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Anderson CJ, Talmane L, Luft J, Connelly J, Nicholson MD, Verburg JC, Pich O, Campbell S, Giaisi M, Wei PC, Sundaram V, Connor F, Ginno PA, Sasaki T, Gilbert DM, López-Bigas N, Semple CA, Odom DT, Aitken SJ, Taylor MS. Strand-resolved mutagenicity of DNA damage and repair. Nature 2024; 630:744-751. [PMID: 38867042 PMCID: PMC11186772 DOI: 10.1038/s41586-024-07490-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 04/30/2024] [Indexed: 06/14/2024]
Abstract
DNA base damage is a major source of oncogenic mutations1. Such damage can produce strand-phased mutation patterns and multiallelic variation through the process of lesion segregation2. Here we exploited these properties to reveal how strand-asymmetric processes, such as replication and transcription, shape DNA damage and repair. Despite distinct mechanisms of leading and lagging strand replication3,4, we observe identical fidelity and damage tolerance for both strands. For small alkylation adducts of DNA, our results support a model in which the same translesion polymerase is recruited on-the-fly to both replication strands, starkly contrasting the strand asymmetric tolerance of bulky UV-induced adducts5. The accumulation of multiple distinct mutations at the site of persistent lesions provides the means to quantify the relative efficiency of repair processes genome wide and at single-base resolution. At multiple scales, we show DNA damage-induced mutations are largely shaped by the influence of DNA accessibility on repair efficiency, rather than gradients of DNA damage. Finally, we reveal specific genomic conditions that can actively drive oncogenic mutagenesis by corrupting the fidelity of nucleotide excision repair. These results provide insight into how strand-asymmetric mechanisms underlie the formation, tolerance and repair of DNA damage, thereby shaping cancer genome evolution.
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Affiliation(s)
- Craig J Anderson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Lana Talmane
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Juliet Luft
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - John Connelly
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
- Edinburgh Pathology, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Laboratory Medicine, NHS Lothian, Edinburgh, UK
| | - Michael D Nicholson
- CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jan C Verburg
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Susan Campbell
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marco Giaisi
- Brain Mosaicism and Tumorigenesis (B400), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pei-Chi Wei
- Brain Mosaicism and Tumorigenesis (B400), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vasavi Sundaram
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Frances Connor
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Paul A Ginno
- Division of Regulatory Genomics and Cancer Evolution (B270), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Takayo Sasaki
- San Diego Biomedical Research Institute, San Diego, CA, USA
| | | | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Colin A Semple
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Division of Regulatory Genomics and Cancer Evolution (B270), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Sarah J Aitken
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - Martin S Taylor
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Chen HJC. Mass Spectrometry Analysis of DNA and Protein Adducts as Biomarkers in Human Exposure to Cigarette Smoking: Acrolein as an Example. Chem Res Toxicol 2023; 36:132-140. [PMID: 36626705 DOI: 10.1021/acs.chemrestox.2c00354] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Acrolein is a major component in cigarette smoke and a product of endogenous lipid peroxidation. It is difficult to distinguish human exposure to acrolein from exogenous sources versus endogenous causes, as components in cigarette smoke can stimulate lipid peroxidation in vivo. Therefore, analysis of acrolein-induced DNA and protein adducts by the highly accurate, sensitive, and specific mass spectrometry-based methods is vital to estimate the degree of damage by this IARC Group 2A carcinogen. This Perspective reviews the analyses of acrolein-induced DNA and protein adducts in humans by mass spectrometry focusing on samples accessible for biomonitoring, including DNA from leukocytes and oral cells and abundant proteins from blood, i.e., hemoglobin and serum albumin.
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Affiliation(s)
- Hauh-Jyun Candy Chen
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection (AIM-HI), National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
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3
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Chen HJC, Cheng SW, Chen NY, Wu DC. Characterization and Quantification of Acrolein-Induced Modifications in Hemoglobin by Mass Spectrometry─Effect of Cigarette Smoking. Chem Res Toxicol 2022; 35:2260-2270. [PMID: 36367988 DOI: 10.1021/acs.chemrestox.2c00262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Exposure to acrolein, the smallest α, β-unsaturated aldehyde, in humans originates from cigarette smoking and other environmental sources, food cooking, and endogenous lipid peroxidation and metabolism. The protein modification caused by acrolein is associated with various diseases, including cancer, cardiovascular, and neurodegenerative diseases. In this study, acrolein-modified human hemoglobin was reduced by sodium borohydride. Thus, three types of modifications, that is, Schiff base, Michael addition, and formyl-dehydropiperidion adducts, were converted to the corresponding stable adducts, leading to mass increases of 40.0313, 58.0419, and 96.0575 Da, respectively. These stable acrolein-modified hemoglobin peptides were identified by nanoflow liquid chromatography coupled to a high-resolution nanoelectrospray ionization tandem mass spectrometry. Among the 26 different types and sites of modifications, 15 of them showed a dose-dependent increase with increasing concentrations of acrolein. To investigate the role of acrolein-induced modifications in smoking and oral cancer, the 15 dose-responsive acrolein-modified peptides, together with three ethylated peptides previously identified, were quantified in oral cancer patients, healthy smokers, and healthy nonsmokers. The results reveal that the relative extents of the Michael-type adduct at α-Lys-16, α-His-50, and β-Lys-59 are significantly higher in smokers (oral cancer and healthy) than in nonsmokers. Areas under the receiver operating characteristic curve of these peptides range from 0.7500 to 0.9375, indicating the ability to discriminate smokers from nonsmokers. Additionally, these acrolein-modified peptides correlate with three ethylated peptides at the N-termini of α- and β-globin, as well as β-His-77, and with the number of cigarettes smoked per day. Therefore, measuring the reduced Michael adducts at α-Lys-16, α-His-50, and β-Lys-59 of hemoglobin from one drop of blood by this sensitive and specific method may reflect the increase of acrolein exposure due to cigarette smoking.
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Affiliation(s)
- Hauh-Jyun Candy Chen
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection (AIM-HI), National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi62142, Taiwan
| | - Shu-Wei Cheng
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection (AIM-HI), National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi62142, Taiwan
| | - Nai-Ying Chen
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection (AIM-HI), National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi62142, Taiwan
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung80708, Taiwan.,Faculty of Medicine, Department of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung80708, Taiwan
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4
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Li Y, Hecht SS. Metabolic Activation and DNA Interactions of Carcinogenic N-Nitrosamines to Which Humans Are Commonly Exposed. Int J Mol Sci 2022; 23:ijms23094559. [PMID: 35562949 PMCID: PMC9105260 DOI: 10.3390/ijms23094559] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
Carcinogenic N-nitrosamine contamination in certain drugs has recently caused great concern and the attention of regulatory agencies. These carcinogens-widely detectable in relatively low levels in food, water, cosmetics, and drugs-are well-established and powerful animal carcinogens. The electrophiles resulting from the cytochrome P450-mediated metabolism of N-nitrosamines can readily react with DNA and form covalent addition products (DNA adducts) that play a central role in carcinogenesis if not repaired. In this review, we aim to provide a comprehensive and updated review of progress on the metabolic activation and DNA interactions of 10 carcinogenic N-nitrosamines to which humans are commonly exposed. Certain DNA adducts such as O6-methylguanine with established miscoding properties play central roles in the cancer induction process, whereas others have been linked to the high incidence of certain types of cancers. We hope the data summarized here will help researchers gain a better understanding of the bioactivation and DNA interactions of these 10 carcinogenic N-nitrosamines and facilitate further research on their toxicologic and carcinogenic properties.
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Affiliation(s)
- Yupeng Li
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA;
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: ; Tel.: +1-612-624-8187
| | - Stephen S. Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA;
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5
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Inhibition of androgen/AR signaling inhibits diethylnitrosamine (DEN) induced tumour initiation and remodels liver immune cell networks. Sci Rep 2021; 11:3646. [PMID: 33574348 PMCID: PMC7878907 DOI: 10.1038/s41598-021-82252-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
A promotional role for androgen receptor (AR) signaling in hepatocellular carcinogenesis is emerging. In pre-clinical models, including diethylnitrosamine- (DEN-) induced hepatocellular carcinoma (HCC), anti-androgen therapies delay hepatocarcinogenesis. However, pharmacologic anti-androgen therapy in advanced HCC patients fails, suggesting that AR plays a role in HCC onset. This study aims to characterize AR expression and function throughout DEN-induced liver inflammation and carcinogenesis and evaluate the efficacy of prophylactic AR antagonism to prevent hepatocarcinogenesis. We demonstrate that pharmacologic AR antagonism with enzalutamide inhibits hepatocellular carcinogenesis. With enzalutamide treatment, we observe decreased CYP2E1 expression, reducing DEN-induced hepatocyte death and DNA ethyl-adducts. AR protein expression analyses show that DEN causes an initial upregulation of AR in portal fibroblasts and leukocytes, but not hepatocytes, suggesting that hepatocyte-autonomous AR signaling is not essential for DEN-induced carcinogenesis. Ablating androgen signaling by surgical castration reduced pre-carcinogen Kupffer cell populations but did not alter DEN-mediated immune cell recruitment nor AR expression. In this study, we identified that anti-androgen interventions modulate mutagenic DNA adducts, tumour initiation, and immune cell composition. Additionally, we find that AR expression in hepatocytes is not present during nor required for early DEN-mediated carcinogenesis.
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6
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He X, Wang P, Wang Y. Mitochondrial Transcription Factor A Binds to and Promotes Mutagenic Transcriptional Bypass of O4-Alkylthymidine Lesions. Anal Chem 2021; 93:1161-1169. [PMID: 33290046 PMCID: PMC7904241 DOI: 10.1021/acs.analchem.0c04224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
O2- and O4-alkylated thymidine lesions are known to be poorly repaired and persist in mammalian tissues. To understand how mammalian cells sense the presence and regulate the repair of these lesions, we employed a quantitative proteomic method to discover regioisomeric O2- and O4-n-butylthymidine (O2- and O4-nBudT)-binding proteins. We were able to identify 21 and 74 candidate DNA damage recognition proteins for O2-nBudT- and O4-nBudT-bearing DNA probes, respectively. Among these proteins, DDB1 and DDB2 selectively bind to O2-nBudT-containing DNA, whereas three high-mobility group (HMG) proteins (i.e., HMGB1, HMGB2, and mitochondrial transcription factor A (TFAM)) exhibit preferential binding to O4-nBudT-bearing DNA. We further demonstrated that TFAM binds directly and selectively with O4-alkyldT-harboring DNA, and the binding capacity depends mainly on the HMG box-A domain of TFAM. We also found that TFAM promotes transcriptional mutagenesis of O4-nBudT and O4-pyridyloxobutylthymidine, which is a DNA adduct induced by tobacco-specific N-nitrosamines, in vitro and in human cells. Together, we explored, for the first time, the interaction proteomes of O-alkyldT lesions, and our study expanded the functions of TFAM by revealing its capability in the recognition of O4-alkyldT-bearing DNA and uncovering its modulation of transcriptional mutagenesis of these lesions in human cells.
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Affiliation(s)
- Xiaomei He
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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Oh J, Xu J, Chong J, Wang D. Molecular basis of transcriptional pausing, stalling, and transcription-coupled repair initiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194659. [PMID: 33271312 DOI: 10.1016/j.bbagrm.2020.194659] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022]
Abstract
Transcription elongation by RNA polymerase II (Pol II) is constantly challenged by numerous types of obstacles that lead to transcriptional pausing or stalling. These obstacles include DNA lesions, DNA epigenetic modifications, DNA binding proteins, and non-B form DNA structures. In particular, lesion-induced prolonged transcriptional blockage or stalling leads to genome instability, cellular dysfunction, and cell death. Transcription-coupled nucleotide excision repair (TC-NER) pathway is the first line of defense that detects and repairs these transcription-blocking DNA lesions. In this review, we will first summarize the recent research progress toward understanding the molecular basis of transcriptional pausing and stalling by different kinds of obstacles. We will then discuss new insights into Pol II-mediated lesion recognition and the roles of CSB in TC-NER.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, United States; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States.
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8
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Liquid chromatography- mass spectrometry for analysis of DNA damages induced by environmental exposure. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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Ma B, Stepanov I, Hecht SS. Recent Studies on DNA Adducts Resulting from Human Exposure to Tobacco Smoke. TOXICS 2019; 7:E16. [PMID: 30893918 PMCID: PMC6468371 DOI: 10.3390/toxics7010016] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/09/2019] [Accepted: 03/13/2019] [Indexed: 12/22/2022]
Abstract
DNA adducts are believed to play a central role in the induction of cancer in cigarette smokers and are proposed as being potential biomarkers of cancer risk. We have summarized research conducted since 2012 on DNA adduct formation in smokers. A variety of DNA adducts derived from various classes of carcinogens, including aromatic amines, polycyclic aromatic hydrocarbons, tobacco-specific nitrosamines, alkylating agents, aldehydes, volatile carcinogens, as well as oxidative damage have been reported. The results are discussed with particular attention to the analytical methods used in those studies. Mass spectrometry-based methods that have higher selectivity and specificity compared to 32P-postlabeling or immunochemical approaches are preferred. Multiple DNA adducts specific to tobacco constituents have also been characterized for the first time in vitro or detected in vivo since 2012, and descriptions of those adducts are included. We also discuss common issues related to measuring DNA adducts in humans, including the development and validation of analytical methods and prevention of artifact formation.
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Affiliation(s)
- Bin Ma
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Irina Stepanov
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Stephen S Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
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10
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Chen HJC, Ip SW. Age-Associated Methylation in Human Hemoglobin and Its Stability on Dried Blood Spots As Analyzed by Nanoflow Liquid Chromatography Tandem Mass Spectrometry. Chem Res Toxicol 2018; 31:1240-1247. [PMID: 30362736 DOI: 10.1021/acs.chemrestox.8b00224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Methylation of biomolecules is involved in many important biological processes. The contributing methylating agents arise from endogenous and exogenous sources (such as cigarette smoking). Human hemoglobin is easily accessible from blood and has been used as a molecular dosimeter for monitoring chemical exposure. We recently developed a method for characterization and quantification of the extents of methylation and ethylation in hemoglobin by nanoflow liquid chromatography tandem mass spectrometry under the selected reaction monitoring mode. Using this method, the relative extents of methylated and ethylated peptides in hemoglobin were quantified in nonsmoking subjects at various ages in this study. Among the nine methylation sites, we found that the extents of methylation were significantly higher in elderly subjects at the N-terminal and His-20 of α-globin, and at the N-terminal and Glu-26 of β-globin. Moreover, the extents of methylation at these sites were significantly correlated with the age of the subjects. On the other hand, no statistically significant difference was found in the ethylated peptides. We also examined the stability of methylated and ethylated hemoglobin when stored on dried blood spot cards. The extents of these modifications on hemoglobin are stable for at least 4 weeks stored at room temperature. Our results suggest that age should be considered as a factor when measuring hemoglobin methylation and that dried blood spot is a valuable biomonitoring technique for hemoglobin modifications in epidemiological studies.
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Affiliation(s)
- Hauh-Jyun Candy Chen
- Department of Chemistry and Biochemistry , National Chung Cheng University , 168 University Road, Ming-Hsiung, Chia-Yi 62142 , Taiwan
| | - Sun Wai Ip
- Department of Chemistry and Biochemistry , National Chung Cheng University , 168 University Road, Ming-Hsiung, Chia-Yi 62142 , Taiwan
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Hu CW, Cooke MS, Chang YJ, Chao MR. Direct-acting DNA ethylating agents associated with tobacco use primarily originate from the tobacco itself, not combustion. JOURNAL OF HAZARDOUS MATERIALS 2018; 358:397-404. [PMID: 30005251 DOI: 10.1016/j.jhazmat.2018.07.011] [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: 04/07/2018] [Revised: 06/27/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
Unburnt tobacco and tobacco smoke contain a variety of carcinogens, exposure to which are causally associated with the incidence of several human cancers. Herein, we used isotope-dilution LC-MS/MS for the quantification of alkylated purines in DNA, following in vitro exposure to aqueous extracts of tobacco itself, and tobacco smoke. Our results demonstrated the presence of direct-acting ethylating agent(s) in unburnt tobacco, which 4.0-6.3 times exceeded that in the particulate phase of sidestream cigarette smoke and 6.8-8.9 times exceeded that in mainstream smoke. Interestingly, particulate phase of sidestream cigarette smoke exhibited higher ethylating potency than that in mainstream smoke. This finding refutes the previous assumptions that the ethylating agent(s) associated with smoking, are derived from cigarette smoke. Indeed, our data show that combustion of tobacco actually decreases the ethylating potency of tobacco. Although the identity of this agent(s) remains unknown, our data suggest that it is highly hydrophilic, and hence likely to be easily extracted by saliva. This would allow intimate contact with the tissues of the oropharyngeal cavity. Taken together, these results have profound implications for tobacco use, in particular for tobacco chewers and passive smokers, whose exposure to ethylating agent(s) is greater than previously thought.
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Affiliation(s)
- Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung 402, Taiwan; Oxidative Stress Group, Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Yuan-Jhe Chang
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Mu-Rong Chao
- Oxidative Stress Group, Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA; Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan; Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan.
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12
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Wu J, Wang P, Li L, You C, Wang Y. Cytotoxic and mutagenic properties of minor-groove O2-alkylthymidine lesions in human cells. J Biol Chem 2018; 293:8638-8644. [PMID: 29685891 DOI: 10.1074/jbc.ra118.003133] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/11/2018] [Indexed: 12/17/2022] Open
Abstract
Endogenous metabolism, environmental exposure, and cancer chemotherapy can lead to alkylation of DNA. It has been well documented that, among the different DNA alkylation products, minor-groove O2-alkylthymidine (O2-alkyldT) lesions are inefficiently repaired. In the present study, we examined how seven O2-alkyldT lesions, with the alkyl group being a Me, Et, nPr, iPr, nBu, iBu, or sBu, are recognized by the DNA replication machinery in human cells. We found that the replication bypass efficiencies of these lesions decrease with increasing length of the alkyl chain, and that these lesions induce substantial frequencies of T→A and T→G mutations. Replication experiments using isogenic cells deficient in specific translesion synthesis (TLS) DNA polymerases revealed that the absence of polymerase η or polymerase ζ, but not polymerase κ or polymerase ι, significantly decreased both the bypass efficiencies and the mutation frequencies for those O2-alkyldT lesions carrying a straight-chain alkyl group. Moreover, the mutagenic properties of the O2-alkyldT lesions were influenced by the length and topology of the alkyl chain and by TLS polymerases. Together, our results provide important new knowledge about the cytotoxic and mutagenic properties of O2-alkyldT lesions, and illustrate the roles of TLS polymerases in replicative bypass of these lesions in human cells.
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Affiliation(s)
- Jun Wu
- From the Department of Chemistry and
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403
| | - Lin Li
- From the Department of Chemistry and
| | | | - Yinsheng Wang
- From the Department of Chemistry and .,Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403
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13
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Hu K, Zhao G, Liu J, Jia L, Xie F, Zhang S, Liu H, Liu M. Simultaneous quantification of three alkylated‑purine adducts in human urine using sulfonic acid poly(glycidyl methacrylate‑divinylbenzene)-based microspheres as sorbent combined with LC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1081-1082:15-24. [DOI: 10.1016/j.jchromb.2018.02.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/06/2018] [Accepted: 02/18/2018] [Indexed: 01/03/2023]
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14
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Chen HJC, Ip SW, Lin FD. Simultaneous Mass Spectrometric Analysis of Methylated and Ethylated Peptides in Human Hemoglobin: Correlation with Cigarette Smoking. Chem Res Toxicol 2017; 30:2074-2083. [DOI: 10.1021/acs.chemrestox.7b00234] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hauh-Jyun Candy Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
| | - Sun Wai Ip
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
| | - Fu-Di Lin
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
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15
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Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis. Proc Natl Acad Sci U S A 2017; 114:E7082-E7091. [PMID: 28784758 DOI: 10.1073/pnas.1708748114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Alkylated DNA lesions, induced by both exogenous chemical agents and endogenous metabolites, interfere with the efficiency and accuracy of DNA replication and transcription. However, the molecular mechanisms of DNA alkylation-induced transcriptional stalling and mutagenesis remain unknown. In this study, we systematically investigated how RNA polymerase II (pol II) recognizes and bypasses regioisomeric O2-, N3-, and O4-ethylthymidine (O2-, N3-, and O4-EtdT) lesions. We observed distinct pol II stalling profiles for the three regioisomeric EtdT lesions. Intriguingly, pol II stalling at O2-EtdT and N3-EtdT sites is exacerbated by TFIIS-stimulated proofreading activity. Assessment for the impact of the EtdT lesions on individual fidelity checkpoints provided further mechanistic insights, where the transcriptional lesion bypass routes for the three EtdT lesions are controlled by distinct fidelity checkpoints. The error-free transcriptional lesion bypass route is strongly favored for the minor-groove O2-EtdT lesion. In contrast, a dominant error-prone route stemming from GMP misincorporation was observed for the major-groove O4-EtdT lesion. For the N3-EtdT lesion that disrupts base pairing, multiple transcriptional lesion bypass routes were found. Importantly, the results from the present in vitro transcriptional studies are well correlated with in vivo transcriptional mutagenesis analysis. Finally, we identified a minor-groove-sensing motif from pol II (termed Pro-Gate loop). The Pro-Gate loop faces toward the minor groove of RNA:DNA hybrid and is involved in modulating the translocation of minor-groove alkylated DNA template after nucleotide incorporation opposite the lesion. Taken together, this work provides important mechanistic insights into transcriptional stalling, lesion bypass, and mutagenesis of alkylated DNA lesions.
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16
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Williams NL, Wang P, Wang Y. Replicative Bypass of O 2-Alkylthymidine Lesions in Vitro. Chem Res Toxicol 2016; 29:1755-1761. [PMID: 27611246 DOI: 10.1021/acs.chemrestox.6b00252] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA alkylation represents a major type of DNA damage and is generally unavoidable due to ubiquitous exposure to various exogenous and endogenous sources of alkylating agents. Among the alkylated DNA lesions, O2-alkylthymidines (O2-alkyldT) are known to be persistent and poorly repaired in mammalian systems and have been shown to accumulate in the esophagus, lung, and liver tissue of rats treated with tobacco-specific N-nitrosamines, i.e., 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N'-nitrosonornicotine (NNN). In this study, we assessed the replicative bypass of a comprehensive set of O2-alkyldT lesions, with the alkyl group being a Me, Et, nPr, iPr, nBu, iBu, or sBu, in template DNA by conducting primer extension assays with the use of major translesion synthesis DNA polymerases. The results showed that human Pol η and, to a lesser degree, human Pol κ, but not human polymerase ι or yeast polymerase ζ, were capable of bypassing all O2-alkyldT lesions and extending the primer to generate full-length replication products. Data from steady-state kinetic measurements showed that human Pol η exhibited high frequencies of misincorporation of dCMP opposite those O2-alkyldT lesions bearing a longer straight-chain alkyl group. However, the nucleotide misincorporation opposite branched-chain lesions was not selective, with dCMP, dGMP, and dTMP being inserted at similar efficiencies, though the total frequencies of nucleotide misincorporation opposite the branched-chain lesions differed and followed the order of O2-iPrdT > O2-iBudT > O2-sBudT. Together, the results from the present study provided important knowledge about the effects of the length and structure of the alkyl group in the O2-alkyldT lesions on the fidelity and efficiency of DNA replication mediated by human Pol η.
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Affiliation(s)
- Nicole L Williams
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
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17
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Wu J, Li L, Wang P, You C, Williams NL, Wang Y. Translesion synthesis of O4-alkylthymidine lesions in human cells. Nucleic Acids Res 2016; 44:9256-9265. [PMID: 27466394 PMCID: PMC5100597 DOI: 10.1093/nar/gkw662] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/13/2016] [Indexed: 12/18/2022] Open
Abstract
Environmental exposure, endogenous metabolism and cancer chemotherapy can give rise to alkylation of DNA, and the resulting alkylated thymidine (alkyldT) lesions were found to be poorly repaired and persistent in mammalian tissues. Unrepaired DNA lesions may compromise genomic integrity by inhibiting DNA replication and inducing mutations in these processes. In this study, we explored how eight O4-alkyldT lesions, with the alkyl group being a Me, Et, nPr, iPr, nBu, iBu, (R)-sBu and (S)-sBu, are recognized by DNA replication machinery in HEK293T human embryonic kidney cells. We found that the O4-alkyldT lesions are moderately blocking to DNA replication, with the bypass efficiencies ranging from 20 to 33% in HEK293T cells, and these lesions induced substantial frequencies T→C transition mutation. We also conducted the replication experiments in the isogenic cells where individual translesion synthesis (TLS) DNA polymerases were depleted by the CRISPR/Cas9 genome editing method. Our results showed that deficiency in Pol η or Pol ζ, but not Pol κ or Pol ι, led to pronounced drops in bypass efficiencies for all the O4-alkyldT lesions except O4-MedT. In addition, depletion of Pol ζ resulted in significant decreases in T→C mutation frequencies for all the O4-alkyldT lesions except O4-MedT and O4-nBudT. Thus, our study provided important new knowledge about the cytotoxic and mutagenic properties of the O4-alkyldT lesions and defined the roles of TLS polymerases in bypassing these lesions in human cells.
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Affiliation(s)
- Jun Wu
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Lin Li
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521-0403, USA
| | - Changjun You
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Nicole L Williams
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521-0403, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA .,Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521-0403, USA
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18
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You C, Wang P, Nay SL, Wang J, Dai X, O’Connor TR, Wang Y. Roles of Aag, Alkbh2, and Alkbh3 in the Repair of Carboxymethylated and Ethylated Thymidine Lesions. ACS Chem Biol 2016; 11:1332-8. [PMID: 26930515 DOI: 10.1021/acschembio.6b00085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Environmental and endogenous genotoxic agents can result in a variety of alkylated and carboxymethylated DNA lesions, including N3-ethylthymidine (N3-EtdT), O(2)-EtdT, and O(4)-EtdT as well as N3-carboxymethylthymidine (N3-CMdT) and O(4)-CMdT. By using nonreplicative double-stranded vectors harboring a site-specifically incorporated DNA lesion, we assessed the potential roles of alkyladenine DNA glycosylase (Aag); alkylation repair protein B homologue 2 (Alkbh2); or Alkbh3 in modulating the effects of N3-EtdT, O(2)-EtdT, O(4)-EtdT, N3-CMdT, or O(4)-CMdT on DNA transcription in mammalian cells. We found that the depletion of Aag did not significantly change the transcriptional inhibitory or mutagenic properties of all five examined lesions, suggesting a negligible role of Aag in the repair of these DNA adducts in mammalian cells. In addition, our results revealed that N3-EtdT, but not other lesions, could be repaired by Alkbh2 and Alkbh3 in mammalian cells. Furthermore, we demonstrated the direct reversal of N3-EtdT by purified human Alkbh2 protein in vitro. These findings provided important new insights into the repair of the carboxymethylated and alkylated thymidine lesions in mammalian cells.
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Affiliation(s)
- Changjun You
- Department
of Chemistry, University of California, Riverside, California, United States
| | - Pengcheng Wang
- Environmental
Toxicology Graduate Program, University of California, Riverside, California, United States
| | - Stephanie L. Nay
- Department
of Cancer Biology, Beckman Research Institute, Duarte, California, United States
| | - Jianshuang Wang
- Department
of Chemistry, University of California, Riverside, California, United States
| | - Xiaoxia Dai
- Department
of Chemistry, University of California, Riverside, California, United States
| | - Timothy R. O’Connor
- Department
of Cancer Biology, Beckman Research Institute, Duarte, California, United States
| | - Yinsheng Wang
- Department
of Chemistry, University of California, Riverside, California, United States
- Environmental
Toxicology Graduate Program, University of California, Riverside, California, United States
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19
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Williams NL, Wang P, Wu J, Wang Y. In Vitro Lesion Bypass Studies of O(4)-Alkylthymidines with Human DNA Polymerase η. Chem Res Toxicol 2016; 29:669-75. [PMID: 27002924 DOI: 10.1021/acs.chemrestox.5b00509] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Environmental exposure and endogenous metabolism can give rise to DNA alkylation. Among alkylated nucleosides, O(4)-alkylthymidine (O(4)-alkyldT) lesions are poorly repaired in mammalian systems and may compromise the efficiency and fidelity of cellular DNA replication. To cope with replication-stalling DNA lesions, cells are equipped with translesion synthesis DNA polymerases that are capable of bypassing various DNA lesions. In this study, we assessed human DNA polymerase η (Pol η)-mediated bypass of various O(4)-alkyldT lesions, with the alkyl group being Me, Et, nPr, iPr, nBu, iBu, (R)-sBu, or (S)-sBu, in template DNA by conducting primer extension and steady-state kinetic assays. Our primer extension assay results revealed that human Pol η, but not human polymerases κ and ι or yeast polymerase ζ, was capable of bypassing all O(4)-alkyldT lesions and extending the primer to generate full-length replication products. Data from steady-state kinetic measurements showed that Pol η preferentially misincorporated dGMP opposite O(4)-alkyldT lesions with a straight-chain alkyl group. The nucleotide misincorporation opposite most lesions with a branched-chain alkyl group was, however, not selective, where dCMP, dGMP, and dTMP were inserted at similar efficiencies opposite O(4)-iPrdT, O(4)-iBudT, and O(4)-(R)-sBudT. These results provide important knowledge about the effects of the length and structure of the alkyl group in O(4)-alkyldT lesions on the fidelity and efficiency of DNA replication mediated by human Pol η.
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Affiliation(s)
- Nicole L Williams
- Environmental Toxicology Graduate Program, ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
| | - Jiabin Wu
- Environmental Toxicology Graduate Program, ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
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20
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You C, Wang J, Dai X, Wang Y. Transcriptional inhibition and mutagenesis induced by N-nitroso compound-derived carboxymethylated thymidine adducts in DNA. Nucleic Acids Res 2015; 43:1012-8. [PMID: 25572317 PMCID: PMC4333421 DOI: 10.1093/nar/gku1391] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
N-nitroso compounds represent a common type of environmental and endogenous DNA-damaging agents. After metabolic activation, many N-nitroso compounds are converted into a diazoacetate intermediate that can react with nucleobases to give carboxymethylated DNA adducts such as N3-carboxymethylthymidine (N3-CMdT) and O4-carboxymethylthymidine (O4-CMdT). In this study, we constructed non-replicative plasmids carrying a single N3-CMdT or O4-CMdT, site-specifically positioned in the transcribed strand, to investigate how these lesions compromise the flow of genetic information during transcription. Our results revealed that both N3-CMdT and O4-CMdT substantially inhibited DNA transcription mediated by T7 RNA polymerase or human RNA polymerase II in vitro and in human cells. In addition, we found that N3-CMdT and O4-CMdT were miscoding lesions and predominantly directed the misinsertion of uridine and guanosine, respectively. Our results also suggested that these carboxymethylated thymidine lesions may constitute efficient substrates for transcription-coupled nucleotide excision repair in human cells. These findings provided important new insights into the biological consequences of the carboxymethylated DNA lesions in living cells.
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Affiliation(s)
- Changjun You
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Jianshuang Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Xiaoxia Dai
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
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21
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You C, Wang P, Dai X, Wang Y. Transcriptional bypass of regioisomeric ethylated thymidine lesions by T7 RNA polymerase and human RNA polymerase II. Nucleic Acids Res 2014; 42:13706-13. [PMID: 25404131 PMCID: PMC4267633 DOI: 10.1093/nar/gku1183] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Alkylative damage to DNA can be induced by environmental chemicals, endogenous metabolites and some commonly prescribed chemotherapeutic agents. The regioisomeric N3-, O(2)- and O(4)-ethylthymidine (N3-, O(2)- and O(4)-EtdT, respectively) represent an important class of ethylated DNA lesions. Using nonreplicative double-stranded vectors containing an N3-EtdT, O(2)-EtdT or O(4)-EtdT at a defined site in the template strand, herein we examined the effects of these lesions on DNA transcription mediated by single-subunit T7 RNA polymerase or multisubunit human RNA polymerase II in vitro and in human cells. We found that O(4)-EtdT is highly mutagenic and exclusively induces the misincorporation of guanine opposite the lesion, whereas N3-EtdT and O(2)-EtdT display promiscuous miscoding properties during transcription. In addition, N3-EtdT and O(2)-EtdT were found to inhibit strongly DNA transcription in vitro and in certain human cells. Moreover, N3-EtdT, but not O(2)-EtdT or O(4)-EtdT, is an efficient substrate for transcription-coupled nucleotide excision repair. These findings provide new important insights into how these alkylated DNA lesions compromise the flow of genetic information, which may help to understand the risk of these lesions in living cells.
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Affiliation(s)
- Changjun You
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521-0403, USA
| | - Xiaoxia Dai
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521-0403, USA
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22
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Zhai Q, Wang P, Cai Q, Wang Y. Syntheses and characterizations of the in vivo replicative bypass and mutagenic properties of the minor-groove O2-alkylthymidine lesions. Nucleic Acids Res 2014; 42:10529-37. [PMID: 25120272 PMCID: PMC4176383 DOI: 10.1093/nar/gku748] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Endogenous metabolism, environmental exposure, and treatment with some chemotherapeutic agents can all give rise to DNA alkylation, which can occur on the phosphate backbone as well as the ring nitrogen or exocyclic nitrogen and oxygen atoms of nucleobases. Previous studies showed that the minor-groove O2-alkylated thymidine (O2-alkyldT) lesions are poorly repaired and persist in mammalian tissues. In the present study, we synthesized oligodeoxyribonucleotides harboring seven O2-alkyldT lesions, with the alkyl group being a Me, Et, nPr, iPr, nBu, iBu or sBu, at a defined site and examined the impact of these lesions on DNA replication in Escherichia coli cells. Our results demonstrated that the replication bypass efficiencies of the O2-alkyldT lesions decreased with the chain length of the alkyl group, and these lesions directed promiscuous nucleotide misincorporation in E. coli cells. We also found that deficiency in Pol V, but not Pol II or Pol IV, led to a marked drop in bypass efficiencies for most O2-alkyldT lesions. We further showed that both Pol IV and Pol V were essential for the misincorporation of dCMP opposite these minor-groove DNA lesions, whereas only Pol V was indispensable for the T→A transversion introduced by these lesions. Depletion of Pol II, however, did not lead to any detectable alterations in mutation frequencies for any of the O2-alkyldT lesions. Thus, our study provided important new knowledge about the cytotoxic and mutagenic properties of the O2-alkyldT lesions and revealed the roles of the SOS-induced DNA polymerases in bypassing these lesions in E. coli cells.
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Affiliation(s)
- Qianqian Zhai
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | - Qian Cai
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
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23
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Dudley E, Bond L. Mass spectrometry analysis of nucleosides and nucleotides. MASS SPECTROMETRY REVIEWS 2014; 33:302-31. [PMID: 24285362 DOI: 10.1002/mas.21388] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/03/2013] [Accepted: 05/03/2013] [Indexed: 05/12/2023]
Abstract
Mass spectrometry has been widely utilised in the study of nucleobases, nucleosides and nucleotides as components of nucleic acids and as bioactive metabolites in their own right. In this review, the application of mass spectrometry to such analysis is overviewed in relation to various aspects regarding the analytical mass spectrometric and chromatographic techniques applied and also the various applications of such analysis.
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Affiliation(s)
- Ed Dudley
- Institute of Mass Spectrometry, College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
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24
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Zhai Q, Wang P, Wang Y. Cytotoxic and mutagenic properties of regioisomeric O²-, N3- and O⁴-ethylthymidines in bacterial cells. Carcinogenesis 2014; 35:2002-6. [PMID: 24710626 DOI: 10.1093/carcin/bgu085] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Exposure to environmental agents and endogenous metabolism can both give rise to DNA alkylation. Thymine is known to be alkylated at O(2), N3 and O(4) positions; however, it remains poorly explored how the regioisomeric alkylated thymidine lesions compromise the flow of genetic information by perturbing DNA replication in cells. Herein, we assessed the differential recognition of the regioisomeric O(2)-, N3- and O(4)-ethylthymidine (O(2)-, N3- and O(4)-EtdT) by the DNA replication machinery of Escherichia coli cells. We found that O(4)-EtdT did not inhibit appreciably DNA replication, whereas O(2)- and N3-EtdT were strongly blocking to DNA replication. In addition, O(4)-EtdT induced a very high frequency of T→C mutation, whereas nucleotide incorporation opposite O(2)- and N3-EtdT was promiscuous. Replication experiments with the use of polymerase-deficient cells revealed that Pol V constituted the major polymerase for the mutagenic bypass of all three EtdT lesions, though Pol IV also contributed to the T→G mutation induced by O(2)- and N3-EtdT. The distinct cytotoxic and mutagenic properties of the three regioisomeric lesions could be attributed to their unique chemical properties.
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Affiliation(s)
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
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25
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Yue L, Wei Y, Chen J, Shi H, Liu Q, Zhang Y, He J, Guo L, Zhang T, Xie J, Peng S. Abundance of Four Sulfur Mustard-DNA Adducts ex Vivo and in Vivo Revealed by Simultaneous Quantification in Stable Isotope Dilution–Ultrahigh Performance Liquid Chromatography–Tandem Mass Spectrometry. Chem Res Toxicol 2014; 27:490-500. [DOI: 10.1021/tx4003403] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Lijun Yue
- State Key Laboratory
of Antitoxic Drugs and Toxicology, and Laboratory of Toxicant Analysis,
Institute of Pharmacology and Toxicology, Academy of Military Medical
Sciences, No. 27 Taiping Road, Haidian District 100850, Beijing, China
- Beijing Institute
for Disease Control and Prevention, No. 20 Dongdajie Street, Fengtai District 100071, Beijing, China
| | - Yuxia Wei
- State Key Laboratory
of Antitoxic Drugs and Toxicology, and Laboratory of Toxicant Analysis,
Institute of Pharmacology and Toxicology, Academy of Military Medical
Sciences, No. 27 Taiping Road, Haidian District 100850, Beijing, China
| | - Jia Chen
- State Key Laboratory
of Antitoxic Drugs and Toxicology, and Laboratory of Toxicant Analysis,
Institute of Pharmacology and Toxicology, Academy of Military Medical
Sciences, No. 27 Taiping Road, Haidian District 100850, Beijing, China
| | - Huiqin Shi
- Beijing Institute
for Disease Control and Prevention, No. 20 Dongdajie Street, Fengtai District 100071, Beijing, China
| | - Qin Liu
- State Key Laboratory
of Antitoxic Drugs and Toxicology, and Laboratory of Toxicant Analysis,
Institute of Pharmacology and Toxicology, Academy of Military Medical
Sciences, No. 27 Taiping Road, Haidian District 100850, Beijing, China
| | - Yajiao Zhang
- State Key Laboratory
of Antitoxic Drugs and Toxicology, and Laboratory of Toxicant Analysis,
Institute of Pharmacology and Toxicology, Academy of Military Medical
Sciences, No. 27 Taiping Road, Haidian District 100850, Beijing, China
| | - Jun He
- Beijing Institute
for Disease Control and Prevention, No. 20 Dongdajie Street, Fengtai District 100071, Beijing, China
| | - Lei Guo
- State Key Laboratory
of Antitoxic Drugs and Toxicology, and Laboratory of Toxicant Analysis,
Institute of Pharmacology and Toxicology, Academy of Military Medical
Sciences, No. 27 Taiping Road, Haidian District 100850, Beijing, China
| | - Tingfen Zhang
- Beijing Institute
for Disease Control and Prevention, No. 20 Dongdajie Street, Fengtai District 100071, Beijing, China
| | - Jianwei Xie
- State Key Laboratory
of Antitoxic Drugs and Toxicology, and Laboratory of Toxicant Analysis,
Institute of Pharmacology and Toxicology, Academy of Military Medical
Sciences, No. 27 Taiping Road, Haidian District 100850, Beijing, China
| | - Shuangqing Peng
- Beijing Institute
for Disease Control and Prevention, No. 20 Dongdajie Street, Fengtai District 100071, Beijing, China
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26
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Chen HJC, Lin CR. Noninvasive measurement of smoking-associated N(3)-ethyladenine and N(7)-ethylguanine in human salivary DNA by stable isotope dilution nanoflow liquid chromatography-nanospray ionization tandem mass spectrometry. Toxicol Lett 2013; 225:27-33. [PMID: 24300169 DOI: 10.1016/j.toxlet.2013.11.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 11/22/2013] [Indexed: 10/25/2022]
Abstract
Evidence showed that ethylating agents are contained in cigarette smoke, which damage DNA producing ethylated DNA adducts, including N(3)-ethyladenine (3-EtAde) and N(7)-ethylguanine (7-EtGua). These two ethylpurines can be depurinated spontaneously and be repaired by enzymes and they have been detected in human urine. In this study, a highly specific and sensitive assay based on stable isotope dilution nanoflow liquid chromatography nanospray ionization tandem mass spectrometry (nanoLC-NSI/MS/MS) was used to measure 3-EtAde and 7-EtGua in human salivary DNA. These ethylpurines were released from DNA by neutral thermal hydrolysis and then enriched by a solid-phase extraction column before nanoLC-NSI/MS/MS analysis. The detection limits (S/N≥3) of 3-EtA and 7-EtG were 15 fg (92 amol) and 10 fg (56 amol), respectively, injected on-column. The lower quantification limits of 3-EtAde and 7-EtGua were both 100 fg, i.e. 620 and 560 amol, respectively, corresponding to 9.4 and 8.6 adducts in 10(9) normal nucleotides, respectively, starting with as little as 20 μg of DNA isolated from an average of 3 mL of saliva. The mean (±SD) levels of 3-EtAde in 15 smokers and 15 nonsmokers were 12.6±7.0 and 9.7±5.3 in 10(8) normal nucleotides, respectively, while those of 7-EtGua were 14.1±8.2 and 3.8±2.8 in 10(8) normal nucleotides in smokers and nonsmokers, respectively. Levels of 7-EtGua, but not 3-EtAde, were statistically significantly higher in smokers than in nonsmokers (p<0.0001). Furthermore, salivary 7-EtGua levels are significantly correlated with the number of cigarettes smoked per day as well as with the smoking index. This highly specific and sensitive stable isotope dilution nanoLC-NSI/MS/MS assay might be feasible in measuring 7-EtGua in human salivary DNA as a noninvasive biomarker for DNA damage induced by cigarette smoking.
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Affiliation(s)
- Hauh-Jyun Candy Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan.
| | - Chao-Ray Lin
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
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27
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Chen HJC, Lin CR. Simultaneous quantification of ethylpurine adducts in human urine by stable isotope dilution nanoflow liquid chromatography nanospray ionization tandem mass spectrometry. J Chromatogr A 2013; 1322:69-73. [DOI: 10.1016/j.chroma.2013.10.092] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/29/2013] [Accepted: 10/29/2013] [Indexed: 11/28/2022]
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28
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Andersen N, Wang P, Wang Y. Replication across regioisomeric ethylated thymidine lesions by purified DNA polymerases. Chem Res Toxicol 2013; 26:1730-8. [PMID: 24134187 DOI: 10.1021/tx4002995] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Causal links exist between smoking cigarettes and cancer development. Some genotoxic agents in cigarette smoke are capable of alkylating nucleobases in DNA, and higher levels of ethylated DNA lesions were observed in smokers than in nonsmokers. In this study, we examined comprehensively how the regioisomeric O(2)-, N3-, and O(4)-ethylthymidine (O(2)-, N3-, and O(4)-EtdT, respectively) perturb DNA replication mediated by purified human DNA polymerases (hPols) η, κ, and ι, yeast DNA polymerase ζ (yPol ζ), and the exonuclease-free Klenow fragment (Kf(-)) of Escherichia coli DNA polymerase I. Our results showed that hPol η and Kf(-) could bypass all three lesions and generate full-length replication products, whereas hPol ι stalled after inserting a single nucleotide opposite the lesions. Bypass conducted by hPol κ and yPol ζ differed markedly among the three lesions. Consistent with its known ability to efficiently bypass the minor groove N(2)-substituted 2'-deoxyguanosine lesions, hPol κ was able to bypass O(2)-EtdT, though it experienced great difficulty in bypassing N3-EtdT and O(4)-EtdT. yPol ζ was only modestly blocked by O(4)-EtdT, but the polymerase was strongly hindered by O(2)-EtdT and N3-EtdT. LC-MS/MS analysis of the replication products revealed that DNA synthesis opposite O(4)-EtdT was highly error-prone, with dGMP being preferentially inserted, while the presence of O(2)-EtdT and N3-EtdT in template DNA directed substantial frequencies of misincorporation of dGMP and, for hPol ι and Kf(-), dTMP. Thus, our results suggested that O(2)-EtdT and N3-EtdT may also contribute to the AT → TA and AT → GC mutations observed in cells and tissues of animals exposed to ethylating agents.
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Affiliation(s)
- Nisana Andersen
- Department of Chemistry and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
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Chen HJC, Lee CR. Detection and simultaneous quantification of three smoking-related ethylthymidine adducts in human salivary DNA by liquid chromatography tandem mass spectrometry. Toxicol Lett 2013; 224:101-7. [PMID: 24140497 DOI: 10.1016/j.toxlet.2013.10.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 11/26/2022]
Abstract
Smoking cigarette increases levels of certain ethylated DNA adducts in certain tissues and urine. Cigarette smoking is a major risk factor of various cancers and DNA ethylation is involved in smoking-related carcinogenesis. Among the ethylated DNA adducts, O(2)-ethylthymidine (O(2)-edT) and the promutagenic O(4)-ethylthymidine (O(4)-edT) are poorly repaired and they can accumulate in vivo. Using an accurate, highly sensitive, and quantitative assay based on stable isotope dilution nanoflow liquid chromatography-nanospray ionization tandem mass spectrometry (nanoLC-NSI/MS/MS), O(2)-edT, N(3)-edT (N(3)-ethylthymidine), and O(4)-edT adducts in human salivary DNA were simultaneous detected and quantified. Saliva is easily accessible and available and it can be a potential target in searching for noninvasive biomarkers. Under the highly selected reaction monitoring (H-SRM) mode, salivary samples from 20 smokers and 13 nonsmokers were analyzed. Starting with 50 μg of DNA isolated from about 3.5 mL of saliva, levels of O(2)-edT, N(3)-edT, and O(4)-edT in 20 smokers' salivary DNA samples were 5.3±6.2, 4.5±5.7, 4.2±8.0 in 10(8) normal nucleotides, respectively, while those in 13 nonsmokers were non-detectable. In addition, statistically significant correlations (p<0.0001) were observed between levels of O(2)-edT and N(3)-edT (γ=0.7388), between levels of O(2)-edT and O(4)-edT (γ=0.8839), and between levels of N(3)-edT, and O(4)-edT (γ=0.7835). To the best of our knowledge, this is the first report of detection and quantification of these three ethylthymidine adducts in human salivary DNA, which might be potential biomarkers for exposure to ethylating agents and possibly for cancer risk assessment.
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Affiliation(s)
- Hauh-Jyun Candy Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan.
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The advantages of microflow LC–MS/MS compared with conventional HPLC–MS/MS for the analysis of methotrexate from human plasma. Bioanalysis 2013; 5:1387-96. [DOI: 10.4155/bio.13.73] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background: In support of bioanalysis, there has always been a desire to improve detection limits and reduce scale. Microflow LC (MFLC) coupled with MS accomplishes both of these goals. Results: As such, MFLC coupled with an MS system was used to generate bioanalytical validation data that met US FDA criteria. The MFLC–MS/MS data was compared with the same method with the use of conventional HPLC–MS/MS and a more than 14× S/N improvement was found with the MFLC–MS/MS method. Methotrexate was used as a model molecule to demonstrate the validation of the method from human plasma. The MFLC–MS/MS method was demonstrated to be accurate (±7%) and precise (12.9% at the LLOQ and a maximum of 11.6% at all other concentrations) across the dynamic range of the assay (1–1000 ng/ml) and compared well with the HPLC–MS/MS method. The MFLC bioanalytical validation was performed at a flow rate of 35 µl/min on a 0.5-mm inner diameter (I.D.) column, whereas, for the same linear velocities on the 2.0-mm I.D. column, the conventional HPLC bioanalytical validation was performed at 700 µl/min. Since the flow rate of the MFLC system is 20-times less than the HPLC system, the consumable solvent and disposal cost to perform the MFLC validation was significantly less. Conclusion: MFLC–MS/MS can be used to perform bioanalytical method validations with increased MS signal, reduced source contamination and reduced solvent consumption.
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Affiliation(s)
- Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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Chen HJC, Liu YF. Simultaneous quantitative analysis of N3-ethyladenine and N7-ethylguanine in human leukocyte deoxyribonucleic acid by stable isotope dilution capillary liquid chromatography-nanospray ionization tandem mass spectrometry. J Chromatogr A 2012; 1271:86-94. [PMID: 23228920 DOI: 10.1016/j.chroma.2012.11.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/07/2012] [Accepted: 11/10/2012] [Indexed: 11/30/2022]
Abstract
Cigarette smoke contains ethylating agents which damage DNA producing ethylated DNA adducts, such as N(3)-ethyladenine (3-EtAde), N(7)-ethylguanine (7-EtGua), and regioisomers of ethylthymine. Among them, 3-EtAde and 7-EtGua are present in human urine and their levels are higher in smokers than in nonsmokers. The amount of ethylated DNA adducts in tissue DNA represents the steady-state levels of DNA adducts resulting from the ethylating agent after repair in vivo. In this study, we have developed a highly sensitive, accurate, and quantitative assay for simultaneous detection and quantification of 3-EtAde and 7-EtGua by stable isotope dilution capillary liquid chromatography-nanospray ionization tandem mass spectrometry (capLC-NSI/MS/MS). Under the highly selective reaction monitoring (H-SRM) mode, the detection limit of 3-EtAde and 7-EtGua injected on-column was 5.0 fg (31 amol) and 10 fg (56 amol), respectively. The quantification limit for the entire assay was 50 and 100 fg of 3-EtAde and 7-EtGua, corresponding to 4.7 and 8.6 adducts in 10(9) normal nucleotides, respectively, starting with 20 μg of DNA isolated from <1 mL of blood and injecting an equivalent of 4 μg of DNA on-column. The mean (±SD) levels of 3-EtAde and 7-EtGua in leukocyte DNA from 20 smokers were 16.0±7.8 and 9.7±8.3 in 10(8) normal nucleotides, respectively, which were statistically significantly higher than those of 5.4±2.6 3-EtAde and 0.3±0.8 7-EtGua in 10(8) normal nucleotides from 20 nonsmokers (p<0.0001). The levels of 3-EtAde and 7-EtGua in these 40 leukocyte DNA samples are positively correlated (γ=0.6970, p<0.0001). Furthermore, there are statistically significant associations between the number of cigarettes smoked per day, as well as the smoking index, and the levels of 3-EtAde and 7-EtGua. Levels of 3-EtAde and 7-EtGua are compared to those of ethylthymidine adducts. To our knowledge, this is the first assay for simultaneous quantification of 3-EtAde and 7-EtGua in the same DNA sample and is the first report of 3-EtAde in human DNA. This highly sensitive and specific stable isotope dilution capLC-NSI/MS/MS assay should be useful in measuring 3-EtAde and 7-EtGua in human leukocyte DNA as potential biomarkers for smoking-related cancers.
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Affiliation(s)
- Hauh-Jyun Candy Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan.
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