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De Graeve M, Van de Walle E, Van Hecke T, De Smet S, Vanhaecke L, Hemeryck LY. Exploration and optimization of extraction, analysis and data normalization strategies for mass spectrometry-based DNA adductome mapping and modeling. Anal Chim Acta 2023; 1274:341578. [PMID: 37455087 DOI: 10.1016/j.aca.2023.341578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Although interest in characterizing DNA damage by means of DNA adductomics has substantially grown, the field of DNA adductomics is still in its infancy, with room for optimization of methods for sample analysis, data processing and DNA adduct identification. In this context, the first objective of this study was to evaluate the use of hydrophilic interaction (HILIC) vs. reversed phase liquid chromatography (RPLC) coupled to high resolution mass spectrometry (HRMS) and thermal acidic vs. enzymatic hydrolysis of DNA followed by DNA adduct purification and enrichment using solid-phase extraction (SPE) or fraction collection for DNA adductome mapping. The second objective was to assess the use of total ion count (TIC) and median intensity (MedI) normalization compared to QC (quality control), iQC (internal QC) and quality control-based robust locally estimated scatterplot smoothing (LOESS) signal correction (QC-RLSC) normalization for processing of the acquired data. The results demonstrate that HILIC compared to RPLC allowed better modeling of the tentative DNA adductome, particularly in combination with thermal acidic hydrolysis and SPE (more valid models, with an average Q2(Y) and R2(Y) of 0.930 and 0.998, respectively). Regarding the need for data normalization and the management of (limited) system instability and signal drift, QC normalization outperformed TIC, MedI, iQC and LOESS normalization. As such, QC normalization can be put forward as the default data normalization strategy. In case of momentous signal drift and/or batch effects however, comparison to other normalization strategies (like e.g. LOESS) is recommended. In future work, further optimization of DNA adductomics may be achieved by merging of HILIC and RPLC datasets and/or application of 2D-LC, as well as the inclusion of Schiff base stabilization and/or fraction collection in the thermal acidic hydrolysis-SPE sample preparation workflow.
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Affiliation(s)
- Marilyn De Graeve
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
| | - Emma Van de Walle
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
| | - Thomas Van Hecke
- Laboratory for Animal Nutrition and Animal Product Quality, Faculty of Bioscience Engineering, Ghent University, Coupure Links, 653, B-9000, Ghent, Belgium.
| | - Stefaan De Smet
- Laboratory for Animal Nutrition and Animal Product Quality, Faculty of Bioscience Engineering, Ghent University, Coupure Links, 653, B-9000, Ghent, Belgium.
| | - Lynn Vanhaecke
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium; Institute for Global Food Security, School of Biological Sciences, Queen's University, University Road, Belfast, United Kingdom.
| | - Lieselot Y Hemeryck
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
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Cui Y, Wang Y. Mass spectrometry-based DNA adductomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Chrétien B, Lelong-Boulouard V, Chantepie S, Sassier M, Bertho M, Brazo P, Humbert X, Alexandre J, Fedrizzi S, Dolladille C. Haematologic malignancies associated with clozapine v. all other antipsychotic agents: a pharmacovigilance study in VigiBase ®. Psychol Med 2021; 51:1459-1466. [PMID: 32036793 DOI: 10.1017/s0033291720000161] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Clozapine is mainly used in patients with treatment-resistant schizophrenia and may lead to potentially severe haematologic adverse events, such as agranulocytosis. Whether clozapine might be associated with haematologic malignancies is unknown. We aimed to assess the association between haematologic malignancies and clozapine using Vigibase®, the WHO pharmacovigilance database. METHODS We performed a disproportionality analysis to compute reporting odds-ratio adjusted for age, sex and concurrent reporting of antineoplastic/immunomodulating agents (aROR) for clozapine and structurally related drugs (loxapine, olanzapine and quetiapine) compared with other antipsychotic drugs. Cases were malignant lymphoma and leukaemia reports. Non-cases were all other reports including at least one antipsychotic report. RESULTS Of the 140 226 clozapine-associated reports, 493 were malignant lymphoma cases, and 275 were leukaemia cases. Clozapine was significantly associated with malignant lymphoma (aROR 9.14, 95% CI 7.75-10.77) and leukaemia (aROR 3.54, 95% CI 2.97-4.22). Patients suffering from those haematologic malignancies were significantly younger in the clozapine treatment group than patients treated with other medicines (p < 0.001). The median time to onset (available for 212 cases) was 5.1 years (IQR 2.2-9.9) for malignant lymphoma and 2.5 years (IQR 0.6-7.4) for leukaemia. The aROR by quartile of dose of clozapine in patients with haematologic malignancies suggested a dose-dependent association. CONCLUSIONS Clozapine was significantly associated with a pharmacovigilance signal of haematologic malignancies. The risk-benefit balance of clozapine should be carefully assessed in patients with risk factors of haematologic malignancies. Clozapine should be used at the lowest effective posology.
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Affiliation(s)
- Basile Chrétien
- Department of Pharmacology, Caen University Hospital, Caen, F-14000, France
- Pharmacovigilance Regional Center, Caen University Hospital, Caen, F-14000, France
| | - Véronique Lelong-Boulouard
- Department of Pharmacology, Caen University Hospital, Caen, F-14000, France
- Normandie Univ, UNICAEN, UFR Santé, INSERM UMR 1075, COMETE-MOBILITES "Vieillissement, Pathologie, Santé", 14000Caen, France
| | - Sylvain Chantepie
- Department of Clinical Haematology, Caen University Hospital, Caen, F-14000, France
| | - Marion Sassier
- Department of Pharmacology, Caen University Hospital, Caen, F-14000, France
- Pharmacovigilance Regional Center, Caen University Hospital, Caen, F-14000, France
| | - Mickael Bertho
- Department of Pharmacology, Caen University Hospital, Caen, F-14000, France
- Pharmacovigilance Regional Center, Caen University Hospital, Caen, F-14000, France
| | - Perrine Brazo
- Department of Psychiatry, Esquirol Center, Caen University Hospital, Caen, F-14000, France
- Normandie Univ, UNICAEN, EA7466, Imagerie et Stratégies Thérapeutiques de la Schizophrénie (ISTS), 14000Caen, France
| | - Xavier Humbert
- Department of Pharmacology, Caen University Hospital, Caen, F-14000, France
- Pharmacovigilance Regional Center, Caen University Hospital, Caen, F-14000, France
- General Practice Department, Normandie Univ, UNICAEN, 14000Caen, France
- Normandie Univ, UNICAEN, EA4650, Signalisation, électrophysiologie et imagerie des lésions d'ischémie-reperfusion myocardique, 14000Caen, France
| | - Joachim Alexandre
- Department of Pharmacology, Caen University Hospital, Caen, F-14000, France
- Pharmacovigilance Regional Center, Caen University Hospital, Caen, F-14000, France
- Normandie Univ, UNICAEN, EA4650, Signalisation, électrophysiologie et imagerie des lésions d'ischémie-reperfusion myocardique, 14000Caen, France
| | - Sophie Fedrizzi
- Department of Pharmacology, Caen University Hospital, Caen, F-14000, France
- Pharmacovigilance Regional Center, Caen University Hospital, Caen, F-14000, France
- Normandie Univ, UNICAEN, EA4650, Signalisation, électrophysiologie et imagerie des lésions d'ischémie-reperfusion myocardique, 14000Caen, France
| | - Charles Dolladille
- Department of Pharmacology, Caen University Hospital, Caen, F-14000, France
- Normandie Univ, UNICAEN, EA4650, Signalisation, électrophysiologie et imagerie des lésions d'ischémie-reperfusion myocardique, 14000Caen, France
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Tang Y, Zhang JL. Recent developments in DNA adduct analysis using liquid chromatography coupled with mass spectrometry. J Sep Sci 2019; 43:31-55. [PMID: 31573133 DOI: 10.1002/jssc.201900737] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/04/2019] [Accepted: 09/27/2019] [Indexed: 12/15/2022]
Abstract
The formation of DNA adducts by genotoxic agents is an early event in cancer development, and it may lead to gene mutations, thereby initiating tumor development. The measurement of DNA adducts can provide critical information about the genotoxic potential of a chemical and its mechanism of carcinogenesis. In recent decades, liquid chromatography coupled with mass spectrometry has become the most important technique for analyzing DNA adducts. The improvements in resolution achievable with new chromatographic separation techniques coupled with the high specificity and sensitivity and wide dynamic range of new mass spectrometry systems have been used for both qualitative and quantitative analyses of DNA adducts. This review discusses the challenges in qualitative and quantitative analyses of DNA adducts by liquid chromatography coupled with mass spectrometry and highlights recent developments towards overcoming the limitations of liquid chromatography coupled with mass spectrometry methods. The key steps and new solutions, such as sample preparation, mass spectrometry fragmentation, and method validation, are summarized. In addition, the fundamental principles and latest advances in DNA adductomic approaches are reviewed.
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Affiliation(s)
- Yu Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Jin-Lan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P. R. China
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Affiliation(s)
- Yang Yu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yuxiang Cui
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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Krais AM, Speksnijder EN, Melis JP, Singh R, Caldwell A, Gamboa da Costa G, Luijten M, Phillips DH, Arlt VM. Metabolic activation of 2-amino-1-methyl-6-phenylimidazo [4,5-b]pyridine and DNA adduct formation depends on p53: Studies in Trp53(+/+),Trp53(+/-) and Trp53(-/-) mice. Int J Cancer 2016; 138:976-82. [PMID: 26335255 PMCID: PMC4832306 DOI: 10.1002/ijc.29836] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/20/2015] [Indexed: 11/07/2022]
Abstract
The expression of the tumor suppressor p53 can influence the bioactivation of, and DNA damage induced by, the environmental carcinogen benzo[a]pyrene, indicating a role for p53 in its cytochrome P450 (CYP)-mediated biotransformation. The carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), which is formed during the cooking of food, is also metabolically activated by CYP enzymes, particularly CYP1A2. We investigated the potential role of p53 in PhIP metabolism in vivo by treating Trp53(+/+), Trp53(+/-) and Trp53(-/-) mice with a single oral dose of 50 mg/kg body weight PhIP. N-(Deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP-C8-dG) levels in DNA, measured by liquid chromatography-tandem mass spectrometry, were significantly lower in liver, colon, forestomach and glandular stomach of Trp53(-/-) mice compared to Trp53(+/+) mice. Lower PhIP-DNA adduct levels in the livers of Trp53(-/-) mice correlated with lower Cyp1a2 enzyme activity (measured by methoxyresorufin-O-demethylase activity) in these animals. Interestingly, PhIP-DNA adduct levels were significantly higher in kidney and bladder of Trp53(-/-) mice compared to Trp53(+/+) mice, which was accompanied by higher sulfotransferase (Sult) 1a1 protein levels and increased Sult1a1 enzyme activity (measured by 2-naphthylsulfate formation from 2-naphthol) in kidneys of these animals. Our study demonstrates a role for p53 in the metabolism of PhIP in vivo, extending previous results on a novel role for p53 in xenobiotic metabolism. Our results also indicate that the impact of p53 on PhIP biotransformation is tissue-dependent and that in addition to Cyp1a enzymes, Sult1a1 can contribute to PhIP-DNA adduct formation.
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Affiliation(s)
- Annette M. Krais
- Analytical and Environmental Sciences Division, MRC‐PHE Centre for Environment and HealthKing's College LondonLondonSE1 9NHUnited Kingdom
- Annette M. Krais current address is: Division of Occupational and Environmental MedicineLund University221 85LundSweden
| | - Ewoud N. Speksnijder
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM)BilthovenMA3721The Netherlands
- Department of Human GeneticsLeiden University Medical CenterLeiden2300The NetherlandsRC
| | - Joost P.M. Melis
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM)BilthovenMA3721The Netherlands
- Department of Human GeneticsLeiden University Medical CenterLeiden2300The NetherlandsRC
| | - Rajinder Singh
- Department of Cancer Studies and Molecular MedicineUniversity of LeicesterLeicesterLE2 7LXUnited Kingdom
| | - Anna Caldwell
- Mass Spectrometry Facility, King's College LondonLondonSE1 9NHUnited Kingdom
| | - Gonçalo Gamboa da Costa
- Division of Biochemical ToxicologyNational Center for Toxicological ResearchJeffersonAR72079
| | - Mirjam Luijten
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM)BilthovenMA3721The Netherlands
- Department of Human GeneticsLeiden University Medical CenterLeiden2300The NetherlandsRC
| | - David H. Phillips
- Analytical and Environmental Sciences Division, MRC‐PHE Centre for Environment and HealthKing's College LondonLondonSE1 9NHUnited Kingdom
| | - Volker M. Arlt
- Analytical and Environmental Sciences Division, MRC‐PHE Centre for Environment and HealthKing's College LondonLondonSE1 9NHUnited Kingdom
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David R, Ebbels T, Gooderham N. Synergistic and Antagonistic Mutation Responses of Human MCL-5 Cells to Mixtures of Benzo[a]pyrene and 2-Amino-1-Methyl-6-Phenylimidazo[4,5-b]pyridine: Dose-Related Variation in the Joint Effects of Common Dietary Carcinogens. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:88-96. [PMID: 26091049 PMCID: PMC4709171 DOI: 10.1289/ehp.1409557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 06/16/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND Chemical carcinogens such as benzo[a]pyrene (BaP) and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) may contribute to the etiology of human diet-associated cancer. Individually, these compounds are genotoxic, but the consequences of exposure to mixtures of these chemicals have not been systematically examined. OBJECTIVES We determined the mutagenic response to mixtures of BaP and PhIP at concentrations relevant to human exposure (micromolar to subnanomolar). METHODS Human MCL-5 cells (metabolically competent) were exposed to BaP or PhIP individually or in mixtures. Mutagenicity was assessed at the thymidine kinase (TK) locus, CYP1A activity was determined by ethoxyresorufin-O-deethylase (EROD) activity and qRT-PCR, and cell cycle was measured by flow cytometry. RESULTS Mixtures of BaP and PhIP produced dose responses different from those of the individual chemicals; we observed remarkably increased mutant frequency (MF) at lower concentrations of the mixtures (not mutagenic individually), and decreased MF at higher concentrations of the mixtures, than the calculated predicted additive MF of the individual chemicals. EROD activity and CYP1A1 mRNA levels were correlated with TK MF, supporting involvement of the CYP1A family in mutation. Moreover, a cell cycle G2/M phase block was observed at high-dose combinations, consistent with DNA damage sensing and repair. CONCLUSIONS Mixtures of these genotoxic chemicals produced mutation responses that differed from those expected for the additive effects of the individual chemicals. The increase in MF for certain combinations of chemicals at low concentrations that were not genotoxic for the individual chemicals, as well as the nonmonotonic dose response, may be important for understanding the mutagenic potential of food and the etiology of diet-associated cancers. CITATION David R, Ebbels T, Gooderham N. 2016. Synergistic and antagonistic mutation responses of human MCL-5 cells to mixtures of benzo[a]pyrene and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine: dose-related variation in the joint effects of common dietary carcinogens. Environ Health Perspect 124:88-96; http://dx.doi.org/10.1289/ehp.1409557.
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Affiliation(s)
| | | | - Nigel Gooderham
- Address correspondence to N. Gooderham, Computational and Systems Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, London, SW7 2AZ, UK. Telephone: 02075943188. E-mail:
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Liu S, Wang Y. Mass spectrometry for the assessment of the occurrence and biological consequences of DNA adducts. Chem Soc Rev 2015; 44:7829-54. [PMID: 26204249 PMCID: PMC4787602 DOI: 10.1039/c5cs00316d] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Exogenous and endogenous sources of chemical species can react, directly or after metabolic activation, with DNA to yield DNA adducts. If not repaired, DNA adducts may compromise cellular functions by blocking DNA replication and/or inducing mutations. Unambiguous identification of the structures and accurate measurements of the levels of DNA adducts in cellular and tissue DNA constitute the first and important step towards understanding the biological consequences of these adducts. The advances in mass spectrometry (MS) instrumentation in the past 2-3 decades have rendered MS an important tool for structure elucidation, quantification, and revelation of the biological consequences of DNA adducts. In this review, we summarized the development of MS techniques on these fronts for DNA adduct analysis. We placed our emphasis of discussion on sample preparation, the combination of MS with gas chromatography- or liquid chromatography (LC)-based separation techniques for the quantitative measurement of DNA adducts, and the use of LC-MS along with molecular biology tools for understanding the human health consequences of DNA adducts. The applications of mass spectrometry-based DNA adduct analysis for predicting the therapeutic outcome of anti-cancer agents, for monitoring the human exposure to endogenous and environmental genotoxic agents, and for DNA repair studies were also discussed.
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Affiliation(s)
- Shuo Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, California, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California, USA and Department of Chemistry, University of California, Riverside, CA 92521-0403, USA.
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Arlt VM, Henderson CJ, Wolf CR, Stiborová M, Phillips DH. The Hepatic Reductase Null (HRN™) and Reductase Conditional Null (RCN) mouse models as suitable tools to study metabolism, toxicity and carcinogenicity of environmental pollutants. Toxicol Res (Camb) 2015. [DOI: 10.1039/c4tx00116h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
This review describes the applicability of the Hepatic Reductase Null (HRN) and Reductase Conditional Null (RCN) mouse models to study carcinogen metabolism.
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Affiliation(s)
- Volker M. Arlt
- Analytical and Environmental Sciences Division
- MRC-PHE Centre for Environment and Health
- King's College London
- London SE1 9NH
- UK
| | - Colin J. Henderson
- Division of Cancer Research
- Medical Research Institute
- Jacqui Wood Cancer Centre
- University of Dundee
- Dundee DD1 9SY
| | - C. Roland Wolf
- Division of Cancer Research
- Medical Research Institute
- Jacqui Wood Cancer Centre
- University of Dundee
- Dundee DD1 9SY
| | - Marie Stiborová
- Department of Biochemistry
- Faculty of Science
- Charles University
- 128 40 Prague 2
- Czech Republic
| | - David H. Phillips
- Analytical and Environmental Sciences Division
- MRC-PHE Centre for Environment and Health
- King's College London
- London SE1 9NH
- UK
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Monien BH, Schumacher F, Herrmann K, Glatt H, Turesky RJ, Chesné C. Simultaneous detection of multiple DNA adducts in human lung samples by isotope-dilution UPLC-MS/MS. Anal Chem 2014; 87:641-8. [PMID: 25423194 PMCID: PMC4287830 DOI: 10.1021/ac503803m] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Recent studies have demonstrated
that various DNA adducts can be
detected in human tissues and fluids using liquid chromatography connected
to tandem mass spectrometry (LC-MS/MS). However, the utility of a
single DNA adduct as a biomarker in risk assessment is debatable because
humans are exposed to many genotoxicants. We established a method
to measure DNA adducts derived from 16 ubiquitous genotoxicants and
developed an analytical technique for their simultaneous quantification
by ultra performance liquid chromatography (UPLC)-MS/MS. Methods for
the enrichment of the analytes from DNA hydrolysates and chromatographic
separation preceding mass spectrometric analysis were optimized, and
the resultant technique was used for the simultaneous analysis of
the 16 DNA adducts in human lung biopsy specimens. Eleven adducts
(formed by benzo[a]pyrene, 1-methylpyrene, 4-aminobiphenyl,
2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine,
1-methoxy-3-indolylmethylglucosinolate, 5-hydroxymethylfurfural, and
malondialdehyde) were not detected in any tissue sample (limits of
detection: 0.02–7.1 adducts/108 nucleosides). 3,N4-etheno-2′-deoxycytidine and 1,N6-etheno-2′-deoxyadenosine, formed from
2,3-epoxyaldehydes of endogenous lipid peroxidation products, were
present in all subjects (16.9–115.3 and 27.2–179/108 nucleosides, respectively). The same was true for N2-(trans-methylisoeugenol-3′-yl)-2′-deoxyguanosine,
the major adduct of methyleugenol (1.7–23.7/108 nucleosides).
A minor adduct of methyleugenol and two adducts of furfuryl alcohol
were detected in several pulmonary specimens. Taken together, we developed
a targeted approach for the simultaneous mass spectrometric analyses
of 16 DNA adducts, which can be easily extended by adducts formed
from other mutagens. The method allowed one to detect adducts of furfuryl
alcohol and methyleugenol in samples of human lung.
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Affiliation(s)
- Bernhard H Monien
- Research Group Genotoxic Food Contaminants, German Institute of Human Nutrition (DIfE) , 14558 Nuthetal, Germany
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Schmeiser HH, Nortier JL, Singh R, Gamboa da Costa G, Sennesael J, Cassuto-Viguier E, Ambrosetti D, Rorive S, Pozdzik A, Phillips DH, Stiborova M, Arlt VM. Exceptionally long-term persistence of DNA adducts formed by carcinogenic aristolochic acid I in renal tissue from patients with aristolochic acid nephropathy. Int J Cancer 2014; 135:502-7. [PMID: 24921086 DOI: 10.1002/ijc.28681] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Aristolochic acid (AA) causes aristolochic acid nephropathy (AAN), first described in women in Belgium accidently prescribed Aristolochia fangchi in a slimming treatment, and also Balkan endemic nephropathy (BEN), through probable dietary contamination with Aristolochia clematitis seeds. Both nephropathies have a high risk of urothelial cancer, with AA being the causative agent. In tissues of AAN and BEN patients, a distinct DNA adduct, 7-(deoxyadenosin-N6-yl)-aristolactam I (dA-AAI), has been detected. DNA adducts can be removed through DNA repair, they can result in mutations through erroneous DNA replication or they can cause cell death. The dA-AAI adduct induces AT to TA transversions in the tumor-suppressor TP53 gene in experimental systems, matching TP53 mutations observed in urothelial tumors from AAN cancer cases. Using thin-layer chromatography 32P-postlabeling and mass spectrometric analysis we report the detection of dA-AAI in renal DNA from 11 Belgian AAN patients over 20 years after exposure to AA had ceased. Our results showed that dA-AAI is an established biomarker of AA exposure, and that this biomarker can be demonstrated to be persistent decades after a distinct AA exposure. Further, the persistence of dA-AAI adducts appears to be a critical determinant for the AA mutational fingerprint frequently found in oncogenes and tumor suppressor genes recently identified by whole genome sequencing of AA-associated urothelial tumors. The potential for exposure to AA worldwide is high; the unprecedented long-term persistence of dA-AAI provides a useful long-term biomarker of exposure and attests to the role of AA in human urothelial malignancy.
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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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Gavina JMA, Yao C, Feng YL. Recent developments in DNA adduct analysis by mass spectrometry: a tool for exposure biomonitoring and identification of hazard for environmental pollutants. Talanta 2014; 130:475-94. [PMID: 25159438 DOI: 10.1016/j.talanta.2014.06.050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/19/2014] [Accepted: 06/22/2014] [Indexed: 02/08/2023]
Abstract
DNA adducts represent an important category of biomarkers for detection and exposure surveillance of potential carcinogenic and genotoxic chemicals in the environment. Sensitive and specific analytical methods are required to detect and differentiate low levels of adducts from native DNA from in vivo exposure. In addition to biomonitoring of environmental pollutants, analytical methods have been developed for structural identification of adducts which provides fundamental information for determining the toxic pathway of hazardous chemicals. In order to achieve the required sensitivity, mass spectrometry has been increasingly utilized to quantify adducts at low levels as well as to obtain structural information. Furthermore, separation techniques such as chromatography and capillary electrophoresis can be coupled to mass spectrometry to increase the selectivity. This review will provide an overview of advances in detection of adducted and modified DNA by mass spectrometry with a focus on the analysis of nucleosides since 2007. Instrument advances, sample and instrument considerations, and recent applications will be summarized in the context of hazard assessment. Finally, advances in biomonitoring applying mass spectrometry will be highlighted. Most importantly, the usefulness of DNA adducts measurement and detection will be comprehensively discussed as a tool for assessment of in vitro and in vivo exposure to environmental pollutants.
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Affiliation(s)
- Jennilee M A Gavina
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9
| | - Chunhe Yao
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9
| | - Yong-Lai Feng
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch, Health Canada, 50 Columbine Driveway, AL: 0800C, Ottawa, Ontario, Canada K1A 0K9.
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14
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Affiliation(s)
- Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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15
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Optimized enzymatic hydrolysis of DNA for LC-MS/MS analyses of adducts of 1-methoxy-3-indolylmethyl glucosinolate and methyleugenol. Anal Biochem 2012; 434:4-11. [PMID: 23142629 DOI: 10.1016/j.ab.2012.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 10/29/2012] [Accepted: 11/01/2012] [Indexed: 01/30/2023]
Abstract
Mass spectrometric analyses of DNA adducts usually require enzymatic digestion of the DNA to nucleosides. The digestive enzymes used in our laboratory included a calf spleen phosphodiesterase, whose marketing was stopped recently. Using DNA adducted with bioactivated methyleugenol and 1-methoxy-3-indolylmethyl glucosinolate-each forming dA and dG adducts-we demonstrate that replacement of calf spleen phosphodiesterase (Merck) with bovine spleen phosphodiesterase (Sigma-Aldrich) leads to unchanged results. Enzyme levels used for DNA digestion are extremely variable in different studies. Therefore, we sequentially varied the level of each of the three enzymes used. All dose (enzyme)-response (adduct level) curves involved a long plateau starting below the enzyme levels employed previously. Thus, we could reduce the amounts of micrococcal nuclease, phosphodiesterase, and alkaline phosphatase for quantitative DNA digestion by factors of 4, 2, and 333, respectively, compared to our previous protocols. Moreover, we observed significant phosphatase activity of both phosphodiesterase preparations used, which may affect the recovery of adducts with methods requiring digestion to 2'-deoxynucleoside-3'-monophosphates (e.g., (32)P-postlabeling). In addition, the phosphodiesterase from Sigma-Aldrich, but not that from Merck, deaminated dA. This was irrelevant for the dA adducts studied, involving bonding at N(6), but might complicate the analysis of other dA adducts.
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Klaene JJ, Sharma VK, Glick J, Vouros P. The analysis of DNA adducts: the transition from (32)P-postlabeling to mass spectrometry. Cancer Lett 2012; 334:10-9. [PMID: 22960573 DOI: 10.1016/j.canlet.2012.08.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 07/20/2012] [Accepted: 08/07/2012] [Indexed: 10/27/2022]
Abstract
The technique of (32)P-postlabeling, which was introduced in 1982 for the analysis of DNA adducts, has long been the method of choice for in vivo studies because of its high sensitivity as it requires only <10μg DNA to achieve the detection of 1 adduct in 10(10) normal bases. (32)P-postlabeling has therefore been utilized in numerous human and animal studies of DNA adduct formation. Like all techniques (32)P-postlabeling does have several disadvantages including the use of radioactive phosphorus, lack of internal standards, and perhaps most significantly does not provide any structural information for positive identification of unknown adducts, a shortcoming that could significantly hamper progress in the field. Structural methods have since been developed to allow for positive identification of DNA adducts, but to this day, the same level of sensitivity and low sample requirements provided by (32)P-postlabeling have not been matched. In this mini review we will discuss the (32)P-postlabeling method and chronicle the transition to mass spectrometry via the hyphenation of gas chromatography, capillary electrophoresis, and ultimately liquid chromatography which, some 30years later, is only just starting to approach the sensitivity and low sample requirements of (32)P-postlabeling. This paper focuses on the detection of bulky carcinogen-DNA adducts, with no mention of oxidative damage or small alkylating agents. This is because the (32)P-postlabeling assay is most compatible with bulky DNA adducts. This will also allow a more comprehensive focus on a subject that has been our particular interest since 1990.
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Affiliation(s)
- Joshua J Klaene
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, MA 02115, United States
| | - Vaneet K Sharma
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, MA 02115, United States
| | - James Glick
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, MA 02115, United States
| | - Paul Vouros
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, MA 02115, United States.
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Ishii Y, Inoue K, Takasu S, Jin M, Matsushita K, Kuroda K, Fukuhara K, Nishikawa A, Umemura T. Determination of Lucidin-Specific DNA Adducts by Liquid Chromatography with Tandem Mass Spectrometry in the Livers and Kidneys of Rats Given Lucidin-3-O-primeveroside. Chem Res Toxicol 2012; 25:1112-8. [DOI: 10.1021/tx300084p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuji Ishii
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Kaoru Inoue
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Shinji Takasu
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Meilan Jin
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Kohei Matsushita
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Ken Kuroda
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Kiyoshi Fukuhara
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Akiyoshi Nishikawa
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
| | - Takashi Umemura
- Division
of Pathology, ‡Division of Organic Chemistry, and §Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku,
Tokyo 158-8501, Japan
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18
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Arlt VM, Singh R, Stiborová M, Gamboa da Costa G, Frei E, Evans JD, Farmer PB, Wolf CR, Henderson CJ, Phillips DH. Effect of hepatic cytochrome P450 (P450) oxidoreductase deficiency on 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine-DNA adduct formation in P450 reductase conditional null mice. Drug Metab Dispos 2011; 39:2169-73. [PMID: 21940903 DOI: 10.1124/dmd.111.041343] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), formed during the cooking of foods, induces colon cancer in rodents. PhIP is metabolically activated by cytochromes P450 (P450s). To evaluate the role of hepatic P450s in the bioactivation of PhIP, we used Reductase Conditional Null (RCN) mice, in which cytochrome P450 oxidoreductase (POR), the unique electron donor to P450s, can be specifically deleted in hepatocytes by pretreatment with 3-methylcholanthrene (3-MC), resulting in the loss of essentially all hepatic P450 function. RCN mice were treated orally with 50 mg/kg b.wt. PhIP daily for 5 days, with and without 3-MC pretreatment. PhIP-DNA adducts (i.e., N-(deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine [dG-C8-PhIP]), measured by liquid chromatography-tandem mass spectrometry, were highest in colon (1362 adducts/10(8) deoxynucleosides), whereas adduct levels in liver were ∼3.5-fold lower. Whereas no differences in PhIP-DNA adduct levels were found in livers with active POR versus inactivated POR, adduct levels were on average ∼2-fold lower in extrahepatic tissues of mice lacking hepatic POR. Hepatic microsomes from RCN mice with or without 3-MC pretreatment were also incubated with PhIP and DNA in vitro. PhIP-DNA adduct formation was ∼8-fold lower with hepatic microsomes from POR-inactivated mice than with those with active POR. Most of the hepatic microsomal activation of PhIP in vitro was attributable to CYP1A. Our results show that PhIP-DNA adduct formation in colon involves hepatic N-oxidation, circulation of activated metabolites via the bloodstream to extrahepatic tissues, and further activation, resulting in the formation of dG-C8-PhIP. Besides hepatic P450s, PhIP may be metabolically activated mainly by a non-P450 pathway in liver.
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Affiliation(s)
- Volker M Arlt
- Section of Molecular Carcinogenesis, Institute of Cancer Research, Brookes Lawley Building, Sutton, Surrey SM2 5NG, UK.
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Turesky RJ, Le Marchand L. Metabolism and biomarkers of heterocyclic aromatic amines in molecular epidemiology studies: lessons learned from aromatic amines. Chem Res Toxicol 2011; 24:1169-214. [PMID: 21688801 PMCID: PMC3156293 DOI: 10.1021/tx200135s] [Citation(s) in RCA: 217] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aromatic amines and heterocyclic aromatic amines (HAAs) are structurally related classes of carcinogens that are formed during the combustion of tobacco or during the high-temperature cooking of meats. Both classes of procarcinogens undergo metabolic activation by N-hydroxylation of the exocyclic amine group to produce a common proposed intermediate, the arylnitrenium ion, which is the critical metabolite implicated in toxicity and DNA damage. However, the biochemistry and chemical properties of these compounds are distinct, and different biomarkers of aromatic amines and HAAs have been developed for human biomonitoring studies. Hemoglobin adducts have been extensively used as biomarkers to monitor occupational and environmental exposures to a number of aromatic amines; however, HAAs do not form hemoglobin adducts at appreciable levels, and other biomarkers have been sought. A number of epidemiologic studies that have investigated dietary consumption of well-done meat in relation to various tumor sites reported a positive association between cancer risk and well-done meat consumption, although some studies have shown no associations between well-done meat and cancer risk. A major limiting factor in most epidemiological studies is the uncertainty in quantitative estimates of chronic exposure to HAAs, and thus, the association of HAAs formed in cooked meat and cancer risk has been difficult to establish. There is a critical need to establish long-term biomarkers of HAAs that can be implemented in molecular epidemioIogy studies. In this review, we highlight and contrast the biochemistry of several prototypical carcinogenic aromatic amines and HAAs to which humans are chronically exposed. The biochemical properties and the impact of polymorphisms of the major xenobiotic-metabolizing enzymes on the biological effects of these chemicals are examined. Lastly, the analytical approaches that have been successfully employed to biomonitor aromatic amines and HAAs, and emerging biomarkers of HAAs that may be implemented in molecular epidemiology studies are discussed.
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Affiliation(s)
- Robert J Turesky
- Division of Environmental Health Sciences, Wadsworth Center , Albany, New York 12201, United States.
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