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Sassa A, Kanemaru Y, Kamoshita N, Honma M, Yasui M. Mutagenic consequences of cytosine alterations site-specifically embedded in the human genome. Genes Environ 2016; 38:17. [PMID: 27588157 PMCID: PMC5007816 DOI: 10.1186/s41021-016-0045-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/06/2016] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Cytosine residues in CpG dinucleotides often undergo various types of modification, such as methylation, deamination, and halogenation. These types of modifications can be pro-mutagenic and can contribute to the formation of mutational hotspots in cells. To analyze mutations induced by DNA modifications in the human genome, we recently developed a system for tracing DNA adducts in targeted mutagenesis (TATAM). In this system, a modified/damaged base is site-specifically introduced into intron 4 of thymidine kinase genes in human lymphoblastoid cells. To further the understanding of the mutagenesis of cytosine modification, we directly introduced different types of altered cytosine residues into the genome and investigated their genomic consequences using the TATAM system. FINDINGS In the genome, the pairing of thymine and 5-bromouracil with guanine, resulting from the deamination of 5-methylcytosine and 5-bromocytosine, respectively, was highly pro-mutagenic compared with the pairing of uracil with guanine, resulting from the deamination of cytosine residues. CONCLUSIONS The deamination of 5-methylcytosine and 5-bromocytosine rather than that of normal cytosine dramatically enhances the mutagenic potential in the human genome.
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Affiliation(s)
- Akira Sassa
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501 Japan
| | - Yuki Kanemaru
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501 Japan.,Present address: Division of Toxicology, Department of Pharmacology, Toxicology and Therapeutics, Showa University School of Pharmacy, Tokyo, 142-8555 Japan
| | - Nagisa Kamoshita
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501 Japan
| | - Masamitsu Honma
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501 Japan
| | - Manabu Yasui
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501 Japan
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Egloff D, Oleinich IA, Freisinger E. Sequence-specific generation of 1,N(6)-ethenoadenine and 3,N(4)-ethenocytosine in single-stranded unmodified DNA. ACS Chem Biol 2015; 10:547-53. [PMID: 25402665 DOI: 10.1021/cb500497p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA lesions such as 1,N(6)-ethenoadenine (εA) and 3,N(4)-ethenocytosine (εC) are ubiquitously present in genomes of different organisms and show increasing levels upon exposure to mutagenic substances or under conditions of chronic inflammations and infections. To facilitate investigations of the mutagenic properties and repair mechanisms of etheno-base adducts, access to oligonucleotides bearing these lesions at defined positions is of great advantage. In this study, we report a new synthetic strategy to sequence-specifically generate etheno-adducts in a single-stranded unmodified DNA sequence making use of a DNA-templated approach that positions the alkylating agent close in space to the respective target base. In contrast to solid-phase synthesis of modified oligonucleotides such DNA-templated methods can be applied to single-stranded nucleic acids of unrestricted lengths. The modular nature of the system allows straightforward adaptation to different sequences.
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Affiliation(s)
- David Egloff
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Igor A. Oleinich
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Eva Freisinger
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Talhaoui I, Couve S, Gros L, Ishchenko AA, Matkarimov B, Saparbaev MK. Aberrant repair initiated by mismatch-specific thymine-DNA glycosylases provides a mechanism for the mutational bias observed in CpG islands. Nucleic Acids Res 2014; 42:6300-13. [PMID: 24692658 PMCID: PMC4041421 DOI: 10.1093/nar/gku246] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 03/09/2014] [Accepted: 03/13/2014] [Indexed: 12/13/2022] Open
Abstract
The human thymine-DNA glycosylase (TDG) initiates the base excision repair (BER) pathway to remove spontaneous and induced DNA base damage. It was first biochemically characterized for its ability to remove T mispaired with G in CpG context. TDG is involved in the epigenetic regulation of gene expressions by protecting CpG-rich promoters from de novo DNA methylation. Here we demonstrate that TDG initiates aberrant repair by excising T when it is paired with a damaged adenine residue in DNA duplex. TDG targets the non-damaged DNA strand and efficiently excises T opposite of hypoxanthine (Hx), 1,N(6)-ethenoadenine, 7,8-dihydro-8-oxoadenine and abasic site in TpG/CpX context, where X is a modified residue. In vitro reconstitution of BER with duplex DNA containing Hx•T pair and TDG results in incorporation of cytosine across Hx. Furthermore, analysis of the mutation spectra inferred from single nucleotide polymorphisms in human population revealed a highly biased mutation pattern within CpG islands (CGIs), with enhanced mutation rate at CpA and TpG sites. These findings demonstrate that under experimental conditions used TDG catalyzes sequence context-dependent aberrant removal of thymine, which results in TpG, CpA→CpG mutations, thus providing a plausible mechanism for the putative evolutionary origin of the CGIs in mammalian genomes.
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Affiliation(s)
- Ibtissam Talhaoui
- Groupe Réparation de l’ADN, Université Paris Sud, Laboratoire Stabilité Génétique et Oncogenèse CNRS, UMR 8200, Gustave Roussy, F-94805 Villejuif Cedex, France
| | - Sophie Couve
- Laboratoire de Génétique Oncologique EPHE, INSERM U753, Gustave Roussy, F-94805 Villejuif, France
| | - Laurent Gros
- Groupe Réparation de l’ADN, Université Paris Sud, Laboratoire Stabilité Génétique et Oncogenèse CNRS, UMR 8200, Gustave Roussy, F-94805 Villejuif Cedex, France
- AB Science SA, 75008 Paris, France
| | - Alexander A. Ishchenko
- Groupe Réparation de l’ADN, Université Paris Sud, Laboratoire Stabilité Génétique et Oncogenèse CNRS, UMR 8200, Gustave Roussy, F-94805 Villejuif Cedex, France
| | - Bakhyt Matkarimov
- Nazarbayev University Research and Innovation System, Astana 010000, Kazakhstan
| | - Murat K. Saparbaev
- Groupe Réparation de l’ADN, Université Paris Sud, Laboratoire Stabilité Génétique et Oncogenèse CNRS, UMR 8200, Gustave Roussy, F-94805 Villejuif Cedex, France
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Sahu PK, Srinivasadesikan V, Jhong ML, Lee SL. Model calculations for the base-pairing specificity of mutagenic exocyclic DNA adduct 1,N 6-ethenoadenine. Struct Chem 2013. [DOI: 10.1007/s11224-013-0318-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Ford KA. Role of electrostatic potential in the in silico prediction of molecular bioactivation and mutagenesis. Mol Pharm 2013; 10:1171-82. [PMID: 23323940 DOI: 10.1021/mp3004385] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Electrostatic potential (ESP) is a useful physicochemical property of a molecule that provides insights into inter- and intramolecular associations, as well as prediction of likely sites of electrophilic and nucleophilic metabolic attack. Knowledge of sites of metabolic attack is of paramount importance in DMPK research since drugs frequently fail in clinical trials due to the formation of bioactivated metabolites which are often difficult to measure experimentally due to their reactive nature and relatively short half-lives. Computational chemistry methods have proven invaluable in recent years as a means to predict and study bioactivated metabolites without the need for chemical syntheses, or testing on experimental animals. Additional molecular properties (heat of formation, heat of solvation and E(LUMO) - E(HOMO)) are discussed in this paper as complementary indicators of the behavior of metabolites in vivo. Five diverse examples are presented (acetaminophen, aniline/phenylamines, imidacloprid, nefazodone and vinyl chloride) which illustrate the utility of this multidimensional approach in predicting bioactivation, and in each case the predicted data agreed with experimental data described in the scientific literature. A further example of the usefulness of calculating ESP, in combination with the molecular properties mentioned above, is provided by an examination of the use of these parameters in providing an explanation for the sites of nucleophilic attack of the nucleic acid cytosine. Exploration of sites of nucleophilic attack of nucleic acids is important as adducts of DNA have the potential to result in mutagenesis.
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Affiliation(s)
- Kevin A Ford
- Safety Assessment, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, USA.
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Nair J, Godschalk RW, Nair U, Owen RW, Hull WE, Bartsch H. Identification of 3,N(4)-etheno-5-methyl-2'-deoxycytidine in human DNA: a new modified nucleoside which may perturb genome methylation. Chem Res Toxicol 2012; 25:162-9. [PMID: 22148471 DOI: 10.1021/tx200392a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methylation of cytidine at dCpdG sequences regulates gene expression and is altered in many chronic inflammatory diseases. Inflammation generates lipid peroxidation (LPO) products which can react with deoxycytidine, deoxyadenosine, and deoxyguanosine in DNA to form pro-mutagenic exocyclic etheno-nucleoside residues. Since 5-methyl-2'-deoxycytidine (5mdC) residues exhibit increased nucleophilicity at N3, they should be even better targets for LPO products. We synthesized and characterized 3,N(4)-etheno-5-methyl-2'-deoxycytidine-3'-phosphate and showed that LPO products can indeed form the corresponding etheno-5mdC (ε5mdC) lesion in DNA in vitro. Our newly developed (32)P-postlabeling method was subsequently used to detect ε5mdC lesions in DNA from human white blood cells, lung, and liver at concentrations 4-10 times higher than that observed for etheno adducts on nonmethylated cytidine. Our new detection method can now be used to explore the hypothesis that this DNA lesion perturbs the DNA methylation status.
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Affiliation(s)
- Jagadeesan Nair
- German Cancer Research Center (DKFZ) , Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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Srinivasadesikan V, Sahu PK, Lee SL. Model calculations for the misincorporation of nucleotides opposite five-membered exocyclic DNA adduct: N(2),3-ethenoguanine. J Phys Chem B 2011; 115:10537-46. [PMID: 21776999 DOI: 10.1021/jp202738v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Five-membered exocyclic DNA adducts are biologically very significant because of their potential to block DNA replication and transcription. N(2),3-Ethenoguanine (N(2,3)-εG) has been identified in the liver DNA of vinyl chloride-exposed rats as a five-membered DNA adduct. Singer et al. ( Carcinogenesis 1987 , 8 , 745 - 747 ) reported that the misincorporation of thymine (T), with two hydrogen bonds to N(2,3)-εG, represents the mutagenic event. Although the base-pairing specificity and mode of misincorporation have been studied experimentally for the N(2),3-ethenoguanine adduct, molecular-level information is not yet clear. In this study, we have considered all four different DNA nucleotides paired with the N(2),3-ethenoguanine adduct for model calculations toward the determination of base-pairing specificity. To provide insight into the mutagenic process of DNA damage based on geometric characteristics and electronic properties, the B3LYP and M06 methods were employed for these model calculations. Single-point energy calculations at the MP2/6-311++G** level on the corresponding optimized geometries were also carried out to better estimate the hydrogen-bonding strengths. The polarizable conductor calculation model (CPCM), which accounts for the overall polarizability of the solvent, was also employed. The computed reaction enthalpy values lie in the order εG-G(2) (10.3 kcal/mol) > εG-G(4) (9.6 kcal/mol) > εG-T(4) (9.2 kcal/mol) > εG-G(1) (9.1 kcal/mol) > εG-A(5) (8.2 kcal/mol) > εG-C(2) (7.9 kcal/mol) at the M06 level, which indicates that guanine and thymine are most favorable for mispairing with the N(2),3-ethenoguanine adduct.
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Liu M, Xu M, Lee JK. The Acidity and Proton Affinity of the Damaged Base 1,N6-Ethenoadenine in the Gas Phase versus in Solution: Intrinsic Reactivity and Biological Implications. J Org Chem 2008; 73:5907-14. [DOI: 10.1021/jo800891c] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Min Liu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Meng Xu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
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Kim MY, Zhou X, Delaney JC, Taghizadeh K, Dedon PC, Essigmann JM, Wogan GN. AlkB influences the chloroacetaldehyde-induced mutation spectra and toxicity in the pSP189 supF shuttle vector. Chem Res Toxicol 2007; 20:1075-83. [PMID: 17658757 DOI: 10.1021/tx700167v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2-Chloroacetaldehyde (CAA), a metabolite of the carcinogen vinyl chloride, reacts with DNA to form cyclic etheno ()-lesions. AlkB, an iron-/alpha-ketoglutarate-dependent dioxygenase, repairs 1, N (6)-ethenodeoxyadenosine (A) and 3, N (4)-ethenodeoxycytidine (C) in site-specifically modified single-stranded viral genomes in vivo and also protects the E. coli genome from the toxic effects of CAA. We examined the role of AlkB as a cellular defense against CAA by characterizing the frequencies, types, and distributions of mutations induced in the double-stranded supF gene of pSP189 damaged in vitro and replicated in AlkB-proficient (AlkB (+)) and AlkB-deficient (AlkB (-)) E. coli. AlkB reduced mutagenic potency and increased the survival of CAA-damaged plasmids. Toxicity and mutagenesis data were benchmarked to levels of -adducts and DNA strand breaks measured by LC-MS/MS and a plasmid nicking assay. CAA treatment caused dose-dependent increases in A, C, and 1, N (2)-ethenodeoxyguanosine (1, N (2)-G) and small increases in strand breaks and abasic sites. Mutation frequency increased in plasmids replicated in both AlkB (+) and AlkB (-) cells; however, at the maximum CAA dose, the mutation frequency was 5-fold lower in AlkB (+) than in AlkB (-) cells, indicating that AlkB protected the genome from CAA lesions. Most induced mutations in AlkB (-) cells were G:C to A:T transitions, with lesser numbers of G:C to T:A transversions and A:T to G:C transitions. G:C to A:T and A:T to G:C transitions were lower in AlkB (+) cells than in AlkB (-) cells. Mutational hotspots at G122, G123, and G160 were common to both cell types. Three additional hotspots were found in AlkB (-) cells (C133, T134, and G159), with a decrease in mutation frequency and change in mutational signature in AlkB (+) cells. These results suggest that the AlkB protein contributes to the elimination of exocyclic DNA base adducts, suppressing the toxic and mutagenic consequences induced by this damage and contributing to genetic stability.
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Affiliation(s)
- Min Young Kim
- Department of Biological Engineering, Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Mishina Y, Yang CG, He C. Direct repair of the exocyclic DNA adduct 1,N6-ethenoadenine by the DNA repair AlkB proteins. J Am Chem Soc 2006; 127:14594-5. [PMID: 16231911 PMCID: PMC2432083 DOI: 10.1021/ja055957m] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The exocyclic DNA base adduct 1,N6-ethenoadenine (epsilonA) is directly repaired by the AlkB proteins in vitro.
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Affiliation(s)
- Yukiko Mishina
- Department of Chemistry, The University of Chicago, Illinois 60637, USA
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Zhu S, Wang A, Xia Z. Polymorphisms of DNA repair gene XPD and DNA damage of workers exposed to vinylchloride monomer. Int J Hyg Environ Health 2005; 208:383-90. [PMID: 16217922 DOI: 10.1016/j.ijheh.2005.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Vinyl chloride monomer (VCM) is a human carcinogen. However, the exact mechanism of carcinogenesis remains unclear. 2-Chloroethylene oxide (CEO) and 2-chloroacetaldehyde (CAA), the metabolic intermediates of VCM, induce DNA damage which is mainly repaired by the nucleotide excision repair (NER) pathway. The XPD gene product and the related XPB protein are DNA helicases that are involved in transcription and NER. Polymorphisms of XPD have been implicated in chemical exposure-related health effects. In order to explore the mechanism of VCM-related health effects, a special matched case-control design (exposed workers with DNA damage and without damage) was used to investigate the association between the gene polymorphisms of XPD and DNA damage in 106 male and 44 female workers occupationally exposed to VCM. Exposure and anthropometrics information was collected through in-person interview. Such information was then used to calculate cumulative exposure doses of the workers. DNA damage in peripheral lymphocytes was measured by the single cell gel electrophoresis (SCGE) assay that identified DNA strand breaks. Genomic DNA from lymphocytes was used in genotyping assays. Genotypes of XPD Ile199Met, XPD Asp312Asn, and XPD Lys751Gln were identified by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) procedure. The results indicate that the genotypes of XPD 751Lys/Gln and Gln/Gln were significantly associated with the expression of DNA damages (OR 2.21, P<0.05, 95% CI 1.01-5.13). An interesting observation is the reduction of DNA damage for workers with high VCM exposure and possessing the XPD Asp/Asn and Asn/Asn genotypes (OR 0.33, 95% CI 0.11-0.95). Polymorphisms of XPD may therefore be a major reason of genetic susceptibility in VCM-induced DNA damage and health consequences.
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Affiliation(s)
- Shoumin Zhu
- Department of Occupational Health and Toxicology, Box 288, School of Public Health, Fudan University, Shanghai 200032, PR China
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