatin remodelling complexes, histone modifiers to bring about dynamic alterations in histone composition, nucleosome positioning, histone modifications. In response to DNA break, modulation of chromatin occurs via various mechanisms including post-translational modification of histones. DNA breaks induce many types of histone modifications, such as phosphorylation, acetylation, methylation and ubiquitylation on specific histone residues which are signal and context dependent. DNA break induced histone modifications have been reported to function in sensing the breaks, activating processing of breaks by specific pathways, and repairing damaged DNA to ensure integrity of the genome. Favourable environment for DSB repair is created by generating open and relaxed chromatin structure. Histone acetylation mediate de-condensation of chromatin and recruitment of DSB repair proteins to their site of action at the DSB to facilitate repair. In this review, we will discuss the current understanding on the critical role of histone acetylation in inducing changes both in chromatin organization and promoting recruitment of DSB repair proteins to sites of DNA damage. It consists of an overview of function and regulation of the deacetylase enzymes which remove these marks and the function of histone acetylation and regulators of acetylation in genome surveillance.
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13
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Qin B, Yu J, Zhao F, Huang J, Zhou Q, Lou Z. Dynamic recruitment of UFM1-specific peptidase 2 to the DNA double-strand breaks regulated by WIP1. GENOME INSTABILITY & DISEASE 2022; 3:217-226. [PMID: 36042814 PMCID: PMC9418083 DOI: 10.1007/s42764-022-00076-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/17/2022] [Accepted: 07/24/2022] [Indexed: 10/29/2022]
Abstract
The ufmylation ligase-UFL1 promotes ATM activation by monoufmylating H4 at K31 in a positive-feedback loop after double-strand breaks (DSB) occur, whereas UFM1 Specific Peptidase 2 (UfSP2) suppresses ATM activation, but the mechanism of recruitment of UfSP2 to the DSB finetuning DNA damage response is still not clear. Here, we report that UfSP2 foci formation is delayed compared to UFL1 foci formation following the radiation insult. Mechanistically, UfSP2 binds to the MRN complex in absence of DSB. Irradiation-induced phosphorylation of UfSP2 by ATM leads to the dissociation of UfSP2 from the MRN complex. This phosphorylation can be removed by the phosphatase WIP1, thereby UfSP2 is recruited to the DSBs, deufmylating H4 and suppressing ATM activation. In summary, we identify a mechanism of delicately negative modulation of ATM activation by UfSP2 and rewires ATM activation pathways.
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Affiliation(s)
- Bo Qin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Jia Yu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905 USA
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14
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Brahme A. Quantifying Cellular Repair, Misrepair and Apoptosis Induced by Boron Ions, Gamma Rays and PRIMA-1 Using the RHR Formulation. Radiat Res 2022; 198:271-296. [PMID: 35834822 DOI: 10.1667/rade-22-00011.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 06/14/2022] [Indexed: 11/03/2022]
Abstract
The recent interaction cross-section-based formulation for radiation-induced direct cellular inactivation, mild and severe sublethal damage, DNA-repair and cell survival have been developed to accurately describe cellular repair, misrepair and apoptosis in TP53 wild-type and mutant cells. The principal idea of this new non-homologous repairable-homologous repairable (RHR) damage formulation is to separately describe the mild damage that can be rapidly handled by the most basic repair processes including the non-homologous end joining (NHEJ), and more complex damage requiring longer repair times and high-fidelity homologous recombination (HR) repair. Taking the interaction between these two key mammalian DNA repair processes more accurately into account has significantly improved the method as indicated in the original publication. Based on the principal mechanisms of 7 repair and 8 misrepair processes presently derived, it has been possible to quite accurately describe the probability that some of these repair processes when unsuccessful can induce cellular apoptosis with increasing doses of γrays, boron ions and PRIMA-1. Interestingly, for all LETs studied (≈0.3-160 eV/nm) the increase in apoptosis saturates when the cell survival reaches about 10% and the fraction of un-hit cells is well below the 1% level. It is shown that most of the early cell kill for low-to-medium LETs are due to apoptosis since the cell survival as well as the non-apoptotic cells agree very well at low doses and other death processes dominate beyond D > 1 Gy. The low-dose apoptosis is due to the fact that the full activation of the checkpoint kinases ATM and Chk2 requires >8 and >18 DSBs per cell to phosphorylate p53 at serine 15 and 20. Therefore, DNA repair is not fully activated until well after 1/2 Gy, and the cellular response may be apoptotic by default before the low-dose hyper sensitivity (LDHS) is replaced by an increased radiation tolerance as the DNA repair processes get maximal efficiency. In effect, simultaneously explaining the LDHS and inverse dose rate phenomena. The partial contributions by the eight newly derived misrepair processes was determined so they together accurately described the experimental apoptosis induction data for γ rays and boron ions. Through these partial misrepair contributions it was possible to predict the apoptotic response based solely on carefully analyzed cell survival data, demonstrating the usefulness of an accurate DNA repair-based cell survival approach. The peak relative biological effectiveness (RBE) of the boron ions was 3.5 at 160 eV/nm whereas the analogous peak relative apoptotic effectiveness (RAE) was 3.4 but at 40 eV/nm indicating the clinical value of the lower LET light ion (15 \le {\rm{LET}} \le 55{\rm{\ eV}}/{\rm{nm}},{\rm{\ }}2 \le Z \le 5) in therapeutic applications to maximize tumor apoptosis and senescence. The new survival expressions were also applied on mouse embryonic fibroblasts with key knocked-out repair genes, showing a good agreement between the principal non-homologous and homologous repair terms and also a reasonable prediction of the associated apoptotic induction. Finally, the formulation was used to estimate the increase in DNA repair and apoptotic response in combination with the mutant p53 reactivating compound PRIMA-1 and γ rays, indicating a 10-2 times increase in apoptosis with 5 μM of the compound reaching apoptosis levels not far from peak apoptosis boron ions in a TP53 mutant cell line. To utilize PRIMA-1 induced apoptosis and cellular sensitization for reactive oxygen species (ROS), concomitant biologically optimized radiation therapy is proposed to maximize the complication free tumor cure for the multitude of TP53 mutant tumors seen in the clinic. The experimental data also indicated the clinically very important high-absorbed dose ROS effect of PRIMA-1.
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Affiliation(s)
- Anders Brahme
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
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15
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HDACs and the epigenetic plasticity of cancer cells: Target the complexity. Pharmacol Ther 2022; 238:108190. [PMID: 35430294 DOI: 10.1016/j.pharmthera.2022.108190] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/11/2022]
Abstract
Cancer cells must adapt to the hostile conditions of the microenvironment in terms of nutrition, space, and immune system attack. Mutations of DNA are the drivers of the tumorigenic process, but mutations must be able to hijack cellular functions to sustain the spread of mutant genomes. Transcriptional control is a key function in this context and is controlled by the rearrangement of the epigenome. Unlike genomic mutations, the epigenome of cancer cells can in principle be reversed. The discovery of the first epigenetic drugs triggered a contaminating enthusiasm. Unfortunately, the complexity of the epigenetic machinery has frustrated this enthusiasm. To develop efficient patient-oriented epigenetic therapies, we need to better understand the nature of this complexity. In this review, we will discuss recent advances in understanding the contribution of HDACs to the maintenance of the transformed state and the rational for their selective targeting.
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16
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Song H, Shen R, Liu X, Yang X, Xie K, Guo Z, Wang D. Histone post-translational modification and the DNA damage response. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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17
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DNA Damage Clustering after Ionizing Radiation and Consequences in the Processing of Chromatin Breaks. Molecules 2022; 27:molecules27051540. [PMID: 35268641 PMCID: PMC8911773 DOI: 10.3390/molecules27051540] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 11/26/2022] Open
Abstract
Charged-particle radiotherapy (CPRT) utilizing low and high linear energy transfer (low-/high-LET) ionizing radiation (IR) is a promising cancer treatment modality having unique physical energy deposition properties. CPRT enables focused delivery of a desired dose to the tumor, thus achieving a better tumor control and reduced normal tissue toxicity. It increases the overall radiation tolerance and the chances of survival for the patient. Further improvements in CPRT are expected from a better understanding of the mechanisms governing the biological effects of IR and their dependence on LET. There is increasing evidence that high-LET IR induces more complex and even clustered DNA double-strand breaks (DSBs) that are extremely consequential to cellular homeostasis, and which represent a considerable threat to genomic integrity. However, from the perspective of cancer management, the same DSB characteristics underpin the expected therapeutic benefit and are central to the rationale guiding current efforts for increased implementation of heavy ions (HI) in radiotherapy. Here, we review the specific cellular DNA damage responses (DDR) elicited by high-LET IR and compare them to those of low-LET IR. We emphasize differences in the forms of DSBs induced and their impact on DDR. Moreover, we analyze how the distinct initial forms of DSBs modulate the interplay between DSB repair pathways through the activation of DNA end resection. We postulate that at complex DSBs and DSB clusters, increased DNA end resection orchestrates an increased engagement of resection-dependent repair pathways. Furthermore, we summarize evidence that after exposure to high-LET IR, error-prone processes outcompete high fidelity homologous recombination (HR) through mechanisms that remain to be elucidated. Finally, we review the high-LET dependence of specific DDR-related post-translational modifications and the induction of apoptosis in cancer cells. We believe that in-depth characterization of the biological effects that are specific to high-LET IR will help to establish predictive and prognostic signatures for use in future individualized therapeutic strategies, and will enhance the prospects for the development of effective countermeasures for improved radiation protection during space travel.
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18
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Karl LA, Peritore M, Galanti L, Pfander B. DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling. Front Genet 2022; 12:821543. [PMID: 35096025 PMCID: PMC8790285 DOI: 10.3389/fgene.2021.821543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.
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Affiliation(s)
- Leonhard Andreas Karl
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martina Peritore
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
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19
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García Fernández F, Fabre E. The Dynamic Behavior of Chromatin in Response to DNA Double-Strand Breaks. Genes (Basel) 2022; 13:genes13020215. [PMID: 35205260 PMCID: PMC8872016 DOI: 10.3390/genes13020215] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
The primary functions of the eukaryotic nucleus as a site for the storage, retrieval, and replication of information require a highly dynamic chromatin organization, which can be affected by the presence of DNA damage. In response to double-strand breaks (DSBs), the mobility of chromatin at the break site is severely affected and, to a lesser extent, that of other chromosomes. The how and why of such movement has been widely studied over the last two decades, leading to different mechanistic models and proposed potential roles underlying both local and global mobility. Here, we review the state of the knowledge on current issues affecting chromatin mobility upon DSBs, and highlight its role as a crucial step in the DNA damage response (DDR).
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Affiliation(s)
- Fabiola García Fernández
- Institut Curie, CNRS UMR3664, Sorbonne Université, F-75005 Paris, France
- Correspondence: (F.G.F.); (E.F.)
| | - Emmanuelle Fabre
- Génomes Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Université de Paris, F-75010 Paris, France
- Correspondence: (F.G.F.); (E.F.)
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20
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Min S, Lee HS, Ji JH, Heo Y, Kim Y, Chae S, Choi YW, Kang HC, Nakanishi M, Cho H. The chromatin remodeler RSF1 coordinates epigenetic marks for transcriptional repression and DSB repair. Nucleic Acids Res 2021; 49:12268-12283. [PMID: 34850117 PMCID: PMC8643642 DOI: 10.1093/nar/gkab1093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 02/06/2023] Open
Abstract
DNA lesions impact on local transcription and the damage-induced transcriptional repression facilitates efficient DNA repair. However, how chromatin dynamics cooperates with these two events remained largely unknown. We here show that histone H2A acetylation at K118 is enriched in transcriptionally active regions. Under DNA damage, the RSF1 chromatin remodeling factor recruits HDAC1 to DSB sites. The RSF1-HDAC1 complex induces the deacetylation of H2A(X)-K118 and its deacetylation is indispensable for the ubiquitination of histone H2A at K119. Accordingly, the acetylation mimetic H2A-K118Q suppressed the H2A-K119ub level, perturbing the transcriptional repression at DNA lesions. Intriguingly, deacetylation of H2AX at K118 also licenses the propagation of γH2AX and recruitment of MDC1. Consequently, the H2AX-K118Q limits DNA repair. Together, the RSF1-HDAC1 complex controls the traffic of the DNA damage response and transcription simultaneously in transcriptionally active chromatins. The interplay between chromatin remodelers and histone modifiers highlights the importance of chromatin versatility in the maintenance of genome integrity.
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Affiliation(s)
- Sunwoo Min
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| | - Ho-Soo Lee
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| | - Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biochemistry and Structural Biology, The University of Texas Health San Antonio, TX 78229-3000, USA
| | - Yungyeong Heo
- Department of Biomedical Sciences, the Graduate School of Ajou University, Suwon, Korea
| | - Yonghyeon Kim
- Department of Biomedical Sciences, the Graduate School of Ajou University, Suwon, Korea
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon 16499, Korea
| | - Yong Won Choi
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, Korea
| | - Ho-Chul Kang
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hyeseong Cho
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
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21
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Yadav UP, Ansari AJ, Arora S, Joshi G, Singh T, Kaur H, Dogra N, Kumar R, Kumar S, Sawant DM, Singh S. Design, synthesis and anticancer activity of 2-arylimidazo[1,2-a]pyridinyl-3-amines. Bioorg Chem 2021; 118:105464. [PMID: 34785441 DOI: 10.1016/j.bioorg.2021.105464] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022]
Abstract
A series of imido-heterocycle compounds were designed, synthesized, characterized, and evaluated for the anticancer potential using breast (MCF-7 and MDA-MB-231), pancreatic (PANC-1), and colon (HCT-116 and HT-29) cancer cell lines and normal cells, while normal cells showed no toxicity. Among the screened compounds, 4h exhibited the best anticancer potential with IC50 values ranging from 1 to 5.5 μM. Compound 4h caused G2/M phase arrest and apoptosis in all the cell lines except MDA-MB-231 mammosphere formation was inhibited. In-vitro enzyme assay showed selective topoisomerase IIα inhibition by compound 4h, leading to DNA damage as observed by fluorescent staining. Cell signalling studies showed decreased expression of cell cycle promoting related proteins while apoptotic proteins were upregulated. Interestingly MDA-MB-231 cells showed only cytostatic effects upon treatment with compound 4h due to defective p53 status. Toxicity study using overexpression of dominant-negative mutant p53 in MCF-7 cells (which have wild type functional p53) showed that anticancer potential of compound 4h is positively correlated with p53 expression.
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Affiliation(s)
- Umesh Prasad Yadav
- Department of Human Genetics and Molecular Medicine, School of Health Sciences Central University of Punjab, Bathinda 151401, India; Department of Biochemistry, All India Institute of Medical Sciences, Patna, India
| | - Arshad J Ansari
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Ajmer 305817, India
| | - Sahil Arora
- Department of Pharmaceutical Sciences and Natural Products, School of Pharmaceutical Sciences, Central University of Punjab, Bathinda 151401, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences and Natural Products, School of Pharmaceutical Sciences, Central University of Punjab, Bathinda 151401, India
| | - Tashvinder Singh
- Department of Human Genetics and Molecular Medicine, School of Health Sciences Central University of Punjab, Bathinda 151401, India
| | - Harsimrat Kaur
- Department of Human Genetics and Molecular Medicine, School of Health Sciences Central University of Punjab, Bathinda 151401, India
| | - Nilambra Dogra
- Centre for Systems Biology & Bioinformatics, Panjab University, Chandigarh 160014, India
| | - Raj Kumar
- Department of Pharmaceutical Sciences and Natural Products, School of Pharmaceutical Sciences, Central University of Punjab, Bathinda 151401, India.
| | - Santosh Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, Patna, India.
| | - Devesh M Sawant
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Ajmer 305817, India.
| | - Sandeep Singh
- Department of Human Genetics and Molecular Medicine, School of Health Sciences Central University of Punjab, Bathinda 151401, India.
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22
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Lan H, Sun Y. Tumor Suppressor FBXW7 and Its Regulation of DNA Damage Response and Repair. Front Cell Dev Biol 2021; 9:751574. [PMID: 34760892 PMCID: PMC8573206 DOI: 10.3389/fcell.2021.751574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/05/2021] [Indexed: 12/21/2022] Open
Abstract
The proper DNA damage response (DDR) and repair are the central molecular mechanisms for the maintenance of cellular homeostasis and genomic integrity. The abnormality in this process is frequently observed in human cancers, and is an important contributing factor to cancer development. FBXW7 is an F-box protein serving as the substrate recognition component of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase. By selectively targeting many oncoproteins for proteasome-mediated degradation, FBXW7 acts as a typical tumor suppressor. Recent studies have demonstrated that FBXW7 also plays critical roles in the process of DDR and repair. In this review, we first briefly introduce the processes of protein ubiquitylation by SCFFBXW7 and DDR/repair, then provide an overview of the molecular characteristics of FBXW7. We next discuss how FBXW7 regulates the process of DDR and repair, and its translational implication. Finally, we propose few future perspectives to further elucidate the role of FBXW7 in regulation of a variety of biological processes and tumorigenesis, and to design a number of approaches for FBXW7 reactivation in a subset of human cancers for potential anticancer therapy.
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Affiliation(s)
- Huiyin Lan
- Department of Thoracic Radiation Oncology, Zhejiang Cancer Hospital, Cancer Hospital of University of Chinese Academy of Sciences, Hangzhou, China.,Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Yi Sun
- Cancer Institute of the Second Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
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23
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Mir US, Bhat A, Mushtaq A, Pandita S, Altaf M, Pandita TK. Role of histone acetyltransferases MOF and Tip60 in genome stability. DNA Repair (Amst) 2021; 107:103205. [PMID: 34399315 DOI: 10.1016/j.dnarep.2021.103205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/01/2021] [Accepted: 08/05/2021] [Indexed: 01/23/2023]
Abstract
The accurate repair of DNA damage specifically the chromosomal double-strand breaks (DSBs) arising from exposure to physical or chemical agents, such as ionizing radiation (IR) and radiomimetic drugs is critical in maintaining genomic integrity. The DNA DSB response and repair is facilitated by hierarchical signaling networks that orchestrate chromatin structural changes specifically histone modifications which impact cell-cycle checkpoints through enzymatic activities to repair the broken DNA ends. Various histone posttranslational modifications such as phosphorylation, acetylation, methylation and ubiquitylation have been shown to play a role in DNA damage repair. Recent studies have provided important insights into the role of histone-specific modifications in sensing DNA damage and facilitating the DNA repair. Histone modifications have been shown to determine the pathway choice for repair of DNA DSBs. This review will summarize the role of important histone acetyltransferases MOF and Tip60 mediated acetylation in repair of DNA DSBs in eukaryotic cells.
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Affiliation(s)
- Ulfat Syed Mir
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, 181143, India
| | - Arjamand Mushtaq
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Shruti Pandita
- Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Mohammad Altaf
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India; Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India.
| | - Tej K Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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24
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Kumimoto RW, Ellison CT, Toruño TY, Bak A, Zhang H, Casteel CL, Coaker G, Harmer SL. XAP5 CIRCADIAN TIMEKEEPER Affects Both DNA Damage Responses and Immune Signaling in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:707923. [PMID: 34659282 PMCID: PMC8517334 DOI: 10.3389/fpls.2021.707923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/30/2021] [Indexed: 06/02/2023]
Abstract
Numerous links have been reported between immune response and DNA damage repair pathways in both plants and animals but the precise nature of the relationship between these fundamental processes is not entirely clear. Here, we report that XAP5 CIRCADIAN TIMEKEEPER (XCT), a protein highly conserved across eukaryotes, acts as a negative regulator of immunity in Arabidopsis thaliana and plays a positive role in responses to DNA damaging radiation. We find xct mutants have enhanced resistance to infection by a virulent bacterial pathogen, Pseudomonas syringae pv. tomato DC3000, and are hyper-responsive to the defense-activating hormone salicylic acid (SA) when compared to wild-type. Unlike most mutants with constitutive effector-triggered immunity (ETI), xct plants do not have increased levels of SA and retain enhanced immunity at elevated temperatures. Genetic analysis indicates XCT acts independently of NONEXPRESSOR OF PATHOGENESIS RELATED GENES1 (NPR1), which encodes a known SA receptor. Since DNA damage has been reported to potentiate immune responses, we next investigated the DNA damage response in our mutants. We found xct seedlings to be hypersensitive to UV-C and γ radiation and deficient in phosphorylation of the histone variant H2A.X, one of the earliest known responses to DNA damage. These data demonstrate that loss of XCT causes a defect in an early step of the DNA damage response pathway. Together, our data suggest that alterations in DNA damage response pathways may underlie the enhanced immunity seen in xct mutants.
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Affiliation(s)
- Roderick W. Kumimoto
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
| | - Cory T. Ellison
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
| | - Tania Y. Toruño
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Aurélie Bak
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Hongtao Zhang
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
| | - Clare L. Casteel
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, United States
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Stacey L. Harmer
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
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Stead ER, Bjedov I. Balancing DNA repair to prevent ageing and cancer. Exp Cell Res 2021; 405:112679. [PMID: 34102225 PMCID: PMC8361780 DOI: 10.1016/j.yexcr.2021.112679] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/25/2021] [Accepted: 04/29/2021] [Indexed: 02/06/2023]
Abstract
DNA damage is a constant stressor to the cell. Persistent damage to the DNA over time results in an increased risk of mutation and an accumulation of mutations with age. Loss of efficient DNA damage repair can lead to accelerated ageing phenotypes or an increased cancer risk, and the trade-off between cancer susceptibility and longevity is often driven by the cell's response to DNA damage. High levels of mutations in DNA repair mutants often leads to excessive cell death and stem cell exhaustion which may promote premature ageing. Stem cells themselves have distinct characteristics that enable them to retain low mutation rates. However, when mutations do arise, stem cell clonal expansion can also contribute to age-related tissue dysfunction as well as heightened cancer risk. In this review, we will highlight increasing DNA damage and mutation accumulation as hallmarks common to both ageing and cancer. We will propose that anti-ageing interventions might be cancer preventative and discuss the mechanisms through which they may act.
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Affiliation(s)
- Eleanor Rachel Stead
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street London, London WC1E 6DD, UK
| | - Ivana Bjedov
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street London, London WC1E 6DD, UK; University College London, Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, Gower Street, London WC1E 6BT, UK.
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26
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Shao BZ, Yao Y, Li JP, Chai NL, Linghu EQ. The Role of Neutrophil Extracellular Traps in Cancer. Front Oncol 2021; 11:714357. [PMID: 34476216 PMCID: PMC8406742 DOI: 10.3389/fonc.2021.714357] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022] Open
Abstract
Neutrophils are vital components of innate and adaptive immunity. It is widely acknowledged that in various pathological conditions, neutrophils are activated and release condensed DNA strands, triggering the formation of neutrophil extracellular traps (NETs). NETs have been shown to be effective in fighting against microbial infections and modulating the pathogenesis and progression of diseases, including malignant tumors. This review describes the current knowledge on the biological characteristics of NETs. Additionally, the mechanisms of NETs in cancer are discussed, including the involvement of signaling pathways and the crosstalk between other cancer-related mechanisms, including inflammasomes and autophagy. Finally, based on previous and current studies, the roles of NET formation and the potential therapeutic targets and strategies related to NETs in several well-studied types of cancers, including breast, lung, colorectal, pancreatic, blood, neurological, and cutaneous cancers, are separately reviewed and discussed.
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Affiliation(s)
| | | | | | - Ning-Li Chai
- Department of Gastroenterology, General Hospital of the Chinese People’s Liberation Army, Beijing, China
| | - En-Qiang Linghu
- Department of Gastroenterology, General Hospital of the Chinese People’s Liberation Army, Beijing, China
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Tatin X, Muggiolu G, Sauvaigo S, Breton J. Evaluation of DNA double-strand break repair capacity in human cells: Critical overview of current functional methods. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108388. [PMID: 34893153 DOI: 10.1016/j.mrrev.2021.108388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 02/05/2023]
Abstract
DNA double-strand breaks (DSBs) are highly deleterious lesions, responsible for mutagenesis, chromosomal translocation or cell death. DSB repair (DSBR) is therefore a critical part of the DNA damage response (DDR) to restore molecular and genomic integrity. In humans, this process is achieved through different pathways with various outcomes. The balance between DSB repair activities varies depending on cell types, tissues or individuals. Over the years, several methods have been developed to study variations in DSBR capacity. Here, we mainly focus on functional techniques, which provide dynamic information regarding global DSB repair proficiency or the activity of specific pathways. These methods rely on two kinds of approaches. Indirect techniques, such as pulse field gel electrophoresis (PFGE), the comet assay and immunofluorescence (IF), measure DSB repair capacity by quantifying the time-dependent decrease in DSB levels after exposure to a DNA-damaging agent. On the other hand, cell-free assays and reporter-based methods directly track the repair of an artificial DNA substrate. Each approach has intrinsic advantages and limitations and despite considerable efforts, there is currently no ideal method to quantify DSBR capacity. All techniques provide different information and can be regarded as complementary, but some studies report conflicting results. Parameters such as the type of biological material, the required equipment or the cost of analysis may also limit available options. Improving currently available methods measuring DSBR capacity would be a major step forward and we present direct applications in mechanistic studies, drug development, human biomonitoring and personalized medicine, where DSBR analysis may improve the identification of patients eligible for chemo- and radiotherapy.
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Affiliation(s)
- Xavier Tatin
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France; LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | | | - Sylvie Sauvaigo
- LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | - Jean Breton
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France.
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Role of Histone Methylation in Maintenance of Genome Integrity. Genes (Basel) 2021; 12:genes12071000. [PMID: 34209979 PMCID: PMC8307007 DOI: 10.3390/genes12071000] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Packaging of the eukaryotic genome with histone and other proteins forms a chromatin structure that regulates the outcome of all DNA mediated processes. The cellular pathways that ensure genomic stability detect and repair DNA damage through mechanisms that are critically dependent upon chromatin structures established by histones and, particularly upon transient histone post-translational modifications. Though subjected to a range of modifications, histone methylation is especially crucial for DNA damage repair, as the methylated histones often form platforms for subsequent repair protein binding at damaged sites. In this review, we highlight and discuss how histone methylation impacts the maintenance of genome integrity through effects related to DNA repair and repair pathway choice.
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29
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Repair pathway choice for double-strand breaks. Essays Biochem 2021; 64:765-777. [PMID: 32648897 DOI: 10.1042/ebc20200007] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022]
Abstract
Deoxyribonucleic acid (DNA) is at a constant risk of damage from endogenous substances, environmental radiation, and chemical stressors. DNA double-strand breaks (DSBs) pose a significant threat to genomic integrity and cell survival. There are two major pathways for DSB repair: nonhomologous end-joining (NHEJ) and homologous recombination (HR). The extent of DNA end resection, which determines the length of the 3' single-stranded DNA (ssDNA) overhang, is the primary factor that determines whether repair is carried out via NHEJ or HR. NHEJ, which does not require a 3' ssDNA tail, occurs throughout the cell cycle. 53BP1 and the cofactors PTIP or RIF1-shieldin protect the broken DNA end, inhibit long-range end resection and thus promote NHEJ. In contrast, HR mainly occurs during the S/G2 phase and requires DNA end processing to create a 3' tail that can invade a homologous region, ensuring faithful gene repair. BRCA1 and the cofactors CtIP, EXO1, BLM/DNA2, and the MRE11-RAD50-NBS1 (MRN) complex promote DNA end resection and thus HR. DNA resection is influenced by the cell cycle, the chromatin environment, and the complexity of the DNA end break. Herein, we summarize the key factors involved in repair pathway selection for DSBs and discuss recent related publications.
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Pescatori S, Berardinelli F, Albanesi J, Ascenzi P, Marino M, Antoccia A, di Masi A, Acconcia F. A Tale of Ice and Fire: The Dual Role for 17β-Estradiol in Balancing DNA Damage and Genome Integrity. Cancers (Basel) 2021; 13:1583. [PMID: 33808099 PMCID: PMC8036963 DOI: 10.3390/cancers13071583] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 12/21/2022] Open
Abstract
17β-estradiol (E2) regulates human physiology both in females and in males. At the same time, E2 acts as a genotoxic substance as it could induce DNA damages, causing the initiation of cellular transformation. Indeed, increased E2 plasma levels are a risk factor for the development of several types of cancers including breast cancer. This paradoxical identity of E2 undermines the foundations of the physiological definition of "hormone" as E2 works both as a homeostatic regulator of body functions and as a genotoxic compound. Here, (i) the molecular circuitries underlying this double face of E2 are reviewed, and (ii) a possible framework to reconcile the intrinsic discrepancies of the E2 function is reported. Indeed, E2 is a regulator of the DNA damage response, which this hormone exploits to calibrate its genotoxicity with its physiological effects. Accordingly, the genes required to maintain genome integrity belong to the E2-controlled cellular signaling network and are essential for the appearance of the E2-induced cellular effects. This concept requires an "upgrade" to the vision of E2 as a "genotoxic hormone", which balances physiological and detrimental pathways to guarantee human body homeostasis. Deregulation of this equilibrium between cellular pathways would determine the E2 pathological effects.
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Affiliation(s)
- Sara Pescatori
- Department of Sciences, Section Biomedical Sciences, and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146 Rome, Italy; (S.P.); (F.B.); (J.A.); (P.A.); (M.M.)
| | - Francesco Berardinelli
- Department of Sciences, Section Biomedical Sciences, and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146 Rome, Italy; (S.P.); (F.B.); (J.A.); (P.A.); (M.M.)
- Neurodevelopment, Neurogenetics and Molecular Neurobiology Unit, IRCCS Santa Lucia Foundation, 00143 Rome, Italy
| | - Jacopo Albanesi
- Department of Sciences, Section Biomedical Sciences, and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146 Rome, Italy; (S.P.); (F.B.); (J.A.); (P.A.); (M.M.)
| | - Paolo Ascenzi
- Department of Sciences, Section Biomedical Sciences, and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146 Rome, Italy; (S.P.); (F.B.); (J.A.); (P.A.); (M.M.)
- Neuroendocrinology, Metabolism and Neuropharmacology Unit, IRCCS Santa Lucia Foundation, 00143 Rome, Italy
| | - Maria Marino
- Department of Sciences, Section Biomedical Sciences, and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146 Rome, Italy; (S.P.); (F.B.); (J.A.); (P.A.); (M.M.)
- Neuroendocrinology, Metabolism and Neuropharmacology Unit, IRCCS Santa Lucia Foundation, 00143 Rome, Italy
| | - Antonio Antoccia
- Department of Sciences, Section Biomedical Sciences, and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146 Rome, Italy; (S.P.); (F.B.); (J.A.); (P.A.); (M.M.)
| | - Alessandra di Masi
- Department of Sciences, Section Biomedical Sciences, and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146 Rome, Italy; (S.P.); (F.B.); (J.A.); (P.A.); (M.M.)
| | - Filippo Acconcia
- Department of Sciences, Section Biomedical Sciences, and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146 Rome, Italy; (S.P.); (F.B.); (J.A.); (P.A.); (M.M.)
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31
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Li T, Petreaca RC, Forsburg SL. Schizosaccharomyces pombe KAT5 contributes to resection and repair of a DNA double-strand break. Genetics 2021; 218:6173406. [PMID: 33723569 DOI: 10.1093/genetics/iyab042] [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: 02/02/2021] [Accepted: 03/04/2021] [Indexed: 11/14/2022] Open
Abstract
Chromatin remodeling is essential for effective repair of a DNA double-strand break (DSB). KAT5 (Schizosaccharomyces pombe Mst1, human TIP60) is a MYST family histone acetyltransferase conserved from yeast to humans that coordinates various DNA damage response activities at a DNA DSB, including histone remodeling and activation of the DNA damage checkpoint. In S. pombe, mutations in mst1+ causes sensitivity to DNA damaging drugs. Here we show that Mst1 is recruited to DSBs. Mutation of mst1+ disrupts recruitment of repair proteins and delays resection. These defects are partially rescued by deletion of pku70, which has been previously shown to antagonize repair by homologous recombination (HR). These phenotypes of mst1 are similar to pht1-4KR, a nonacetylatable form of histone variant H2A.Z, which has been proposed to affect resection. Our data suggest that Mst1 functions to direct repair of DSBs toward HR pathways by modulating resection at the DSB.
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Affiliation(s)
- Tingting Li
- Program of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA
| | - Ruben C Petreaca
- Program of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA
- Department of Molecular Genetics, Ohio State University, Marion, OH 43302, USA
| | - Susan L Forsburg
- Program of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA
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Brancolini C, Di Giorgio E, Formisano L, Gagliano T. Quis Custodiet Ipsos Custodes (Who Controls the Controllers)? Two Decades of Studies on HDAC9. Life (Basel) 2021; 11:life11020090. [PMID: 33513699 PMCID: PMC7912504 DOI: 10.3390/life11020090] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding how an epigenetic regulator drives different cellular responses can be a tricky task. Very often, their activities are modulated by large multiprotein complexes, the composition of which is context- and time-dependent. As a consequence, experiments aimed to unveil the functions of an epigenetic regulator can provide different outcomes and conclusions, depending on the circumstances. HDAC9 (histone deacetylase), an epigenetic regulator that influences different differentiating and adaptive responses, makes no exception. Since its discovery, different phenotypes and/or dysfunctions have been observed after the artificial manipulation of its expression. The cells and the microenvironment use multiple strategies to control and monitor HDAC9 activities. To date, some of the genes under HDAC9 control have been identified. However, the exact mechanisms through which HDAC9 can achieve all the different tasks so far described, remain mysterious. Whether it can assemble into different multiprotein complexes and how the cells modulate these complexes is not clearly defined. In summary, despite several cellular responses are known to be affected by HDAC9, many aspects of its network of interactions still remain to be defined.
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Affiliation(s)
- Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy; (E.D.G.); (T.G.)
- Correspondence:
| | - Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy; (E.D.G.); (T.G.)
| | - Luigi Formisano
- Department of Neuroscience, School of Medicine, “Federico II” University of Naples, Via Pansini, 5, 80131 Naples, Italy;
| | - Teresa Gagliano
- Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy; (E.D.G.); (T.G.)
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33
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Rauscher S, Greil R, Geisberger R. Re-Sensitizing Tumor Cells to Cancer Drugs with Epigenetic Regulators. Curr Cancer Drug Targets 2021; 21:353-359. [PMID: 33423645 DOI: 10.2174/1568009620666210108102723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/13/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
Cancer drug resistance is a major problem for cancer therapy. While many drugs can be effective in first-line treatments, cancer cells can become resistant due to genetic (mutations and chromosomal aberrations) but also epigenetic changes. Hence, many research studies addressed epigenetic drugs in circumventing resistance to conventional therapeutics in different tumor entities and in increasing the efficiency of immune checkpoint therapies. Furthermore, repositioning of already approved drugs in combination with epigenetic modifiers could potentiate their efficacy and thus could be an attractive strategy for cancer treatment. Summarizing, we recapitulate current data on epigenetic drugs and their targets in modulating sensitivity towards conventional and immune therapies, providing evidence that altering expression profiles by epigenetic modifiers holds great potential to improve the clinical outcome of cancer patients.
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Affiliation(s)
- Stefanie Rauscher
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Salzburg, Austria, Cancer Cluster Salzburg, 5020Salzburg, Austria
| | - Richard Greil
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Salzburg, Austria, Cancer Cluster Salzburg, 5020Salzburg, Austria
| | - Roland Geisberger
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Salzburg, Austria, Cancer Cluster Salzburg, 5020Salzburg, Austria
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Oleksiewicz U, Machnik M. Causes, effects, and clinical implications of perturbed patterns within the cancer epigenome. Semin Cancer Biol 2020; 83:15-35. [PMID: 33359485 DOI: 10.1016/j.semcancer.2020.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
Somatic mutations accumulating over a patient's lifetime are well-defined causative factors that fuel carcinogenesis. It is now clear, however, that epigenomic signature is also largely perturbed in many malignancies. These alterations support the transcriptional program crucial for the acquisition and maintenance of cancer hallmarks. Epigenetic instability may arise due to the genetic mutations or transcriptional deregulation of the proteins implicated in epigenetic signaling. Moreover, external stimulation and physiological aging may also participate in this phenomenon. The epigenomic signature is frequently associated with a cell of origin, as well as with tumor stage and differentiation, which all reflect its high heterogeneity across and within various tumors. Here, we will overview the current understanding of the causes and effects of the altered and heterogeneous epigenomic landscape in cancer. We will focus mainly on DNA methylation and post-translational histone modifications as the key regulatory epigenetic signaling marks. In addition, we will describe how this knowledge is translated into the clinic. We will particularly concentrate on the applicability of epigenetic alterations as biomarkers for improved diagnosis, prognosis, and prediction. Finally, we will also review current developments regarding epi-drug usage in clinical and experimental settings.
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Affiliation(s)
- Urszula Oleksiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, Poznan, Poland; Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Poznan, Poland.
| | - Marta Machnik
- Department of Cancer Immunology, Poznan University of Medical Sciences, Poznan, Poland; Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Poznan, Poland
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Sauty SM, Shaban K, Yankulov K. Gene repression in S. cerevisiae-looking beyond Sir-dependent gene silencing. Curr Genet 2020; 67:3-17. [PMID: 33037902 DOI: 10.1007/s00294-020-01114-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/24/2020] [Indexed: 01/09/2023]
Abstract
Gene silencing by the SIR (Silent Information Region) family of proteins in S. cerevisiae has been extensively studied and has served as a founding paradigm for our general understanding of gene repression and its links to histone deacetylation and chromatin structure. In recent years, our understanding of other mechanisms of gene repression in S.cerevisiae was significantly advanced. In this review, we focus on such Sir-independent mechanisms of gene repression executed by various Histone Deacetylases (HDACs) and Histone Methyl Transferases (HMTs). We focus on the genes regulated by these enzymes and their known mechanisms of action. We describe the cooperation and redundancy between HDACs and HMTs, and their involvement in gene repression by non-coding RNAs or by their non-histone substrates. We also propose models of epigenetic transmission of the chromatin structures produced by these enzymes and discuss these in the context of gene repression phenomena in other organisms. These include the recycling of the epigenetic marks imposed by HMTs or the recycling of the complexes harboring HDACs.
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Affiliation(s)
- Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada.
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Progress towards improving homing and engraftment of hematopoietic stem cells for clinical transplantation. Curr Opin Hematol 2020; 26:266-272. [PMID: 31045644 DOI: 10.1097/moh.0000000000000510] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW Hematopoietic cell transplantation (HCT) is a life-saving treatment for a variety of hematological and nonhematological disorders. Successful clinical outcomes after transplantation rely on adequate hematopoietic stem cell (HSC) numbers, and the homing and subsequent short-term and long-term engraftment of these cells in the bone marrow. Enhancing the homing capability of HSCs has the potential for high impact on improving HCT and patient survival. RECENT FINDINGS There are a number of ways to enhance HSC engraftment. Neutralizing negative epigenetic regulation by histone deacetylase 5 (HDAC5) increases surface CXCR4 expression and promotes human HSC homing and engraftment in immune-deficient NSG (NOD.Cg-Prkdc IL2rgt/Sz) mice. Short-term treatment of cells with glucocorticoids, pharmacological stabilization of hypoxia-inducible factor (HIF)-1α, increasing membrane lipid raft aggregation, and inhibition of dipeptidyl peptidase 4 (DPP4) facilitates HSC homing and engraftment. Added to these procedures, modulating the mitochondria permeability transition pore (MPTP) to mitigate ambient air-induced extra physiological oxygen stress/shock (EPHOSS) by hypoxic harvest and processing, or using cyclosporine A during air collection increases functional HSC numbers and improves HSC engraftment. SUMMARY A better understanding of the regulation of human HSC homing mediated by various signaling pathways will facilitate development of more efficient means to enhance HCT efficacy.
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PAICS contributes to gastric carcinogenesis and participates in DNA damage response by interacting with histone deacetylase 1/2. Cell Death Dis 2020; 11:507. [PMID: 32632107 PMCID: PMC7338359 DOI: 10.1038/s41419-020-2708-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 02/06/2023]
Abstract
Phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS), an essential enzyme involved in de novo purine biosynthesis, is connected with formation of various tumors. However, the specific biological roles and related mechanisms of PAICS in gastric cancer (GC) remain unclear. In the present study, we identified for the first time that PAICS was significantly upregulated in GC and high expression of PAICS was correlated with poor prognosis of patients with GC. In addition, knockdown of PAICS significantly induced cell apoptosis, and inhibited GC cell growth both in vitro and in vivo. Mechanistic studies first found that PAICS was engaged in DNA damage response, and knockdown of PAICS in GC cell lines induced DNA damage and impaired DNA damage repair efficiency. Further explorations revealed that PAICS interacted with histone deacetylase HDAC1 and HDAC2, and PAICS deficiency decreased the expression of DAD51 and inhibited its recruitment to DNA damage sites by impairing HDAC1/2 deacetylase activity, eventually preventing DNA damage repair. Consistently, PAICS deficiency enhanced the sensitivity of GC cells to DNA damage agent, cisplatin (CDDP), both in vitro and in vivo. Altogether, our findings demonstrate that PAICS plays an oncogenic role in GC, which act as a novel diagnosis and prognostic biomarker for patients with GC.
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Zhang Y, Shi J, Liu X, Xiao Z, Lei G, Lee H, Koppula P, Cheng W, Mao C, Zhuang L, Ma L, Li W, Gan B. H2A Monoubiquitination Links Glucose Availability to Epigenetic Regulation of the Endoplasmic Reticulum Stress Response and Cancer Cell Death. Cancer Res 2020; 80:2243-2256. [PMID: 32273282 DOI: 10.1158/0008-5472.can-19-3580] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/11/2020] [Accepted: 04/06/2020] [Indexed: 02/06/2023]
Abstract
Epigenetic regulation of gene transcription has been shown to coordinate with nutrient availability, yet the mechanisms underlying this coordination remain incompletely understood. Here, we show that glucose starvation suppresses histone 2A K119 monoubiquitination (H2Aub), a histone modification that correlates with gene repression. Glucose starvation suppressed H2Aub levels independently of energy stress-mediated AMP-activated protein kinase activation and possibly through NADPH depletion and subsequent inhibition of BMI1, an integral component of polycomb-repressive complex 1 (PRC1) that catalyzes H2Aub on chromatin. Integrated transcriptomic and epigenomic analyses linked glucose starvation-mediated H2Aub repression to the activation of genes involved in the endoplasmic reticulum (ER) stress response. We further showed that this epigenetic mechanism has a role in glucose starvation-induced cell death and that pharmacologic inhibition of glucose transporter 1 and PRC1 synergistically promoted ER stress and suppressed tumor growth in vivo. Together, these results reveal a hitherto unrecognized epigenetic mechanism coupling glucose availability to the ER stress response. SIGNIFICANCE: These findings link glucose deprivation and H2A ubiquitination to regulation of the ER stress response in tumor growth and demonstrate pharmacologic susceptibility to inhibition of polycomb and glucose transporters.
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Affiliation(s)
- Yilei Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiejun Shi
- Department of Biological Chemistry, University of California, Irvine, Irvine, California.,Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Xiaoguang Liu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhenna Xiao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guang Lei
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hyemin Lee
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pranavi Koppula
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas
| | - Weijie Cheng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chao Mao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Li Zhuang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas
| | - Wei Li
- Department of Biological Chemistry, University of California, Irvine, Irvine, California. .,Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Boyi Gan
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas
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Glanzner WG, Gutierrez K, Rissi VB, de Macedo MP, Lopez R, Currin L, Dicks N, Baldassarre H, Agellon LB, Bordignon V. Histone Lysine Demethylases KDM5B and KDM5C Modulate Genome Activation and Stability in Porcine Embryos. Front Cell Dev Biol 2020; 8:151. [PMID: 32211412 PMCID: PMC7076052 DOI: 10.3389/fcell.2020.00151] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/24/2020] [Indexed: 12/16/2022] Open
Abstract
The lysine demethylases KDM5B and KDM5C are highly, but transiently, expressed in porcine embryos around the genome activation stage. Attenuation of KDM5B and KDM5C mRNA hampered embryo development to the blastocyst stage in fertilized, parthenogenetically activated and nuclear transfer embryos. While KDM5B attenuation increased H3K4me2-3 levels on D3 embryos and H3K4me1-2-3 on D5 embryos, KDM5C attenuation increased H3K9me1 on D3 embryos, and H3K9me1 and H3K4me1 on D5 embryos. The relative mRNA abundance of EIF1AX and EIF2A on D3 embryos, and the proportion of D4 embryos presenting a fluorescent signal for uridine incorporation were severely reduced in both KDM5B- and KDM5C-attenuated compared to control embryos, which indicate a delay in the initiation of the embryo transcriptional activity. Moreover, KDM5B and KDM5C attenuation affected DNA damage response and increased DNA double-strand breaks (DSBs), and decreased development of UV-irradiated embryos. Findings from this study revealed that both KDM5B and KDM5C are important regulators of early development in porcine embryos as their attenuation altered H3K4 and H3K9 methylation patterns, perturbed embryo genome activation, and decreased DNA damage repair capacity.
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Affiliation(s)
- Werner Giehl Glanzner
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Karina Gutierrez
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Vitor Braga Rissi
- Laboratory of Biotechnology and Animal Reproduction - BioRep, Federal University of Santa Maria (UFSM), Santa Maria, Brazil
| | | | - Rosalba Lopez
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Luke Currin
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Naomi Dicks
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Hernan Baldassarre
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Luis B Agellon
- School of Human Nutrition, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Vilceu Bordignon
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
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Schizosaccharomyces pombe Assays to Study Mitotic Recombination Outcomes. Genes (Basel) 2020; 11:genes11010079. [PMID: 31936815 PMCID: PMC7016768 DOI: 10.3390/genes11010079] [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: 12/20/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 01/16/2023] Open
Abstract
The fission yeast—Schizosaccharomyces pombe—has emerged as a powerful tractable system for studying DNA damage repair. Over the last few decades, several powerful in vivo genetic assays have been developed to study outcomes of mitotic recombination, the major repair mechanism of DNA double strand breaks and stalled or collapsed DNA replication forks. These assays have significantly increased our understanding of the molecular mechanisms underlying the DNA damage response pathways. Here, we review the assays that have been developed in fission yeast to study mitotic recombination.
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Chromatin Profiling of the Repetitive and Nonrepetitive Genomes of the Human Fungal Pathogen Candida albicans. mBio 2019; 10:mBio.01376-19. [PMID: 31337722 PMCID: PMC6650553 DOI: 10.1128/mbio.01376-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The fungus Candida albicans is an opportunistic pathogen that normally lives on the human body without causing any harm. However, C. albicans is also a dangerous pathogen responsible for millions of infections annually. C. albicans is such a successful pathogen because it can adapt to and thrive in different environments. Chemical modifications of chromatin, the structure that packages DNA into cells, can allow environmental adaptation by regulating gene expression and genome organization. Surprisingly, the contribution of chromatin modification to C. albicans biology is still largely unknown. For the first time, we analyzed C. albicans chromatin modifications on a genome-wide basis. We demonstrate that specific chromatin states are associated with distinct regions of the C. albicans genome and identify the roles of the chromatin modifiers Sir2 and Set1 in shaping C. albicans chromatin and gene expression. Eukaryotic genomes are packaged into chromatin structures that play pivotal roles in regulating all DNA-associated processes. Histone posttranslational modifications modulate chromatin structure and function, leading to rapid regulation of gene expression and genome stability, key steps in environmental adaptation. Candida albicans, a prevalent fungal pathogen in humans, can rapidly adapt and thrive in diverse host niches. The contribution of chromatin to C. albicans biology is largely unexplored. Here, we generated the first comprehensive chromatin profile of histone modifications (histone H3 trimethylated on lysine 4 [H3K4me3], histone H3 acetylated on lysine 9 [H3K9Ac], acetylated lysine 16 on histone H4 [H4K16Ac], and γH2A) across the C. albicans genome and investigated its relationship to gene expression by harnessing genome-wide sequencing approaches. We demonstrated that gene-rich nonrepetitive regions are packaged into canonical euchromatin in association with histone modifications that mirror their transcriptional activity. In contrast, repetitive regions are assembled into distinct chromatin states; subtelomeric regions and the ribosomal DNA (rDNA) locus are assembled into heterochromatin, while major repeat sequences and transposons are packaged in chromatin that bears features of euchromatin and heterochromatin. Genome-wide mapping of γH2A, a marker of genome instability, identified potential recombination-prone genomic loci. Finally, we present the first quantitative chromatin profiling in C. albicans to delineate the role of the chromatin modifiers Sir2 and Set1 in controlling chromatin structure and gene expression. This report presents the first genome-wide chromatin profiling of histone modifications associated with the C. albicans genome. These epigenomic maps provide an invaluable resource to understand the contribution of chromatin to C. albicans biology and identify aspects of C. albicans chromatin organization that differ from that of other yeasts.
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