1
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Tire B, Talibova G, Ozturk S. The crosstalk between telomeres and DNA repair mechanisms: an overview to mammalian somatic cells, germ cells, and preimplantation embryos. J Assist Reprod Genet 2024; 41:277-291. [PMID: 38165506 PMCID: PMC10894803 DOI: 10.1007/s10815-023-03008-2] [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: 07/10/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024] Open
Abstract
Telomeres are located at the ends of linear chromosomes and play a critical role in maintaining genomic stability by preventing premature activation of DNA repair mechanisms. Because of exposure to various genotoxic agents, telomeres can undergo shortening and genetic changes. In mammalian cells, the basic DNA repair mechanisms, including base excision repair, nucleotide excision repair, double-strand break repair, and mismatch repair, function in repairing potential damages in telomeres. If these damages are not repaired correctly in time, the unfavorable results such as apoptosis, cell cycle arrest, and cancerous transition may occur. During lifespan, mammalian somatic cells, male and female germ cells, and preimplantation embryos experience a number of telomeric damages. Herein, we comprehensively reviewed the crosstalk between telomeres and the DNA repair mechanisms in the somatic cells, germ cells, and embryos. Infertility development resulting from possible defects in this crosstalk is also discussed in the light of existing studies.
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Affiliation(s)
- Betul Tire
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey
| | - Gunel Talibova
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey.
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2
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Chen J, Potlapalli R, Quan H, Chen L, Xie Y, Pouriyeh S, Sakib N, Liu L, Xie Y. Exploring DNA Damage and Repair Mechanisms: A Review with Computational Insights. BIOTECH 2024; 13:3. [PMID: 38247733 PMCID: PMC10801582 DOI: 10.3390/biotech13010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/21/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
DNA damage is a critical factor contributing to genetic alterations, directly affecting human health, including developing diseases such as cancer and age-related disorders. DNA repair mechanisms play a pivotal role in safeguarding genetic integrity and preventing the onset of these ailments. Over the past decade, substantial progress and pivotal discoveries have been achieved in DNA damage and repair. This comprehensive review paper consolidates research efforts, focusing on DNA repair mechanisms, computational research methods, and associated databases. Our work is a valuable resource for scientists and researchers engaged in computational DNA research, offering the latest insights into DNA-related proteins, diseases, and cutting-edge methodologies. The review addresses key questions, including the major types of DNA damage, common DNA repair mechanisms, the availability of reliable databases for DNA damage and associated diseases, and the predominant computational research methods for enzymes involved in DNA damage and repair.
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Affiliation(s)
- Jiawei Chen
- College of Letter and Science, University of California, Berkeley, CA 94720, USA;
| | - Ravi Potlapalli
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Heng Quan
- Department of Civil and Urban Engineering, New York University, New York, NY 11201, USA;
| | - Lingtao Chen
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Ying Xie
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Seyedamin Pouriyeh
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Nazmus Sakib
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Lichao Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA 94304, USA;
| | - Yixin Xie
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
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3
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An L, Li Y, Yaq L, Wang Y, Dai Q, Du S, Ru Y, Zhoucuo Q, Wang J. Transcriptome analysis reveals molecular regulation mechanism of Tibet sheep tolerance to high altitude oxygen environment. Anim Biotechnol 2023; 34:5097-5112. [PMID: 37729444 DOI: 10.1080/10495398.2023.2258953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
As one of the most important livestock breeds on the Qinghai-Tibet Plateau, Tibetan sheep are of great importance to the local economy, agriculture and culture. Its adaptive mechanism in low temperature and low oxygen at highland altitudes has not been reported. In this study, transcriptome sequencing was used to analyze the heart, liver, spleen, lung, kidney, and muscle tissue of sheep at low and highland altitudes. LOC101112291, SELENOW, COL3A1, GPX1, TMSB4X and HSF4 were selected as candidate genes for adapting to plateau characteristics in Tibet Sheep. Besides, glutathione metabolism, arachidonic acid metabolism, nucleotide excision repair, regulation of actin cytoskeleton, protein digestion and absorption, thyroid hormone synthesis, relaxation signaling pathways may play important roles in the adaptation to plateau hypoxia, and cold tolerance. Structural analysis also showed that sequencing genes related to the adaptation mechanism of Tibet sheep to highland altitude. This study will lay a certain foundation for Tibet sheep research.
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Affiliation(s)
- Li An
- College of Life Science and Biotechnology, Mianyang Teacher's College, Mianyang, China
- Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest University for Nationalities, Chengdu, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu, China
| | - Yanyan Li
- Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest University for Nationalities, Chengdu, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu, China
| | - Lin Yaq
- Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest University for Nationalities, Chengdu, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu, China
| | - Yong Wang
- Key Laboratory of Qinghai-Tibet Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest University for Nationalities, Chengdu, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu, China
| | - Qilin Dai
- School of Life Science and Engineering, Southwest University of Science and Technology, Mian Yang, China
| | - Shizhang Du
- College of Life Science and Biotechnology, Mianyang Teacher's College, Mianyang, China
| | - Yi Ru
- Ruo'ergai Bureau of Agriculture and Animal Husbandry, Ruo'ergai, China
| | - Qi Zhoucuo
- Huzhu Tu Autonomous County of Comprehensive Law Enforcement Brigade of Agricultural Administration, Huzhu Tu Autonomous County, China
| | - Jinling Wang
- College of Life Science and Biotechnology, Mianyang Teacher's College, Mianyang, China
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4
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Ribeiro JH, Altinisik N, Rajan N, Verslegers M, Baatout S, Gopalakrishnan J, Quintens R. DNA damage and repair: underlying mechanisms leading to microcephaly. Front Cell Dev Biol 2023; 11:1268565. [PMID: 37881689 PMCID: PMC10597653 DOI: 10.3389/fcell.2023.1268565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023] Open
Abstract
DNA-damaging agents and endogenous DNA damage constantly harm genome integrity. Under genotoxic stress conditions, the DNA damage response (DDR) machinery is crucial in repairing lesions and preventing mutations in the basic structure of the DNA. Different repair pathways are implicated in the resolution of such lesions. For instance, the non-homologous DNA end joining and homologous recombination pathways are central cellular mechanisms by which eukaryotic cells maintain genome integrity. However, defects in these pathways are often associated with neurological disorders, indicating the pivotal role of DDR in normal brain development. Moreover, the brain is the most sensitive organ affected by DNA-damaging agents compared to other tissues during the prenatal period. The accumulation of lesions is believed to induce cell death, reduce proliferation and premature differentiation of neural stem and progenitor cells, and reduce brain size (microcephaly). Microcephaly is mainly caused by genetic mutations, especially genes encoding proteins involved in centrosomes and DNA repair pathways. However, it can also be induced by exposure to ionizing radiation and intrauterine infections such as the Zika virus. This review explains mammalian cortical development and the major DNA repair pathways that may lead to microcephaly when impaired. Next, we discuss the mechanisms and possible exposures leading to DNA damage and p53 hyperactivation culminating in microcephaly.
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Affiliation(s)
- Jessica Honorato Ribeiro
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Nazlican Altinisik
- Laboratory for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Nicholas Rajan
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Mieke Verslegers
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jay Gopalakrishnan
- Laboratory for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Roel Quintens
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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5
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Alrayes L, Stout J, Schroeder D. Arabidopsis RAD16 Homologues Are Involved in UV Tolerance and Growth. Genes (Basel) 2023; 14:1552. [PMID: 37628604 PMCID: PMC10454142 DOI: 10.3390/genes14081552] [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: 06/30/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
In plants, prolonged exposure to ultraviolet (UV) radiation causes harmful DNA lesions. Nucleotide excision repair (NER) is an important DNA repair mechanism that operates via two pathways: transcription coupled repair (TC-NER) and global genomic repair (GG-NER). In plants and mammals, TC-NER is initiated by the Cockayne Syndrome A and B (CSA/CSB) complex, whereas GG-NER is initiated by the Damaged DNA Binding protein 1/2 (DDB1/2) complex. In the yeast Saccharomyces cerevisiae (S. cerevisiae), GG-NER is initiated by the Radiation Sensitive 7 and 16, (RAD7/16) complex. Arabidopsis thaliana has two homologues of yeast RAD16, At1g05120 and At1g02670, which we named AtRAD16 and AtRAD16b, respectively. In this study, we characterized the roles of AtRAD16 and AtRAD16b. Arabidopsis rad16 and rad16b null mutants exhibited increased UV sensitivity. Moreover, AtRAD16 overexpression increased plant UV tolerance. Thus, AtRAD16 and AtRAD16b contribute to plant UV tolerance and growth. Additionally, we found physical interaction between AtRAD16 and AtRAD7. Thus, the Arabidopsis RAD7/16 complex is functional in plant NER. Furthermore, AtRAD16 makes a significant contribution to Arabidopsis UV tolerance compared to the DDB1/2 and the CSB pathways. This is the first time the role and interaction of DDB1/2, RAD7/16, and CSA/CSB components in a single system have been studied.
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Affiliation(s)
- Linda Alrayes
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (J.S.); (D.S.)
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6
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Naumenko NV, Petruseva IO, Lavrik OI. Bulky Adducts in Clustered DNA Lesions: Causes of Resistance to the NER System. Acta Naturae 2022; 14:38-49. [PMID: 36694906 PMCID: PMC9844087 DOI: 10.32607/actanaturae.11741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/18/2022] [Indexed: 01/22/2023] Open
Abstract
The nucleotide excision repair (NER) system removes a wide range of bulky DNA lesions that cause significant distortions of the regular double helix structure. These lesions, mainly bulky covalent DNA adducts, are induced by ultraviolet and ionizing radiation or the interaction between exogenous/endogenous chemically active substances and nitrogenous DNA bases. As the number of DNA lesions increases, e.g., due to intensive chemotherapy and combination therapy of various diseases or DNA repair impairment, clustered lesions containing bulky adducts may occur. Clustered lesions are two or more lesions located within one or two turns of the DNA helix. Despite the fact that repair of single DNA lesions by the NER system in eukaryotic cells has been studied quite thoroughly, the repair mechanism of these lesions in clusters remains obscure. Identification of the structural features of the DNA regions containing irreparable clustered lesions is of considerable interest, in particular due to a relationship between the efficiency of some antitumor drugs and the activity of cellular repair systems. In this review, we analyzed data on the induction of clustered lesions containing bulky adducts, the potential biological significance of these lesions, and methods for quantification of DNA lesions and considered the causes for the inhibition of NER-catalyzed excision of clustered bulky lesions.
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Affiliation(s)
- N. V. Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - I. O. Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - O. I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
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7
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Ramírez-Gamboa D, Díaz-Zamorano AL, Meléndez-Sánchez ER, Reyes-Pardo H, Villaseñor-Zepeda KR, López-Arellanes ME, Sosa-Hernández JE, Coronado-Apodaca KG, Gámez-Méndez A, Afewerki S, Iqbal HMN, Parra-Saldivar R, Martínez-Ruiz M. Photolyase Production and Current Applications: A Review. Molecules 2022; 27:molecules27185998. [PMID: 36144740 PMCID: PMC9505440 DOI: 10.3390/molecules27185998] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The photolyase family consists of flavoproteins with enzyme activity able to repair ultraviolet light radiation damage by photoreactivation. DNA damage by the formation of a cyclobutane pyrimidine dimer (CPD) and a pyrimidine-pyrimidone (6-4) photoproduct can lead to multiple affections such as cellular apoptosis and mutagenesis that can evolve into skin cancer. The development of integrated applications to prevent the negative effects of prolonged sunlight exposure, usually during outdoor activities, is imperative. This study presents the functions, characteristics, and types of photolyases, their therapeutic and cosmetic applications, and additionally explores some photolyase-producing microorganisms and drug delivery systems.
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Affiliation(s)
- Diana Ramírez-Gamboa
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | | | - Humberto Reyes-Pardo
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | | | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Karina G. Coronado-Apodaca
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Ana Gámez-Méndez
- Department of Basic Sciences, Universidad de Monterrey, Av. Ignacio Morones Prieto 4500 Pte, San Pedro Garza Garcia 66238, Mexico
| | - Samson Afewerki
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Roberto Parra-Saldivar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
- Correspondence: (R.P.-S.); (M.M.-R.)
| | - Manuel Martínez-Ruiz
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
- Correspondence: (R.P.-S.); (M.M.-R.)
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8
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Zuo C, Lv X, Liu T, Yang L, Yang Z, Yu C, Chen H. Polymorphisms in ERCC4 and ERCC5 and risk of cancers: Systematic research synopsis, meta-analysis, and epidemiological evidence. Front Oncol 2022; 12:951193. [PMID: 36033436 PMCID: PMC9404303 DOI: 10.3389/fonc.2022.951193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/20/2022] [Indexed: 12/24/2022] Open
Abstract
The variants of DNA repair genes have been widely reported to be associated with cancer risk in the past decades. As were two crucial members of nucleotide excision repair pathway, ERCC4 and ERCC5 polymorphisms are linked with susceptibility to multiple cancers, but the conclusions were controversial. In this updated meta-analysis concerned with ERCC4 and ERCC5 single-nucleotide polymorphisms (SNPs), 160 eligible publications were identified, and we exerted the meta-analysis of correlations between 24 variants and 19 types of cancer. Venice criteria and the false-positive report probability were used to evaluate a cumulative evidence of significant associations. We conducted functional annotations for those strong associations using data from the Encyclopedia of DNA Elements (ENCODE) Project. We obtained 11 polymorphisms significantly related to changed susceptibility to 11 cancers (p < 0.05). Strong evidence was assigned to four variant-related cancer risks in Asians (ERCC4 rs744154 with bladder cancer, ERCC5 rs2296147 with esophageal cancer, ERCC5 rs17655 with laryngeal cancer and uterine cancer, and ERCC5 rs751402 with gastric cancer), moderate to six SNPs with a risk of eight cancers, and weak to nine SNPs with nine cancers. Data from ENCODE and other public databases showed that the loci of these SNPs with strong evidence might fall in putative functional regions. In conclusion, this paper summarizes comprehensive evidence that common variants of ERCC4 and ERCC5 genes are strongly associated with the risk of bladder cancer, esophageal cancer, laryngeal cancer, uterine cancer, and gastric cancer and elucidates the crucial role of the DNA repair genes in the genetic predisposition to human cancers.
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Affiliation(s)
- Chunjian Zuo
- Department of Thoracic Surgery, Army Medical Center of PLA, Chongqing, China
| | - Xiaolong Lv
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tianyu Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lei Yang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zelin Yang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Cao Yu
- Department of Cardiothoracic Surgery, The Jiang Jin Central Hospital of Chongqing, Chongqing, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Huanwen Chen,
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9
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Fu I, Mu H, Geacintov NE, Broyde S. Mechanism of lesion verification by the human XPD helicase in nucleotide excision repair. Nucleic Acids Res 2022; 50:6837-6853. [PMID: 35713557 PMCID: PMC9262607 DOI: 10.1093/nar/gkac496] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/11/2022] [Accepted: 05/25/2022] [Indexed: 01/19/2023] Open
Abstract
In nucleotide excision repair (NER), the xeroderma pigmentosum D helicase (XPD) scans DNA searching for bulky lesions, stalls when encountering such damage to verify its presence, and allows repair to proceed. Structural studies have shown XPD bound to its single-stranded DNA substrate, but molecular and dynamic characterization of how XPD translocates on undamaged DNA and how it stalls to verify lesions remains poorly understood. Here, we have performed extensive all-atom MD simulations of human XPD bound to undamaged and damaged ssDNA, containing a mutagenic pyrimidine (6-4) pyrimidone UV photoproduct (6-4PP), near the XPD pore entrance. We characterize how XPD responds to the presence of the DNA lesion, delineating the atomistic-scale mechanism that it utilizes to discriminate between damaged and undamaged nucleotides. We identify key amino acid residues, including FeS residues R112, R196, H135, K128, Arch residues E377 and R380, and ATPase lobe 1 residues 215-221, that are involved in damage verification and show how movements of Arch and ATPase lobe 1 domains relative to the FeS domain modulate these interactions. These structural and dynamic molecular depictions of XPD helicase activity with unmodified DNA and its inhibition by the lesion elucidate how the lesion is verified by inducing XPD stalling.
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Affiliation(s)
- Iwen Fu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Hong Mu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Nicholas E Geacintov
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Suse Broyde
- To whom correspondence should be addressed. Tel: +1 212 998 8231;
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10
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hSSB2 (NABP1) is required for the recruitment of RPA during the cellular response to DNA UV damage. Sci Rep 2021; 11:20256. [PMID: 34642383 PMCID: PMC8511049 DOI: 10.1038/s41598-021-99355-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022] Open
Abstract
Maintenance of genomic stability is critical to prevent diseases such as cancer. As such, eukaryotic cells have multiple pathways to efficiently detect, signal and repair DNA damage. One common form of exogenous DNA damage comes from ultraviolet B (UVB) radiation. UVB generates cyclobutane pyrimidine dimers (CPD) that must be rapidly detected and repaired to maintain the genetic code. The nucleotide excision repair (NER) pathway is the main repair system for this type of DNA damage. Here, we determined the role of the human Single-Stranded DNA Binding protein 2, hSSB2, in the response to UVB exposure. We demonstrate that hSSB2 levels increase in vitro and in vivo after UVB irradiation and that hSSB2 rapidly binds to chromatin. Depletion of hSSB2 results in significantly decreased Replication Protein A (RPA32) phosphorylation and impaired RPA32 localisation to the site of UV-induced DNA damage. Delayed recruitment of NER protein Xeroderma Pigmentosum group C (XPC) was also observed, leading to increased cellular sensitivity to UVB. Finally, hSSB2 was shown to have affinity for single-strand DNA containing a single CPD and for duplex DNA with a two-base mismatch mimicking a CPD moiety. Altogether our data demonstrate that hSSB2 is involved in the cellular response to UV exposure.
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11
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Naumenko NV, Petruseva IO, Lomzov AA, Lavrik OI. Recognition and removal of clustered DNA lesions via nucleotide excision repair. DNA Repair (Amst) 2021; 108:103225. [PMID: 34562718 DOI: 10.1016/j.dnarep.2021.103225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/25/2021] [Accepted: 09/05/2021] [Indexed: 10/20/2022]
Abstract
Clustered damage of DNA consists of two or more lesions located within one or two turns of the DNA helix. Clusters consisting of lesions of various structures can arise under the influence of strong damaging factors, especially if the cells have a compromised repair status. In this work, we analyzed how the presence of an analog of the apurinic/apyrimidinic site - a non-nucleoside residue consisting of diethylene glycol phosphodiester (DEG) - affects the recognition and removal of a bulky lesion (a non-nucleoside site of the modified DNA strand containing a fluorescein residue, nFlu) from DNA by a mammalian nucleotide excision repair system. Here we demonstrated that the efficiency of nFlu removal decreases in the presence of DEG in the complementary strand and is completely suppressed when the DEG is located opposite the nFlu. By contrast, protein factor XPC-RAD23B, which initiates global genomic nucleotide excision repair, has higher affinity for DNA containing clustered damage as compared to DNA containing a single bulky lesion; the affinity of XPC strengthens as the positions of DEG and nFlu become closer. The changes in the double-stranded DNA's geometry caused by the presence of clustered damage were also assessed. The obtained experimental data together with the results of molecular dynamics simulations make it possible to get insight into the structural features of DNA containing clustered lesions that determine the efficiency of repair. Speaking more broadly, this study should help to understand the probable fate of bulky adduct-containing clusters of various topologies in the mammalian cell.
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Affiliation(s)
- N V Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - I O Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.
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12
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Wang H, Lautrup S, Caponio D, Zhang J, Fang EF. DNA Damage-Induced Neurodegeneration in Accelerated Ageing and Alzheimer's Disease. Int J Mol Sci 2021; 22:ijms22136748. [PMID: 34201700 PMCID: PMC8268089 DOI: 10.3390/ijms22136748] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/18/2022] Open
Abstract
DNA repair ensures genomic stability to achieve healthy ageing, including cognitive maintenance. Mutations on genes encoding key DNA repair proteins can lead to diseases with accelerated ageing phenotypes. Some of these diseases are xeroderma pigmentosum group A (XPA, caused by mutation of XPA), Cockayne syndrome group A and group B (CSA, CSB, and are caused by mutations of CSA and CSB, respectively), ataxia-telangiectasia (A-T, caused by mutation of ATM), and Werner syndrome (WS, with most cases caused by mutations in WRN). Except for WS, a common trait of the aforementioned progerias is neurodegeneration. Evidence from studies using animal models and patient tissues suggests that the associated DNA repair deficiencies lead to depletion of cellular nicotinamide adenine dinucleotide (NAD+), resulting in impaired mitophagy, accumulation of damaged mitochondria, metabolic derailment, energy deprivation, and finally leading to neuronal dysfunction and loss. Intriguingly, these features are also observed in Alzheimer’s disease (AD), the most common type of dementia affecting more than 50 million individuals worldwide. Further studies on the mechanisms of the DNA repair deficient premature ageing diseases will help to unveil the mystery of ageing and may provide novel therapeutic strategies for AD.
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Affiliation(s)
- Heling Wang
- Department of Clinical Molecular Biology, Akershus University Hospital, University of Oslo, 1478 Lørenskog, Norway; (H.W.); (S.L.); (D.C.); (J.Z.)
| | - Sofie Lautrup
- Department of Clinical Molecular Biology, Akershus University Hospital, University of Oslo, 1478 Lørenskog, Norway; (H.W.); (S.L.); (D.C.); (J.Z.)
| | - Domenica Caponio
- Department of Clinical Molecular Biology, Akershus University Hospital, University of Oslo, 1478 Lørenskog, Norway; (H.W.); (S.L.); (D.C.); (J.Z.)
| | - Jianying Zhang
- Department of Clinical Molecular Biology, Akershus University Hospital, University of Oslo, 1478 Lørenskog, Norway; (H.W.); (S.L.); (D.C.); (J.Z.)
- Xiangya School of Stomatology, Central South University, Changsha 410083, China
| | - Evandro F. Fang
- Department of Clinical Molecular Biology, Akershus University Hospital, University of Oslo, 1478 Lørenskog, Norway; (H.W.); (S.L.); (D.C.); (J.Z.)
- The Norwegian Centre on Healthy Ageing (NO-Age), 0010 Oslo, Norway
- Correspondence:
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13
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Zeng Y, Li J, Guo W, Luo W, Liu X, He R, Hu Z, Duan L, Xia C, Luo D. AKR1B10 protects against UVC-induced DNA damage in breast cancer cells. Acta Biochim Biophys Sin (Shanghai) 2021; 53:726-738. [PMID: 33913495 DOI: 10.1093/abbs/gmab045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Indexed: 11/13/2022] Open
Abstract
The cellular response to DNA damage is crucial for maintaining the integrity and stability of molecular structure. To maintain genome stability, DNA-damaged cells should be arrested so that mutations can be repaired before replication. Although several key components required for this arrest have been discovered, the majority of the pathways are still unclear. Through a number of assays, including cell viability, colony formation, and apotheosis assay, we found that AKR1B10 protected cells from UVC-induced DNA damage. Surprisingly, UVC-induced γH2AX foci and DNA double-strand breaks in the AKR1B10-overexpressing cells were ∼4-5 folds lower than those in the control group. The expression levels of AKR1B10, p53, chk1, chk2, nuclear factor (NF)-κB, and p65 showed dynamic changes in response to UVC irradiation. Our results suggested that AKR1B10 is involved in the pathway of cell cycle checkpoint and NF-κB in DNA damage. Taken together, our results suggest that AKR1B10 is involved in the repair of the DNA double-strand break, which provides a new insight into the role of AKR1B10 in DNA damage repair and indicates a new trail in tumorigenesis and cancer drug resistance.
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Affiliation(s)
- Yuanqing Zeng
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, University of South China, Chenzhou 423000, China
- Department of Clinical Laboratory, Zhuhai Hospital, Guangdong Hospital of Traditional Chinese Medicine, Zhuhai 519015, China
| | - Jia Li
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, University of South China, Chenzhou 423000, China
| | - Wangyuan Guo
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, University of South China, Chenzhou 423000, China
| | - Weihao Luo
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, University of South China, Chenzhou 423000, China
| | - Xiangting Liu
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, University of South China, Chenzhou 423000, China
| | - Rongzhang He
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, University of South China, Chenzhou 423000, China
| | - Zheng Hu
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, University of South China, Chenzhou 423000, China
| | - Lili Duan
- Translational Medicine Institute, The First People’s Hospital of Chenzhou, University of South China, Chenzhou 423000, China
| | - Chenglai Xia
- Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan 528000, China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 520150, China
| | - Dixian Luo
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen 518000, China
- Center for Laboratory and Pathology, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, The First People’s Hospital of Chenzhou, Southern Medical University, Chenzhou 423000, China
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14
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Kara A, Özgür A, Nalbantoğlu S, Karadağ A. DNA repair pathways and their roles in drug resistance for lung adenocarcinoma. Mol Biol Rep 2021; 48:3813-3825. [PMID: 33856604 DOI: 10.1007/s11033-021-06314-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/24/2021] [Indexed: 01/24/2023]
Abstract
Lung cancer is the leading cancer type of death rate. The lung adenocarcinoma subtype is responsible for almost half of the total lung cancer deaths. Despite the improvements in cancer treatment in recent years, lung adenocarcinoma patients' overall survival rate remains poor. Immunetherapy and chemotherapy are two of the most widely used options for the treatment of cancer. Although many cancer types initially respond to these treatments, the development of resistance is inevitable. The rapid development of drug resistance mainly characterizes lung adenocarcinoma. Despite being the subject of many studies in recent years, the resistance initiation and progression mechanism is still unclear. In this review, we have examined the role of the primary DNA repair pathways (non-homologous end joining (NHEJ) pathway, homologous-recombinant repair (HR) pathway, base excision repair (BER) pathway, and nucleotide excision repair (NER) pathway and transactivation mechanisms of tumor protein 53 (TP53) in drug resistance development. This review suggests that mentioned pathways have essential roles in developing the resistance against chemotherapy and immunotherapy in lung adenocarcinoma patients.
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Affiliation(s)
- Altan Kara
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey.
| | - Aykut Özgür
- Laboratory and Veterinary Health Program, Department of Veterinary Medicine, Artova Vocational School, Tokat Gaziosmanpaşa University, Tokat, Turkey
| | - Sinem Nalbantoğlu
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey
| | - Abdullah Karadağ
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey
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15
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Regulation of ddb2 expression in blind cavefish and zebrafish reveals plasticity in the control of sunlight-induced DNA damage repair. PLoS Genet 2021; 17:e1009356. [PMID: 33544716 PMCID: PMC7891740 DOI: 10.1371/journal.pgen.1009356] [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: 06/22/2020] [Revised: 02/18/2021] [Accepted: 01/12/2021] [Indexed: 11/19/2022] Open
Abstract
We have gained considerable insight into the mechanisms which recognize and repair DNA damage, but how they adapt to extreme environmental challenges remains poorly understood. Cavefish have proven to be fascinating models for exploring the evolution of DNA repair in the complete absence of UV-induced DNA damage and light. We have previously revealed that the Somalian cavefish Phreatichthys andruzzii, lacks photoreactivation repair via the loss of light, UV and ROS-induced photolyase gene transcription mediated by D-box enhancer elements. Here, we explore whether other systems repairing UV-induced DNA damage have been similarly affected in this cavefish model. By performing a comparative study using P. andruzzii and the surface-dwelling zebrafish, we provide evidence for a conservation of sunlight-regulated Nucleotide Excision Repair (NER). Specifically, the expression of the ddb2 gene which encodes a key NER recognition factor is robustly induced following exposure to light, UV and oxidative stress in both species. As in the case of the photolyase genes, D-boxes in the ddb2 promoter are sufficient to induce transcription in zebrafish. Interestingly, despite the loss of D-box-regulated photolyase gene expression in P. andruzzii, the D-box is required for ddb2 induction by visible light and oxidative stress in cavefish. However, in the cavefish ddb2 gene this D-box-mediated induction requires cooperation with an adjacent, highly conserved E2F element. Furthermore, while in zebrafish UV-induced ddb2 expression results from transcriptional activation accompanied by stabilization of the ddb2 mRNA, in P. andruzzii UV induces ddb2 expression exclusively via an increase in mRNA stability. Thus, we reveal plasticity in the transcriptional and post transcriptional mechanisms regulating the repair of sunlight-induced DNA damage under long-term environmental challenges.
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16
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Costa MB, Farias IR, da Silva Monte C, Filho LIPF, de Paula Borges D, de Oliveira RTG, Ribeiro-Junior HL, Magalhães SMM, Pinheiro RF. Chromosomal abnormalities and dysregulated DNA repair gene expression in farmers exposed to pesticides. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 82:103564. [PMID: 33326828 DOI: 10.1016/j.etap.2020.103564] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/24/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Exposure to pesticides is considered a major factor underlying increased risk of hematological disorders in agricultural workers due to its carcinogenic potential. However, genotoxic impact of pesticides in DNA integrity of bone marrow stem cells (BMSC) of farmers exposed is not yet well known. We evaluated presence of chromosomal abnormalities (CA) and mRNA expression of DNA repair targets (ATM, BRCA1, BRCA2, RAD51, XRCC5, XRCC6, LIG4, CSA, CSB, XPA, XPC, XPG) in 90 bone marrow samples of farmers divided into three groups: commercial farming (CF), family farming (FF) and organic farming (OF). Our results showed that farmers in CF (72.7 %) and FF (27.3 %) groups had significantly higher values of CA when compared to OF group (0.0 %; p = 0.003). CF showed lower XPG (p = 0.008), CSA (p < 0.001), ATM (p = 0.036) and LIG4 (p = 0.004) mRNA expression than OF. FF presented lower XPG (p = 0.012) and LIG4 (p = 0.004) expression than OF. CF + FF individual with ≥12 years of exposure to pesticides showed decreased mRNA expression of XPC (p = 0.001), XPG (p = 0.010), CSB (p = 0.05), ATM (p = 0.030) and LIG4 (p = 0.044) than those who have been exposed for <12 years. CF + FF with CA showed a lower expression of BRCA2 when compared to CF + FF group without CA (p = 0.007). These results highlight that genotoxic exposure to pesticides negatively affects expression profile of important DNA repair genes in BMSC, favoring irreparable chromosomal lesions.
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Affiliation(s)
- Marilia Braga Costa
- Post-Graduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, Ceará, Brazil; Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Izabelle Rocha Farias
- Post-Graduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, Ceará, Brazil; Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Cristiane da Silva Monte
- Post-Graduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, Ceará, Brazil; Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Luiz Ivando Pires Ferreira Filho
- Post-Graduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, Ceará, Brazil; Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Daniela de Paula Borges
- Post-Graduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, Ceará, Brazil; Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Roberta Taiane Germano de Oliveira
- Post-Graduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, Ceará, Brazil; Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Howard Lopes Ribeiro-Junior
- Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil; Post-Graduate Program in Translational Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil; Post-Graduate Program in Pathology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Silvia Maria Meira Magalhães
- Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil; Clinical Medicine Department, Federal University of Ceara, Fortaleza, Ceara, Brazil
| | - Ronald Feitosa Pinheiro
- Cancer Cytogenomic Laboratory, Federal University of Ceará, Fortaleza, Ceará, Brazil; Clinical Medicine Department, Federal University of Ceara, Fortaleza, Ceara, Brazil; Post-Graduate Program in Translational Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil; Post-Graduate Program in Pathology, Federal University of Ceará, Fortaleza, Ceará, Brazil.
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17
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Shiu JL, Wu CK, Chang SB, Sun YJ, Chen YJ, Lai CC, Chiu WT, Chang WT, Myung K, Su WP, Liaw H. The HLTF-PARP1 interaction in the progression and stability of damaged replication forks caused by methyl methanesulfonate. Oncogenesis 2020; 9:104. [PMID: 33281189 PMCID: PMC7719709 DOI: 10.1038/s41389-020-00289-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/04/2020] [Accepted: 11/17/2020] [Indexed: 11/27/2022] Open
Abstract
Human HLTF participates in the lesion-bypass mechanism through the fork reversal structure, known as template switching of post-replication repair. However, the mechanism by which HLTF promotes the replication progression and fork stability of damaged forks remains unclear. Here, we identify a novel protein–protein interaction between HLTF and PARP1. The depletion of HLTF and PARP1 increases chromosome breaks, further reduces the length of replication tracks, and concomitantly increases the number of stalled forks after methyl methanesulfonate treatment according to a DNA fiber analysis. The progression of replication also depends on BARD1 in the presence of MMS treatment. By combining 5-ethynyl-2′-deoxyuridine with a proximity ligation assay, we revealed that the HLTF, PARP1, and BRCA1/BARD1/RAD51 proteins were initially recruited to damaged forks. However, prolonged stalling of damaged forks results in fork collapse. HLTF and PCNA dissociate from the collapsed forks, with increased accumulation of PARP1 and BRCA1/BARD1/RAD51 at the collapsed forks. Our results reveal that HLTF together with PARP1 and BARD1 participates in the stabilization of damaged forks, and the PARP1–BARD1 interaction is further involved in the repair of collapse forks.
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Affiliation(s)
- Jia-Lin Shiu
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Cheng-Kuei Wu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, Tainan City, 704, Taiwan
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Yan-Jhih Sun
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Yen-Ju Chen
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, College of Life Science, National Chung Hsing University, No.145 Xingda Rd. South Dist., Taichung City, Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Wen-Tsan Chang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Kyungjae Myung
- IBS Center for Genomic Integrity, UNIST-gil 50, Ulsan, 689-798, Republic of Korea
| | - Wen-Pin Su
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, Tainan City, 704, Taiwan. .,Departments of Oncology and Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, 704, Taiwan.
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan.
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18
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Rahimian E, Amini A, Alikarami F, Pezeshki SMS, Saki N, Safa M. DNA repair pathways as guardians of the genome: Therapeutic potential and possible prognostic role in hematologic neoplasms. DNA Repair (Amst) 2020; 96:102951. [PMID: 32971475 DOI: 10.1016/j.dnarep.2020.102951] [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: 04/02/2020] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 11/30/2022]
Abstract
DNA repair pathways, which are also identified as guardians of the genome, protect cells from frequent damage that can lead to DNA breaks. The most deleterious types of damage are double-strand breaks (DSBs), which are repaired by homologous recombination (HR) and non-homologous end joining (NHEJ). Single strand breaks (SSBs) can be corrected through base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). Failure to restore DNA lesions or inappropriately repaired DNA damage culminates in genomic instability and changes in the regulation of cellular functions. Intriguingly, particular mutations and translocations are accompanied by special types of leukemia. Besides, expression patterns of certain repair genes are altered in different hematologic malignancies. Moreover, analysis of mutations in key mediators of DNA damage repair (DDR) pathways, as well as investigation of their expression and function, may provide us with emerging biomarkers of response/resistance to treatment. Therefore, defective DDR pathways can offer a rational starting point for developing DNA repair-targeted drugs. In this review, we address genetic alterations and gene/protein expression changes, as well as provide an overview of DNA repair pathways.
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Affiliation(s)
- Elahe Rahimian
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Amini
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Alikarami
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia (CHOP), Philadelphia, PA 19104, USA
| | - Seyed Mohammad Sadegh Pezeshki
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran; Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
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19
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Yang S, Liu JDH, Diem M, Wesseling S, Vervoort J, Oostenbrink C, Rietjens IMCM. Molecular Dynamics and In Vitro Quantification of Safrole DNA Adducts Reveal DNA Adduct Persistence Due to Limited DNA Distortion Resulting in Inefficient Repair. Chem Res Toxicol 2020; 33:2298-2309. [PMID: 32786539 DOI: 10.1021/acs.chemrestox.0c00097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The formation and repair of N2-(trans-isosafrol-3'-yl)-2'-deoxyguanosine (S-3'-N2-dG) DNA adduct derived from the spice and herbal alkenylbenzene constituent safrole were investigated. DNA adduct formation and repair were studied in vitro and using molecular dynamics (MD) simulations. DNA adduct formation was quantified using liquid chromatography-mass spectrometry (LCMS) in wild type and NER (nucleotide excision repair) deficient CHO cells and also in HepaRG cells and primary rat hepatocytes after different periods of repair following exposure to safrole or 1'-hydroxysafrole (1'-OH safrole). The slower repair of the DNA adducts found in NER deficient cells compared to that in CHO wild type cells indicates a role for NER in repair of S-3'-N2-dG DNA adducts. However, DNA repair in liver cell models appeared to be limited, with over 90% of the adducts remaining even after 24 or 48 h recovery. In our further studies, MD simulations indicated that S-3'-N2-dG adduct formation causes only subtle changes in the DNA structure, potentially explaining inefficient activation of NER. Inefficiency of NER mediated repair of S-3'-N2-dG adducts points at persistence and potential bioaccumulation of safrole DNA adducts upon daily dietary exposure.
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Affiliation(s)
- Shuo Yang
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jakob D H Liu
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Matthias Diem
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Sebastiaan Wesseling
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jacques Vervoort
- Division of Biochemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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20
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Prasad RR, Paudel S, Raina K, Agarwal R. Silibinin and non-melanoma skin cancers. J Tradit Complement Med 2020; 10:236-244. [PMID: 32670818 PMCID: PMC7340873 DOI: 10.1016/j.jtcme.2020.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 01/20/2023] Open
Abstract
Skin is the largest human organ that shields the inner body from contact with xenobiotic and genotoxic agents, and in this process, the skin's cellular genome faces continuous stress due to direct exposure to these noxious factors. Accumulation of genetic stress results in genomic alterations leading to undesirable gene or protein alteration/expression in skin cells, which eventually causes the formation of non-melanoma skin cancers (NMSCs). Ultraviolet B (UVB) radiation from sun is the most prominent factor contributing to ∼5 million skin cancer cases (which are mostly NMSCs) in the United States (US) and western countries. UVB exposure causes aberrations in a range of biochemical and molecular pathways such as: thymine dimer formation, DNA damage, oxidative stress, inflammatory responses, altered cellular signaling, which ultimately contribute to the development of NMSCs. The focus of this review is to summarize the protective and preventive potential of silymarin and/or silibinin against UVB-induced NMSC in pre-clinical skin cancer studies. Over two decades of research has shown the strong potential of silibinin, a biologically active flavonolignan (crude form Silymarin) derived from milk thistle plant, against a wide range of cancers, including NMSCs. Silibinin protects against UVB-induced thymine dimer formation and in turn promotes DNA repair and/or initiates apoptosis in damaged cells via an increase in p53 levels. Additionally, silibinin has shown strong efficacy against NMSCs via its potential to target aberrant signaling pathways, and induction of anti-inflammatory responses. Overall, completed comprehensive studies suggest the potential use of silibinin to prevent and/or manage NMSCs in humans.
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Affiliation(s)
- Ram Raj Prasad
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Sandeep Paudel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Komal Raina
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, USA
| | - Rajesh Agarwal
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO, 80045, USA
- University of Colorado Comprehensive Cancer Center, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO, 80045, USA
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21
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Long LJ, Lee PH, Small EM, Hillyer C, Guo Y, Osley MA. Regulation of UV damage repair in quiescent yeast cells. DNA Repair (Amst) 2020; 90:102861. [PMID: 32403026 DOI: 10.1016/j.dnarep.2020.102861] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/10/2020] [Accepted: 04/15/2020] [Indexed: 12/27/2022]
Abstract
Non-growing quiescent cells face special challenges when repairing lesions produced by exogenous DNA damaging agents. These challenges include the global repression of transcription and translation and a compacted chromatin structure. We investigated how quiescent yeast cells regulated the repair of DNA lesions produced by UV irradiation. We found that UV lesions were excised and repaired in quiescent cells before their re-entry into S phase, and that lesion repair was correlated with high levels of Rad7, a recognition factor in the global genome repair sub-pathway of nucleotide excision repair (GGR-NER). UV exposure led to an increased frequency of mutations that included C->T transitions and T > A transversions. Mutagenesis was dependent on the error-prone translesion synthesis (TLS) DNA polymerase, Pol zeta, which was the only DNA polymerase present in detectable levels in quiescent cells. Across the genome of quiescent cells, UV-induced mutations showed an association with exons that contained H3K36 or H3K79 trimethylation but not with those bound by RNA polymerase II. Together, the data suggest that the distinct physiological state and chromatin structure of quiescent cells contribute to its regulation of UV damage repair.
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Affiliation(s)
- Lindsey J Long
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Po-Hsuen Lee
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Eric M Small
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Cory Hillyer
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Yan Guo
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Mary Ann Osley
- Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
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Alhmoud JF, Woolley JF, Al Moustafa AE, Malki MI. DNA Damage/Repair Management in Cancers. Cancers (Basel) 2020; 12:E1050. [PMID: 32340362 PMCID: PMC7226105 DOI: 10.3390/cancers12041050] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
DNA damage is well recognized as a critical factor in cancer development and progression. DNA lesions create an abnormal nucleotide or nucleotide fragment, causing a break in one or both chains of the DNA strand. When DNA damage occurs, the possibility of generated mutations increases. Genomic instability is one of the most important factors that lead to cancer development. DNA repair pathways perform the essential role of correcting the DNA lesions that occur from DNA damaging agents or carcinogens, thus maintaining genomic stability. Inefficient DNA repair is a critical driving force behind cancer establishment, progression and evolution. A thorough understanding of DNA repair mechanisms in cancer will allow for better therapeutic intervention. In this review we will discuss the relationship between DNA damage/repair mechanisms and cancer, and how we can target these pathways.
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Affiliation(s)
- Jehad F. Alhmoud
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Al-Ahliyya Amman University, Amman 19328, Jordan
| | - John F. Woolley
- Department of Molecular & Clinical Pharmacology, Liverpool University, Liverpool L69 3GE, UK;
| | | | - Mohammed Imad Malki
- College of Medicine, QU Health, Qatar University, Doha P. O. Box 2713, Qatar;
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CRL4 Ubiquitin Pathway and DNA Damage Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:225-239. [PMID: 31898231 DOI: 10.1007/978-981-15-1025-0_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
DNA damage occurs in a human cell at an average frequency of 10,000 incidences per day by means of external and internal culprits, damage that triggers sequential cellular responses and stalls the cell cycle while activating specific DNA repair pathways. Failure to remove DNA lesions would compromise genomic integrity, leading to human diseases such as cancer and premature aging. If DNA damage is extensive and cannot be repaired, cells undergo apoptosis. DNA damage response (DDR) often entails posttranslational modifications of key DNA repair and DNA damage checkpoint proteins, including phosphorylation and ubiquitination. Cullin-RING ligase 4 (CRL4) enzyme has been found to target multiple DDR proteins for ubiquitination. In this chapter, we will discuss key repair and checkpoint proteins that are subject to ubiquitin-dependent regulation by members of the CRL4 family during ultraviolet light (UV)-induced DNA damage.
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Genetic diversity and functional effect of common polymorphisms in genes involved in the first heterodimeric complex of the Nucleotide Excision Repair pathway. DNA Repair (Amst) 2019; 86:102770. [PMID: 31865061 DOI: 10.1016/j.dnarep.2019.102770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/25/2019] [Accepted: 12/09/2019] [Indexed: 01/26/2023]
Abstract
Nucleotide excision repair is a multistep process that recognizes and eliminates a spectrum of DNA damages. Five proteins, namely XPC, RAD23, Centrin 2, DDB1 and DDB2 act as a heterodimeric complex at the early steps of the NER pathway and play a crucial role in the removal of DNA lesions. Several exonic mutations on genes coding for these proteins have been identified as associated with Xeroderma-pigmentosum (XP), a rare monogenic disorder. However, the role of regulatory polymorphisms in disease development and inter-ethnic diversity is still not well documented. Due to the high incidence rate of XP in Tunisia, we performed a genotyping analysis of 140 SNPs found on these 5 genes in a set of 135-subjects representing the general Tunisian-population. An inter-ethnic comparison based on the genotype frequency of these SNPs have been also conducted. For the most relevant variants, we performed a comprehensive assessment of their functional effects. Linkage disequilibrium and principal component analysis showed that the Tunisian-population is an admixed and intermediate population between Sub-Saharan Africans and Europeans. Using variable factor maps, we identified a list of 20 polymorphisms that contribute considerably to the inter-ethnic diversity of the NER complex. In-silico functional analysis showed that SNPs on XPC, DDB1 and DDB2 are associated with eQTLs mainly DDB2-rs10838681 that seems to decrease significantly the expression level of ACP2 (p = 6.1 × 10-26). Statistical analysis showed that the allelic frequency of DDB2-rs10838681 in Tunisia is significantly different from all other populations. Using rVarBase, we identified 5 variants on XPC, DDB1 and DDB2 that seem to alter the binding sites of several transcription factors considered as key players in DNA-repair pathways. Results presented in this study provide the first report on regulatory polymorphisms of the NER-complex genes in Tunisia. These results may also help to establish a baseline database for future association and functional studies.
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da Silva Sergio LP, Mencalha AL, de Souza da Fonseca A, de Paoli F. DNA repair and genomic stability in lungs affected by acute injury. Biomed Pharmacother 2019; 119:109412. [PMID: 31514069 PMCID: PMC9170240 DOI: 10.1016/j.biopha.2019.109412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 12/28/2022] Open
Abstract
Acute pulmonary injury, or acute respiratory distress syndrome, has a high incidence in elderly individuals and high mortality in its most severe degree, becoming a challenge to public health due to pathophysiological complications and increased economic burden. Acute pulmonary injury can develop from sepsis, septic shock, and pancreatitis causing reduction of alveolar airspace due to hyperinflammatory response. Oxidative stress acts directly on the maintenance of inflammation, resulting in tissue injury, as well as inducing DNA damages. Once the DNA is damaged, enzymatic DNA repair mechanisms act on lesions in order to maintain genomic stability and, consequently, contribute to cell viability and homeostasis. Although palliative treatment based on mechanical ventilation and antibiotic using have a kind of efficacy, therapies based on modulation of DNA repair and genomic stability could be effective for improving repair and recovery of lung tissue in patients with acute pulmonary injury.
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Affiliation(s)
- Luiz Philippe da Silva Sergio
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Vila Isabel, Rio de Janeiro, 20551030, Brazil.
| | - Andre Luiz Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Vila Isabel, Rio de Janeiro, 20551030, Brazil
| | - Adenilson de Souza da Fonseca
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Vila Isabel, Rio de Janeiro, 20551030, Brazil; Departamento de Ciências Fisiológicas, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rua Frei Caneca, 94, Rio de Janeiro, 20211040, Brazil; Centro de Ciências da Saúde, Centro Universitário Serra dos Órgãos, Avenida Alberto Torres, 111, Teresópolis, Rio de Janeiro, 25964004, Brazil
| | - Flavia de Paoli
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer - s/n, Campus Universitário, São Pedro, Juiz de Fora, Minas Gerais, 36036900, Brazil
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Armando RG, Mengual Gomez DL, Maggio J, Sanmartin MC, Gomez DE. Telomeropathies: Etiology, diagnosis, treatment and follow-up. Ethical and legal considerations. Clin Genet 2019; 96:3-16. [PMID: 30820928 DOI: 10.1111/cge.13526] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/12/2019] [Accepted: 02/26/2019] [Indexed: 12/13/2022]
Abstract
Telomeropathies involve a wide variety of infrequent genetic diseases caused by mutations in the telomerase maintenance mechanism or the DNA damage response (DDR) system. They are considered a family of rare diseases that often share causes, molecular mechanisms and symptoms. Generally, these diseases are not diagnosed until the symptoms are advanced, diminishing the survival time of patients. Although several related syndromes may still be unrecognized this work describes those that are known, highlighting that because they are rare diseases, physicians should be trained in their early diagnosis. The etiology and diagnosis are discussed for each telomeropathy and the treatments when available, along with a new classification of this group of diseases. Ethical and legal issues related to this group of diseases are also considered.
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Affiliation(s)
- Romina G Armando
- Laboratory of Molecular Oncology, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Diego L Mengual Gomez
- Laboratory of Molecular Oncology, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Julián Maggio
- Laboratory of Molecular Oncology, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - María C Sanmartin
- Laboratory of Molecular Oncology, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Daniel E Gomez
- Laboratory of Molecular Oncology, Universidad Nacional de Quilmes, Buenos Aires, Argentina
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Crystal structure of the yeast Rad7-Elc1 complex and assembly of the Rad7-Rad16-Elc1-Cul3 complex. DNA Repair (Amst) 2019; 77:1-9. [PMID: 30840920 DOI: 10.1016/j.dnarep.2019.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 01/30/2019] [Accepted: 02/21/2019] [Indexed: 11/20/2022]
Abstract
Nucleotide excision repair (NER) is a versatile system that deals with various bulky and helix-distorting DNA lesions caused by UV and environmental mutagens. Based on how lesion recognition occurs, NER has been separated into global genome repair (GGR) and transcription-coupled repair (TCR). The yeast Rad7-Rad16 complex is indispensable for the GGR sub-pathway. Rad7-Rad16 binds to UV-damaged DNA in a synergistic fashion with Rad4, the main lesion recognizer, to achieve efficient recognition of lesions. In addition, Rad7-Rad16 associates with Elc1 and Cul3 to form an EloC-Cul-SOCS-box (ECS)-type E3 ubiquitin ligase complex that ubiquitinates Rad4 in response to UV radiation. However, the structure and architecture of the Rad7-Rad16-Elc1-Cul3 complex remain unsolved. Here, we determined the structure of the Rad7-Elc1 complex and revealed key interaction regions responsible for the formation of the Rad7-Rad16-Elc1-Cul3 complex. These results provide new insights into the assembly of the Rad7-Rad16-Elc1-Cul3 complex and structural framework for further studies.
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Lahari T, Lazaro J, Marcus JM, Schroeder DF. RAD7 homologues contribute to Arabidopsis UV tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:267-277. [PMID: 30466592 DOI: 10.1016/j.plantsci.2018.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/07/2018] [Accepted: 09/21/2018] [Indexed: 06/09/2023]
Abstract
Frequent exposure of plants to solar ultraviolet radiation (UV) results in damaged DNA. One mechanism of DNA repair is the light independent pathway Global Genomic Nucleotide Excision Repair (GG-NER), which repairs UV damaged DNA throughout the genome. In mammals, GG-NER DNA damage recognition is performed by the Damaged DNA Binding protein 1 and 2 (DDB1/2) complex which recruits the Xeroderma Pigmentosa group C (XPC) / RAD23D complex. In the yeast Saccharomyces cerevisiae, distinct proteins, Radiation sensitive 7 and 16 (Rad7p and Rad16p), recognize the damaged DNA strand and then recruit the XPC homologue, Rad4p, and Rad23p. The remainder of the proteins involved GG-NER are well conserved. DDB1, DDB2, XPC/RAD4, and RAD23 homologues have been described in the model plant Arabidopsis thaliana. In this study we characterize three Arabidopsis RAD7 homologues, RAD7a, RAD7b, and RAD7c. Loss of function alleles of each of the three RAD7 homologues result in increased UV sensitivity. In addition, RAD7b and RAD7c overexpression lines exhibited increased UV tolerance. Thus RAD7 homologues contribute to UV tolerance in plants as well as in yeast. This is the first time any system has been shown to utilize both the DDB1/2 and RAD7/16 damage recognition complexes.
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Affiliation(s)
- Triparna Lahari
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Janelle Lazaro
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Jeffrey M Marcus
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Dana F Schroeder
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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Low-power laser alters mRNA levels from DNA repair genes in acute lung injury induced by sepsis in Wistar rats. Lasers Med Sci 2018; 34:157-168. [DOI: 10.1007/s10103-018-2656-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/30/2018] [Indexed: 01/08/2023]
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Lawania S, Sharma S, Singh N, Behera D. XPF polymorphism toward lung cancer susceptibility and survival in patients treated with platinum-based chemotherapy. Future Oncol 2018; 14:1071-1089. [PMID: 29741112 DOI: 10.2217/fon-2017-0569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To evaluate the association of three XPF polymorphic variants (673 C>T, 11985 A>G, G415A) with lung cancer, overall survival and clinical response in North Indians. METHODS Genotyping was performed using PCR-restriction fragment length polymorphism. RESULTS A total of 673 C>T polymorphism was associated with 1.5-fold increased lung cancer risk for heterozygous genotype (CT; p = 0.03). Adenocarcinoma patients with 673 C>T polymorphism carrying heterozygous genotype (CT) had a lower hazard ratio (p = 0.01). Classification and regression tree analysis predicted XPF 673 C>T (M) as the strongest risk factor for the lung cancer (p = 0.003). For 11985 A>G polymorphism, lung cancer subjects treated with irinotecan cisplatin/carboplatin regimen having heterozygous genotype (AG) was associated with high mortality risk (p = 0.0001). CONCLUSION 673 C>T polymorphism was associated with increased lung cancer risk.
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Affiliation(s)
- Shweta Lawania
- Department of Biotechnology, Thapar University, Punjab 147002, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar University, Punjab 147002, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education & Research (PGIMER), Sector 14, Chandigarh, India
| | - Digamber Behera
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education & Research (PGIMER), Sector 14, Chandigarh, India
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Lukyanchikova NV, Petruseva IO, Evdokimov AN, Koroleva LS, Lavrik OI. DNA Bearing Bulky Fluorescent and Photoreactive Damage in Both Strands as Substrates of the Nucleotide Excision Repair System. Mol Biol 2018. [DOI: 10.1134/s0026893318020061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Sameer AS, Nissar S. XPD-The Lynchpin of NER: Molecule, Gene, Polymorphisms, and Role in Colorectal Carcinogenesis. Front Mol Biosci 2018; 5:23. [PMID: 29616226 PMCID: PMC5869190 DOI: 10.3389/fmolb.2018.00023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/27/2018] [Indexed: 01/17/2023] Open
Abstract
In mammals the bulky DNA adduct lesions known to result in deleterious phenotypes are acted upon and removed from the genomic DNA by nucleotide excision repair (NER) pathway. TFIIH multi-protein complex with its important helicase–Xeroderma Pigmentosum Protein (XPD) serves as the pivotal factor for opening up of the damaged lesion DNA site and carry out the repair process. The initial damage verification step of the TFIIH is in part dependent upon the helicase activity of XPD. Besides, XPD is also actively involved in the initiation steps of transcription and in the regulation of the cell cycle and apoptosis. In this review, we will be exploring the new insights in scientific research on the functioning of the NER pathway, the role of TFIIH as the central complex of NER, the pivotal helicase XPD as the lynchpin of NER and the effects of various single nucleotide polymorphisms (SNPs) of XPD on its functioning and their consequent role in colorectal carcinogenesis.
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Affiliation(s)
- Aga Syed Sameer
- Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Saniya Nissar
- Department of Biochemistry, Kashmir University, Srinagar, India
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Evdokimov AN, Tsidulko AY, Popov AV, Vorobiev YN, Lomzov AA, Koroleva LS, Silnikov VN, Petruseva IO, Lavrik OI. Structural basis for the recognition and processing of DNA containing bulky lesions by the mammalian nucleotide excision repair system. DNA Repair (Amst) 2018; 61:86-98. [DOI: 10.1016/j.dnarep.2017.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 10/05/2017] [Accepted: 10/23/2017] [Indexed: 11/30/2022]
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Sergio LPDS, de Paoli F, Mencalha AL, da Fonseca ADS. Chronic Obstructive Pulmonary Disease: From Injury to Genomic Stability. COPD 2017; 14:439-450. [DOI: 10.1080/15412555.2017.1332025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Luiz Philippe da Silva Sergio
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Vila Isabel, Rio de Janeiro, Brazil
| | - Flavia de Paoli
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, São Pedro, Juiz de Fora, Minas Gerais, Brazil
| | - Andre Luiz Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Vila Isabel, Rio de Janeiro, Brazil
| | - Adenilson de Souza da Fonseca
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Vila Isabel, Rio de Janeiro, Brazil
- Departamento de Ciências Fisiológicas, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
- Centro de Ciências da Saúde, Centro Universitário Serra dos Órgãos, Teresópolis, Rio de Janeiro, Brazil
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Lukyanchikova NV, Petruseva IO, Evdokimov AN, Silnikov VN, Lavrik OI. DNA with Damage in Both Strands as Affinity Probes and Nucleotide Excision Repair Substrates. BIOCHEMISTRY (MOSCOW) 2017; 81:263-74. [PMID: 27262196 DOI: 10.1134/s0006297916030093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nucleotide excision repair (NER) is a multistep process of recognition and elimination of a wide spectrum of damages that cause significant distortions in DNA structure, such as UV-induced damage and bulky chemical adducts. A series of model DNAs containing new bulky fluoro-azidobenzoyl photoactive lesion dC(FAB) and well-recognized nonnucleoside lesions nFlu and nAnt have been designed and their interaction with repair proteins investigated. We demonstrate that modified DNA duplexes dC(FAB)/dG (probe I), dC(FAB)/nFlu+4 (probe II), and dC(FAB)/nFlu-3 (probe III) have increased (as compared to unmodified DNA, umDNA) structure-dependent affinity for XPC-HR23B (Kdum > KdI > KdII ≈ KdIII) and differentially crosslink to XPC and proteins of NER-competent extracts. The presence of dC(FAB) results in (i) decreased melting temperature (ΔTm = -3°C) and (ii) 12° DNA bending. The extended dC(FAB)/dG-DNA (137 bp) was demonstrated to be an effective NER substrate. Lack of correlation between the affinity to XPC-HR23B and substrate properties of the model DNA suggests a high impact of the verification stage on the overall NER process. In addition, DNAs containing closely positioned, well-recognized lesions in the complementary strands represent hardly repairable (dC(FAB)/nFlu+4, dC(FAB)/nFlu-3) or irreparable (nFlu/nFlu+4, nFlu/nFlu-3, nAnt/nFlu+4, nAnt/nFlu-3) structures. Our data provide evidence that the NER system of higher eukaryotes recognizes and eliminates damaged DNA fragments on a multi-criterion basis.
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Affiliation(s)
- N V Lukyanchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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Zhang J, Shim G, de Toledo SM, Azzam EI. The Translationally Controlled Tumor Protein and the Cellular Response to Ionizing Radiation-Induced DNA Damage. Results Probl Cell Differ 2017; 64:227-253. [DOI: 10.1007/978-3-319-67591-6_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Stratigi K, Chatzidoukaki O, Garinis GA. DNA damage-induced inflammation and nuclear architecture. Mech Ageing Dev 2016; 165:17-26. [PMID: 27702596 DOI: 10.1016/j.mad.2016.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/20/2016] [Accepted: 09/25/2016] [Indexed: 12/12/2022]
Abstract
Nuclear architecture and the chromatin state affect most-if not all- DNA-dependent transactions, including the ability of cells to sense DNA lesions and restore damaged DNA back to its native form. Recent evidence points to functional links between DNA damage sensors, DNA repair mechanisms and the innate immune responses. The latter raises the question of how such seemingly disparate processes operate within the intrinsically complex nuclear landscape and the chromatin environment. Here, we discuss how DNA damage-induced immune responses operate within chromatin and the distinct sub-nuclear compartments highlighting their relevance to chronic inflammation.
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Affiliation(s)
- Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Ourania Chatzidoukaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece; Department of Biology, University of Crete, Vassilika Vouton, GR71409, Heraklion, Crete, Greece.
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Liu L, Zheng YH, Han L, Qin SK. Efficacy and safety of the oxaliplatin-based chemotherapy in the treatment of advanced primary hepatocellular carcinoma: A meta-analysis of prospective studies. Medicine (Baltimore) 2016; 95:e4993. [PMID: 27749557 PMCID: PMC5059059 DOI: 10.1097/md.0000000000004993] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Many clinical studies have demonstrated the survival benefits of oxaliplatin-based chemotherapy for advanced hepatocellular carcinoma patients. Therefore, we aim to evaluate the efficacy and safety of oxaliplatin-based chemotherapy in patients with advanced hepatocellular carcinoma by conducting a meta-analysis of prospective studies. METHODS A comprehensive literature search was performed using the PubMed, Cochrane Library, EMBASE, and Web of Science databases from their inception to June 2016. Only prospective studies evaluating oxaliplatin-based chemotherapy in patients with advanced hepatocellular carcinoma were selected. The main outcomes included objective response rate (ORR), progression-free survival (PFS), overall survival (OS), and main adverse events. RESULTS Ten prospective studies involving 525 patients were included. The pooled ORR, 1-year PFS, and OS were 14.4% (95% confidence interval [CI] 9.2-19.6%), 9.3% (95%CI 10-28%), and 35.7% (95%CI 27-44%), respectively, for oxaliplatin-based chemotherapy. The median PFS and OS were 4.7 and 9.4 months, respectively. The incidences of grade 3/4 toxicities of neutropenia, thrombopenia, anemia, neurotoxicity, diarrhea, and nausea/vomiting were 17.2%, 9.2%, 6.0%, 4.8%, 3.1%, and 1.8%, respectively. Subgroup analysis revealed that the pooled ORR was 13.9% (95%CI 6.8-21%) in Asian patients and 12.8% (95%CI 6.8-18.7%) in Western patients. For Asian patients, the median PFS and OS were 4.2 and 9.2 months, and the 1-year PFS and OS were 12.5% and 30.5%, respectively. For Western patients, the median PFS and OS were 4.7 and 9.5 months, and the 1-year PFS and OS were 19.6% and 42.4%, respectively. There were no significant differences in the ORR, 1-year PFS, and OS (P > 0.05) between Asian and Western patients. CONCLUSIONS Oxaliplatin-based chemotherapy appears to be effective and safe for the treatment of advanced hepatocellular carcinoma.
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Affiliation(s)
- Lin Liu
- Department of Oncology, Zhong-Da Hospital, School of Medicine, Southeast University
- Department of Oncology, 81st Hospital of the Chinese People's Liberation Army, Nanjing, Jiangsu, China
- Correspondence: Lin Liu, Department of Oncology, Zhong-Da Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China (e-mail: ); Shu-Kui Qin, Department of Oncology, the 81 Hospital of the Chinese People's Liberation Army, Nanjing, Jiangsu, China (e-mail: )
| | - Ying-hui Zheng
- Department of Oncology, Zhong-Da Hospital, School of Medicine, Southeast University
| | - Li Han
- Department of Oncology, Zhong-Da Hospital, School of Medicine, Southeast University
| | - Shu-Kui Qin
- Department of Oncology, 81st Hospital of the Chinese People's Liberation Army, Nanjing, Jiangsu, China
- Correspondence: Lin Liu, Department of Oncology, Zhong-Da Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China (e-mail: ); Shu-Kui Qin, Department of Oncology, the 81 Hospital of the Chinese People's Liberation Army, Nanjing, Jiangsu, China (e-mail: )
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Evangelisti C, Cenni V, Lattanzi G. Potential therapeutic effects of the MTOR inhibitors for preventing ageing and progeria-related disorders. Br J Clin Pharmacol 2016; 82:1229-1244. [PMID: 26952863 PMCID: PMC5061804 DOI: 10.1111/bcp.12928] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 03/02/2016] [Accepted: 03/02/2016] [Indexed: 12/25/2022] Open
Abstract
The mammalian target of rapamycin (mTOR) pathway is an highly conserved signal transduction axis involved in many cellular processes, such as cell growth, survival, transcription, translation, apoptosis, metabolism, motility and autophagy. Recently, this signalling pathway has come to the attention of the scientific community owing to the unexpected finding that inhibition of mTOR by rapamycin, an antibiotic with immunosuppressant and chemotherapeutic properties, extends lifespan in diverse animal models. Moreover, rapamycin has been reported to rescue the cellular phenotype in a progeroid syndrome [Hutchinson–Gilford Progeria syndrome (HGPS)] that recapitulates most of the traits of physiological ageing. The promising perspectives raised by these results warrant a better understanding of mTOR signalling and the potential applications of mTOR inhibitors to counteract ageing‐associated diseases and increase longevity. This review is focused on these issues.
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Affiliation(s)
- Camilla Evangelisti
- CNR Institute for Molecular Genetics, Unit of Bologna, Bologna, Italy.,Rizzoli Orthopedic Institute, Laboratory of Musculoskeletal Cell Biology, Bologna, Italy
| | - Vittoria Cenni
- CNR Institute for Molecular Genetics, Unit of Bologna, Bologna, Italy.,Rizzoli Orthopedic Institute, Laboratory of Musculoskeletal Cell Biology, Bologna, Italy
| | - Giovanna Lattanzi
- CNR Institute for Molecular Genetics, Unit of Bologna, Bologna, Italy. .,Rizzoli Orthopedic Institute, Laboratory of Musculoskeletal Cell Biology, Bologna, Italy.
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40
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Zafeer M, Mahjabeen I, Kayani MA. Increased expression of ERCC2 gene in head and neck cancer is associated with aggressive tumors: a systematic review and case-control study. Int J Biol Markers 2016; 31:e17-25. [PMID: 26659720 DOI: 10.5301/jbm.5000186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2015] [Indexed: 11/20/2022]
Abstract
INTRODUCTION The excision repair cross-complementation group 2 (ERCC2) ATP-dependent helicase is an essential member of the DNA repair pathway. It has been observed to be differentially expressed in different cancers, which shows its involvement in carcinogenesis. AIM In the present study we have tried to determine the association of expression patterns of this gene with head and neck carcinogenesis. METHOD We first carried out a systematic review of the available studies on the role of ERCC2 in head and neck cancer (HNC). In order to test the hypothesis that the expression patterns of XPD/ERCC2 play a critical role in HNC pathogenesis, we then conducted a population based case-control study on 81 head and neck tumor samples and adjacent normal-tissue control samples. Reverse transcriptase polymerase chain reaction (RT-PCR) and quantitative polymerase chain reaction (qPCR) were used to assess ERCC2 deregulation at the mRNA level. RESULT Expression analysis showed that the ERCC2 expression level was significantly upregulated (p<0.05) in HNC tissues compared with adjacent normal tissues. Furthermore, the expression pattern of ERCC2 was correlated with the expression pattern of Ki-67 and a significant correlation (r = 0.230, p<0.03) was observed between ERCC2 and Ki-67. Spearman's correlation also showed a significant correlation between ERCC2 expression and tumor stage (r = 0.271, p<0.02) and grade (r = 0.228, p<0.02) of HNC. CONCLUSIONS Our data suggest that deregulation of ERCC2 in HNC has the potential to predict a more aggressive cancer phenotype and may be considered a possible biomarker for improved diagnosis and prognosis of HNC.
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Affiliation(s)
- Maryam Zafeer
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad - Pakistan
| | - Ishrat Mahjabeen
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad - Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad - Pakistan
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Angelika Ihle M, Merkelbach-Bruse S, Hartmann W, Bauer S, Ratner N, Sonobe H, Nishio J, Larsson O, Åman P, Pedeutour F, Taguchi T, Wardelmann E, Buettner R, Schildhaus HU. HR23b expression is a potential predictive biomarker for HDAC inhibitor treatment in mesenchymal tumours and is associated with response to vorinostat. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2016; 2:59-71. [PMID: 27499916 PMCID: PMC4907056 DOI: 10.1002/cjp2.35] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 12/13/2015] [Accepted: 12/17/2015] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDAC) are key players in epigenetic regulation of gene expression and HDAC inhibitor (HDACi) treatment seems to be a promising anticancer therapy in many human tumours, including soft tissue sarcomas. HR23b has been shown to be a potential biomarker for sensitivity to HDACi therapy in cutaneous T‐cell lymphoma and hepatocellular carcinoma. We aimed to evaluate HR23b as a candidate biomarker for HDACi response in sarcomas and gastrointestinal stromal tumours (GIST). Therefore, HR23b expression was analysed comprehensively by western blot in sarcoma and GIST cell lines covering all major clinically relevant subtypes. MTT assay and ApoTox‐GloTM Triplex assay were performed after treatment with vorinostat, belinostat, mocetinostat and entinostat. HR23b protein expression was measured under HDACi treatment. Furthermore, HR23b expression levels were immunohistochemically determined in a large set of 523 clinical samples from sarcoma and GIST patients. Western blot analyses showed that sarcomas differ significantly in their expression of HR23b protein. All HDACi were able to regulate proliferation and apoptosis in vitro. Sensitivity to vorinostat correlated significantly with HR23b protein expression. Immunohistochemical prevalence screening in clinical samples of relevant adult‐type tumours revealed that 12.5% of sarcomas (among them malignant peripheral nerve sheath tumours, pleomorphic liposarcomas, leiomyosarcomas, dedifferentiated liposarcomas, synovial sarcomas and angiosarcomas) and 23.2% of GIST show high HR23b expression. Therefore, HDACi have antiproliferative and proapoptotic effects in sarcomas depending on the expression level of HR23b. These findings suggest that HR23b represents a candidate biomarker for HDACi sensitivity in certain sarcoma types and in GIST.
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Affiliation(s)
| | | | - Wolfgang Hartmann
- Institute of Pathology, University Hospital CologneCologneGermany; Gerhard Domagk Institute of Pathology, University Hospital MünsterMünsterGermany
| | - Sebastian Bauer
- Sarcoma Center, West German Cancer Center, University of Essen Essen Germany
| | - Nancy Ratner
- US Department of Pediatrics Cincinnati Children's Hospital Medical Centre Cincinnati OH USA
| | - Hiroshi Sonobe
- Department of Laboratory Medicine Chugoku Central Hospital Fukuyama Hiroshima Japan
| | - Jun Nishio
- Faculty of Medicine, Department of Orthopaedic Surgery Fukuoka University Fukuoka Japan
| | - Olle Larsson
- Department of Oncology and Pathology The Karolinska Institute Stockholm Sweden
| | - Pierre Åman
- Sahlgrenska Cancer Centre, University of Gothenburg Gothenburg Sweden
| | - Florence Pedeutour
- Faculty of Medicine, Laboratory of Genetics of Solid Tumours Institute for Research on Cancer and Aging Nice France
| | - Takahiro Taguchi
- Division of Human Health & Medical Science, Graduate School of Kuroshio Science Kochi University Nankoku Kochi Japan
| | - Eva Wardelmann
- Institute of Pathology, University Hospital CologneCologneGermany; Gerhard Domagk Institute of Pathology, University Hospital MünsterMünsterGermany
| | | | - Hans-Ulrich Schildhaus
- Institute of Pathology, University Hospital CologneCologneGermany; Institute of Pathology, University Hospital GöttingenGöttingenGermany
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Sergio LPS, Campos VMA, Vicentini SC, Mencalha AL, de Paoli F, Fonseca AS. Low-intensity red and infrared lasers affect mRNA expression of DNA nucleotide excision repair in skin and muscle tissue. Lasers Med Sci 2016; 31:429-35. [DOI: 10.1007/s10103-016-1870-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 01/04/2016] [Indexed: 01/08/2023]
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Architecture of the human XPC DNA repair and stem cell coactivator complex. Proc Natl Acad Sci U S A 2015; 112:14817-22. [PMID: 26627236 PMCID: PMC4672820 DOI: 10.1073/pnas.1520104112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The Xeroderma pigmentosum complementation group C (XPC) complex is a versatile factor involved in both nucleotide excision repair and transcriptional coactivation as a critical component of the NANOG, OCT4, and SOX2 pluripotency gene regulatory network. Here we present the structure of the human holo-XPC complex determined by single-particle electron microscopy to reveal a flexible, ear-shaped structure that undergoes localized loss of order upon DNA binding. We also determined the structure of the complete yeast homolog Rad4 holo-complex to find a similar overall architecture to the human complex, consistent with their shared DNA repair functions. Localized differences between these structures reflect an intriguing phylogenetic divergence in transcriptional capabilities that we present here. Having positioned the constituent subunits by tagging and deletion, we propose a model of key interaction interfaces that reveals the structural basis for this difference in functional conservation. Together, our findings establish a framework for understanding the structure-function relationships of the XPC complex in the interplay between transcription and DNA repair.
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Abstract
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Xeroderma
pigmentosum complementation group A (XPA) protein plays
a critical role in the repair of DNA damage via the nucleotide excision
repair (NER) pathway. XPA serves as a scaffold for NER, interacting
with several other NER proteins as well as the DNA substrate. The
critical importance of XPA is underscored by its association with
the most severe clinical phenotypes of the genetic disorder Xeroderma
pigmentosum. Many of these disease-associated mutations map to the
XPA98–219 DNA-binding domain (DBD) first reported
∼20 years ago. Although multiple solution NMR structures of
XPA98–219 have been determined, the molecular basis
for the interaction of this domain with DNA is only poorly characterized.
In this report, we demonstrate using a fluorescence anisotropy DNA-binding
assay that the previously reported XPA DBD binds DNA with substantially
weaker affinity than the full-length protein. In-depth analysis of
the XPA sequence suggested that the original DBD construct lacks critical
basic charge and helical elements at its C-terminus. Generation and
analysis of a series of C-terminal extensions beyond residue 219 yielded
a stable, soluble human XPA98–239 construct that
binds to a Y-shaped ssDNA–dsDNA junction and other substrates
with the same affinity as the full-length protein. Two-dimensional 15N–1H NMR suggested XPA98–239 contains the same globular core as XPA98–219 and
likely undergoes a conformational change upon binding DNA. Together,
our results demonstrate that the XPA DBD should be redefined and that
XPA98–239 is a suitable model to examine the DNA
binding activity of human XPA.
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Affiliation(s)
- Norie Sugitani
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37232-8725, United States
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