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Zhang X, Leng J, Lv L, Song D, Lv X. Advances in the mechanistic understanding, biological consequences, and measurement of DNA adducts induced by tobacco smoke and e-cigarette aerosol: A review. Int J Biol Macromol 2025; 306:141574. [PMID: 40023427 DOI: 10.1016/j.ijbiomac.2025.141574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 02/23/2025] [Accepted: 02/26/2025] [Indexed: 03/04/2025]
Abstract
Components in tobacco smoke and electronic cigarette (e-cigarette) aerosol form adducts with DNA, which can cause DNA mutations and affect repair of DNA damage. Numerous studies have shown a strong association between inhaled smoke and lung cancer. The presence of DNA adducts can indicate chemical components of smoke. Therefore, DNA adducts are significant biomarkers of tobacco exposure that might predict lung disease status and serve as precursors to lung cancer, since they trigger DNA mutations and impair biological processes such as DNA replication and transcription. To date, no systematic review has compared tobacco smoke and e-cigarette aerosol in terms of the fate of DNA adducts. We reviewed recent studies comparing the formation of DNA adducts on exposure to components from conventional cigarette smoke versus e-cigarette aerosol. The aims of the review were threefold: (1) to summarize components of tobacco smoke and e-cigarette aerosol in relation to mechanisms for the formation of DNA adducts; (2) to highlight the biological consequences of exposure to tobacco smoke and e-cigarette aerosol; and (3) to summarize advances in understanding of the primary detection methods of DNA adducts in tobacco exposure studies. The findings of this review should benefit environmental toxicology studies of tobacco exposure.
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Affiliation(s)
- Xinyun Zhang
- Comprehensive Exposure Research Center, School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian 116600, China
| | - Jiapeng Leng
- Comprehensive Exposure Research Center, School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian 116600, China.
| | - Ling Lv
- Comprehensive Exposure Research Center, School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian 116600, China
| | - Danjun Song
- First Clinical College of Liaoning University of Traditional Chinese Medicine, Shenyang 110847, China
| | - Xiaodong Lv
- Comprehensive Exposure Research Center, School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian 116600, China.
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2
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Chao MR, Chang YJ, Cooke MS, Hu CW. Multi-adductomics: Advancing mass spectrometry techniques for comprehensive exposome characterization. Trends Analyt Chem 2024; 180:117900. [PMID: 39246549 PMCID: PMC11375889 DOI: 10.1016/j.trac.2024.117900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
Adductomics, an emerging field within the 'omics sciences, focuses on the formation and prevalence of DNA, RNA, and protein adducts induced by endogenous and exogenous agents in biological systems. These modifications often result from exposure to environmental pollutants, dietary components, and xenobiotics, impacting cellular functions and potentially leading to diseases such as cancer. This review highlights advances in mass spectrometry (MS) that enhance the detection of these critical modifications and discusses current and emerging trends in adductomics, including developments in MS instrument use, screening techniques, and the study of various biomolecular modifications from mono-adducts to complex hybrid crosslinks between different types of biomolecules. The review also considers challenges, including the need for specialized MS spectra databases and multi-omics integration, while emphasizing techniques to distinguish between exogenous and endogenous modifications. The future of adductomics possesses significant potential for enhancing our understanding of health in relation to environmental exposures and precision medicine.
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Affiliation(s)
- Mu-Rong Chao
- 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
| | - Yuan-Jhe Chang
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung 402, Taiwan
- Department of Family and Community Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan
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3
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Xu R, Zhang Y, Gao Y, Jia S, Choi S, Xu Y, Gong J. Development of a targeted method for DNA adductome and its application as sensitive biomarkers of ambient air pollution exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135018. [PMID: 38959829 DOI: 10.1016/j.jhazmat.2024.135018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/11/2024] [Accepted: 06/22/2024] [Indexed: 07/05/2024]
Abstract
DNA adducts are widely recognized as biomarkers of exposure to environmental carcinogens and associated health effects in toxicological and epidemiological studies. This study presents a targeted and sensitive method for comprehensive DNA adductome analysis using ultra-high-performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (UHPLC-QqQ-MS/MS). The method was developed using calf thymus DNA, with careful optimization of mass spectrometric parameters, chromatographic separation conditions, and pretreatment methods. Ultimately, a targeted method was established for 41 DNA adducts, which showed good linearity (R2 ≥0.992), recovery (80.1-119.4 %), accuracy (81.3-117.8 %), and precision (relative standard deviation <14.2 %). The established method was employed to analyze DNA adducts in peripheral blood cells from pregnant women in Shanxi and Beijing. Up to 23 DNA adducts were successfully detected in samples of varying sizes. From 2 μg of maternal DNA samples, seven specific adducts were identified: 5-methyl-2'-deoxycytidine (5-MedC), 5-hydroxymethyl-2'-deoxycytidine (5-HmdC), N6-methyl-2'-deoxyadenosine (N6-MedA), 8-hydroxy-2'-deoxyguanosine (8-OHdG), 5-hydroxy-2'-deoxycytidine (5-OHdC), 1,N6-etheno-2'-deoxyadenosine (1,N6-εdA), and N2-methyl-2'-deoxyguanosine (N2-MedG). This study reveals that exposure to higher concentrations of ambient air pollutants may elevate the levels of DNA methylation and oxidative damage at different base sites, highlighting the application potential of DNA adducts as sensitive biomarkers of air pollution exposure.
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Affiliation(s)
- Ruiwei Xu
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Yi Zhang
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Yingfeng Gao
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Shuyu Jia
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Seokho Choi
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Yifan Xu
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Jicheng Gong
- SKL-ESPC & SEPKL-AERM, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China.
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4
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Möller C, Virzi J, Chang YJ, Keidel A, Chao MR, Hu CW, Cooke MS. DNA modifications: Biomarkers for the exposome? ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2024; 108:104449. [PMID: 38636743 DOI: 10.1016/j.etap.2024.104449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
The concept of the exposome is the encompassing of all the environmental exposures, both exogenous and endogenous, across the life course. Many, if not all, of these exposures can result in the generation of reactive species, and/or the modulation of cellular processes, that can lead to a breadth of modifications of DNA, the nature of which may be used to infer their origin. Because of their role in cell function, such modifications have been associated with various major human diseases, including cancer, and so their assessment is crucial. Historically, most methods have been able to only measure one or a few DNA modifications at a time, limiting the information available. With the development of DNA adductomics, which aims to determine the totality of DNA modifications, a far more comprehensive picture of the DNA adduct burden can be gained. Importantly, DNA adductomics can facilitate a "top-down" investigative approach whereby patterns of adducts may be used to trace and identify the originating exposure source. This, together with other 'omic approaches, represents a major tool for unraveling the complexities of the exposome and hence allow a better a understanding of the environmental origins of disease.
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Affiliation(s)
- Carolina Möller
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
| | - Jazmine Virzi
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Yuan-Jhe Chang
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Alexandra Keidel
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Mu-Rong Chao
- 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
| | - Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA; College of Public Health, University of South Florida, Tampa, FL 33620, USA; Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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5
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Chen Z, Luo G, Ren J, Wang Q, Zhao X, Wei L, Wang Y, Liu Y, Deng Y, Li S. Recent Advances in and Application of Fluorescent Microspheres for Multiple Nucleic Acid Detection. BIOSENSORS 2024; 14:265. [PMID: 38920569 PMCID: PMC11201543 DOI: 10.3390/bios14060265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
Traditional single nucleic acid assays can only detect one target while multiple nucleic acid assays can detect multiple targets simultaneously, providing comprehensive and accurate information. Fluorescent microspheres in multiplexed nucleic acid detection offer high sensitivity, specificity, multiplexing, flexibility, and scalability advantages, enabling precise, real-time results and supporting clinical diagnosis and research. However, multiplexed assays face challenges like complexity, costs, and sample handling issues. The review explores the recent advancements and applications of fluorescent microspheres in multiple nucleic acid detection. It discusses the versatility of fluorescent microspheres in various fields, such as disease diagnosis, drug screening, and personalized medicine. The review highlights the possibility of adjusting the performance of fluorescent microspheres by modifying concentrations and carrier forms, allowing for tailored applications. It emphasizes the potential of fluorescent microsphere technology in revolutionizing nucleic acid detection and advancing health, disease treatment, and medical research.
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Affiliation(s)
- Zhu Chen
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Gaoming Luo
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Jie Ren
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Qixuan Wang
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xinping Zhao
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Linyu Wei
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yue Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China;
| | - Yuan Liu
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Yan Deng
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Song Li
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
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6
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Kibar G, Sarıarslan B, Doğanay S, Yıldız G, Usta OB, Çetin B. Novel 3D-Printed Microfluidic Magnetic Platform for Rapid DNA Isolation. Anal Chem 2024; 96:1985-1992. [PMID: 38254336 DOI: 10.1021/acs.analchem.3c04412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
This study presents a novel miniaturized device as a 3D-printed microfluidic magnetic platform specifically designed to manipulate magnetic microparticles in a microfluidic chip for rapid deoxyribonucleic acid (DNA) isolation. The novel design enables the movement of the magnetic particles in the same or opposite directions with the flow or suspends them in continuous flow. A computational model was developed to assess the effectiveness of the magnetic manipulation of the particles. Superparamagnetic monodisperse silica particles synthesized in-house are utilized for the isolation of fish sperm DNA and human placenta DNA. It was demonstrated that the proposed platform can perform DNA isolation within 10 min with an isolation efficiency of 50% at optimum operating conditions.
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Affiliation(s)
- Güneş Kibar
- Department of Materials Science and Engineering, Adana Alparslan Türkeş Science and Technology University, Adana 01250, Turkey
- Center for Engineering in Medicine and Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- UNAM─National Nanotechnology Research Center and Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Büşra Sarıarslan
- UNAM─National Nanotechnology Research Center and Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
- Microfluidics & Lab-on-a-chip Research Group, Mechanical Engineering Department, Bilkent University, Ankara 06800, Turkey
| | - Serkan Doğanay
- Mechatronics Engineering Department İzmir Katip Çelebi University, İzmir 35620, Turkey
| | - Gökay Yıldız
- TEKGEN Healthcare Services Inc., Ümraniye, İstanbul 34775, Turkey
| | - O Berk Usta
- Center for Engineering in Medicine and Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Shriners Children's Hospital, Boston, Massachusetts 02114, United States
| | - Barbaros Çetin
- UNAM─National Nanotechnology Research Center and Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
- Microfluidics & Lab-on-a-chip Research Group, Mechanical Engineering Department, Bilkent University, Ankara 06800, Turkey
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7
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Wu H, Zhang Y, Xu H, Xu B, Chen J, Guo L, Liu Q, Xie J. Urinary Profile of Alkylated DNA Adducts and DNA Oxidative Damage in Sulfur Mustard-Exposed Rats Revealed by Mass Spectrometry Quantification. Chem Res Toxicol 2023; 36:1495-1502. [PMID: 37625021 DOI: 10.1021/acs.chemrestox.3c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Alkylation reagents, represented by sulfur mustard (SM), can damage DNA molecules directly as well as lead to oxidative stress, causing DNA lesions indirectly. Correspondingly, two types of biomarkers including alkylated DNA adducts and oxidative DNA adducts are commonly involved in the research of DNA damage evaluation caused by these agents. However, the correlations and differences of the occurrence, duration, severity, and traceability between alkylation and oxidation lesions on the DNA molecular level reflected by these two types of biomarkers have not been systematically studied. A simultaneous determination method for four alkylated DNA adducts, i.e., N7-(2-hydroxyethylthioethyl)2'-guanine (N7-HETEG), O6-(2-hydroxyethylthioethyl)-2'-guanine (O6-HETEG), N3-(2-hydroxyethylthioethyl)-2'-adenine (N3-HETEA), and bis(2-ethyl-N7-guanine)thioether (Bis-G), and the oxidative adduct 8-hydroxy-2'-deoxyguanosine (8-OH-dG) in urine samples by isotope-dilution high-performance liquid chromatography-tandem mass spectrometry (ID-HPLC-MS/MS) was built with a lower limit of detection of 0.02 ng/mL (except Bis-G, 0.05 ng/mL) and a recovery of 79-111%. The profile of these adducts was simultaneously monitored in urine samples after SD rats' dermal exposure to SM in three dose levels (1, 3, and 10 mg/kg). The time-effect and dose-effect experiments revealed that when exposed to SM, DNA alkylation lesions would happen earlier than those of oxidation. For the two types of biomarkers, alkylated DNA adducts showed an obvious dose-effect relationship and could be used as internal exposure dose and effect biomarkers, while 8-OH-dG did not show a correlation with exposure dose, demonstrating that it was more suitable as a biomarker for DNA oxidative lesions but not an indicator for the extent of cytotoxicity and internal exposure.
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Affiliation(s)
- Haijiang Wu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Yajiao Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Hua Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Bin Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Jia Chen
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Lei Guo
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Qin Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Jianwei Xie
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
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8
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Martella G, Motwani NH, Khan Z, Sousa PFM, Gorokhova E, Motwani HV. Simultaneous RNA and DNA Adductomics Using Single Data-Independent Acquisition Mass Spectrometry Analysis. Chem Res Toxicol 2023; 36:1471-1482. [PMID: 37566384 PMCID: PMC10523582 DOI: 10.1021/acs.chemrestox.3c00041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Indexed: 08/12/2023]
Abstract
Adductomics studies are used for the detection and characterization of various chemical modifications (adducts) of nucleic acids and proteins. The advancements in liquid chromatography coupled with high-resolution tandem mass spectrometry (HRMS/MS) have resulted in efficient methods for qualitative and quantitative adductomics. We developed an HRMS-based method for the simultaneous analysis of RNA and DNA adducts in a single run and demonstrated its application using Baltic amphipods, useful sentinels of environmental disturbances, as test organisms. The novelty of this method is screening for RNA and DNA adducts by a single injection on an Orbitrap HRMS instrument using full scan and data-independent acquisition. The MS raw files were processed with an open-source program, nLossFinder, to identify and distinguish RNA and DNA adducts based on the characteristic neutral loss of ribonucleosides and 2'-deoxyribonucleosides, respectively. In the amphipods, in addition to the nearly 150 putative DNA adducts characterized earlier, we detected 60 putative RNA adducts. For the structural identification of the detected RNA adducts, the MODOMICS database was used. The identified RNA adducts included simple mono- and dimethylation and other larger functional groups on different ribonucleosides and deaminated product inosine. However, 54 of these RNA adducts are not yet structurally identified, and further work on their characterization may uncover new layers of information related to the transcriptome and help understand their biological significance. Considering the susceptibility of nucleic acids to environmental factors, including pollutants, the developed multi-adductomics methodology with further advancement has the potential to provide biomarkers for diagnostics of pollution effects in biota.
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Affiliation(s)
- Giulia Martella
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - Nisha H. Motwani
- School
of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge SE-14189, Sweden
| | - Zareen Khan
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - Pedro F. M. Sousa
- Department
of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Elena Gorokhova
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - Hitesh V. Motwani
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
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9
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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: 5] [Impact Index Per Article: 2.5] [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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10
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Yin M, Hu Y, Fan H, Wang Q, Wang M, Wang W, Shi C. Method for trace determination of N-nitrosamines impurities in metronidazole benzoate using high-performance liquid chromatography coupled with atmospheric-pressure chemical ionization tandem mass spectrometry. J Sep Sci 2023; 46:e2200225. [PMID: 36562102 DOI: 10.1002/jssc.202200225] [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: 03/17/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Genotoxic impurity control has been a great concern in the pharmaceutical industry since the recall of the large round of sartans worldwide in 2018. In these sartans, N-nitrosamines were the main contaminants in active pharmaceutical ingredients and formulations. Numerous analytical methods have been developed to detect N-nitrosamines in food, drugs, and environmental samples. In this study, a sensitive method is developed for the trace determination of N-nitrosamine impurities in metronidazole benzoate pharmaceuticals using high-performance liquid chromatography/atmospheric-pressure chemical ionization tandem mass spectrometry in the multiple reaction monitoring mode. The method was validated regarding system suitability, selectivity, linearity, accuracy, precision, sensitivity, solution stability, and robustness. The method showed good linearity with R2 ≥ 0.999 and FMandel < Ftab(95%) ranging from 0.33 to 8.00 ng/ml. The low limits of detection of N-nitrosamines were in the range of 0.22-0.80 ng/ml (0.0014-0.0050 ppm). The low limits of quantification were in the range of 0.33-1.20 ng/ml (0.0021-0.0075 ppm), which were lower than the acceptable limits in metronidazole benzoate pharmaceuticals and indicated the high sensitivity of the method. The recoveries of N-nitrosamines ranged from 84% to 97%. Thus, this method exhibits good selectivity, sensitivity, and accuracy. Moreover, it is a simple, convenient, and scientific strategy for detecting N-nitrosamine impurities in pharmaceuticals to support the development of the pharmaceutical industry.
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Affiliation(s)
- Mingxing Yin
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Yinuo Hu
- Hubei Hongyuan Pharmaceutical Technology Ltd., Huanggang, P. R. China
| | - Huajun Fan
- ICAS Testing Technology Service (Shanghai) Ltd., Shanghai, P. R. China
| | - Qiulan Wang
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Mengdie Wang
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wenqing Wang
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Chunyang Shi
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
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11
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Krassnig SC, Mäser M, Probst NA, Werner J, Schlett C, Schumann N, von Scheven G, Mangerich A, Bürkle A. Comparative analysis of chlorambucil-induced DNA lesion formation and repair in a spectrum of different human cell systems. Toxicol Rep 2023; 10:171-189. [PMID: 36714466 PMCID: PMC9881385 DOI: 10.1016/j.toxrep.2023.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023] Open
Abstract
Chlorambucil (CLB) belongs to the class of nitrogen mustards (NMs), which are highly reactive bifunctional alkylating agents and were the first chemotherapeutic agents developed. They form DNA interstrand crosslinks (ICLs), which cause a blockage of DNA strand separation, inhibiting essential processes in DNA metabolism like replication and transcription. In fast replicating cells, e.g., tumor cells, this can induce cell death. The upregulation of ICL repair is thought to be a key factor for the resistance of tumor cells to ICL-inducing cytostatic agents including NMs. To monitor induction and repair of CLB-induced ICLs, we adjusted the automated reversed fluorometric analysis of alkaline DNA unwinding assay (rFADU) for the detection of ICLs in adherent cells. For the detection of monoalkylated DNA bases we established an LC-MS/MS method. We performed a comparative analysis of adduct formation and removal in five human cell lines and in peripheral blood mononuclear cells (PBMCs) after treatment with CLB. Dose-dependent increases in adduct formation were observed, and suitable treatment concentrations were identified for each cell line, which were then used for monitoring the kinetics of adduct formation. We observed significant differences in the repair kinetics of the cell lines tested. For example, in A2780 cells, hTERT immortalized VH10 cells, and in PBMCs a time-dependent repair of the two main monoalkylated DNA-adducts was confirmed. Regarding ICLs, repair was observed in all cell systems except for PBMCs. In conclusion, LC-MS/MS analyses combined with the rFADU technique are powerful tools to study the molecular mechanisms of NM-induced DNA damage and repair. By applying these methods to a spectrum of human cell systems of different origin and transformation status, we obtained insight into the cell-type specific repair of different CLB-induced DNA lesions, which may help identify novel resistance mechanisms of tumors and define molecular targets for therapeutic interventions.
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Key Words
- BER, base excision repair
- CLB, chlorambucil
- Chlorambucil
- DNA repair kinetics
- ICL, interstrand crosslink
- Interstrand crosslink
- MS, mass spectrometry
- Mass spectrometry
- Monoalkylated DNA adducts
- NER, nucleotide excision repair
- NM, Nitrogen mustard
- Nitrogen mustard
- PBMCs, peripheral blood mononuclear cells
- PI, propidium iodide
- RPE-1, human retinal pigment epithelial
- SD, standard deviation
- VH10, human foreskin fibroblasts
- dG, 2'-deoxyguanosine
- hTERT, human telomerase reverse transcriptase
- rFADU, reverse fluorometric analysis of alkaline DNA unwinding
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Affiliation(s)
- Sarah Ceylan Krassnig
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Marina Mäser
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Nicola Anna Probst
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Jens Werner
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Charlotte Schlett
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Nina Schumann
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Gudrun von Scheven
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
| | - Aswin Mangerich
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
- Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, D-14558 Nuthetal, Germany
| | - Alexander Bürkle
- Molecular Toxicology, Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
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12
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Wróblewska AM, Gos N, Zajda J, Ruzik L, Matczuk M. Drawbacks in the efficient monitoring of gold nanoparticle-based cisplatin delivery systems formation by HPLC-ICP-MS. METALLOMICS : INTEGRATED BIOMETAL SCIENCE 2023; 15:6985008. [PMID: 36631296 DOI: 10.1093/mtomcs/mfad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023]
Abstract
Since chemotherapy suffers many limitations related to side effects of anticancer drugs (e.g. cisplatin - CDDP), nanoparticles are probed as carriers in targeted drug delivery. Gold nanoparticles (AuNPs) are broadly investigated due to their biocompatibility, nontoxicity, and tunable surface. Despite many AuNPs-cisplatin systems (AuNP-CS) reports found in the literature, only a few include studies of their synthesis and formation efficiency using analytical tools providing simultaneously qualitative and quantitative analytical information. Therefore, this research continues our previous study of AuNP-CS formation investigated by capillary electrophoresis with inductively coupled plasma mass spectrometry (ICP-MS). Namely, it presents the analogical approach but employs the coupling of another separation technique: isocratic reversed-phase high-performance liquid chromatography. The study concerns the difficulties of analytical method optimization path and contains a discussion of the observed problematic issues related to the analysis and preparation of AuNP-CS. Moreover, the presented work confronts the performance and applicability of both tools for the scrutiny of AuNP-CS, especially considering the comparison of their resolution power.
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Affiliation(s)
- Anna M Wróblewska
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
| | - Nina Gos
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
| | - Joanna Zajda
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
| | - Lena Ruzik
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
| | - Magdalena Matczuk
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland
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13
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Song X, Song X, Lai W, Wang H. Hyperactive DNA Cutting for Unbiased UHPLC-MS/MS Quantification of Epigenetic DNA Marks by Engineering DNase I Mutants. Anal Chem 2022; 94:17670-17676. [PMID: 36490323 DOI: 10.1021/acs.analchem.2c04485] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic DNA modifications, such as 5-methylcytosine, 5-hydroxymethylcytosine, and 5-formylcytosine, are associated with a variety of diseases and potential biomarkers for cancer diagnosis and therapy. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays are considered to be the gold standard for qualitative and quantitative detection of DNA modifications. DNA digestion for converting long DNA polymer into 2'-deoxynucleosides is an important preprocessing step to achieve sensitive and accurate LC-MS/MS quantification. Here, we showed that, as stimulated by divalent metal ions, Mg2+ and Mn2+, the engineered human DNase I Q9R:E13R:N74K mutant can efficiently digest DNA in the presence of monovalent metal ions at a high concentration (e.g., 1 M NaCl), showing hyperactivity on DNA cutting. We also found that the engineered DNase I mutants display exceptional DNA-cutting activity over a wider pH range (5.5-9.5). Due to their hyperactivity and high salt tolerance, the engineered DNase I mutants cut DNA 5mC and dC efficiently. Benefitting from this DNA-cutting hyperactivity, we demonstrated an LC-MS/MS assay for unbiased and accurate quantification of DNA 5mC.
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Affiliation(s)
- Xingrui Song
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xinyue Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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14
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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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15
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Fan Y, Sun G, Kaw HY, Zhu L, Wang W. Analytical characterization of nucleotides and their concentration variation in drinking water treatment process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:152510. [PMID: 34968603 DOI: 10.1016/j.scitotenv.2021.152510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Nucleotides, as the basic building blocks of nucleic acids, widely exist in aqueous environment. In this study, we developed a solid phase extraction-high performance liquid chromatography-tandem mass spectrometry (SPE-UPLC-MS/MS) method for the analysis of 5'-adenosine monophosphate (AMP), 5'-uridine monophosphate (UMP), 5'-cytidine monophosphate (CMP) and 5'-guanosine monophosphate (GMP). The method achieved limits of detection (LODs) of 0.1-1.0 ng/L, and recoveries of 85-95% for the four tested nucleotides. The occurrence and concentrations of the four nucleotides in water from eight representative drinking water treatment and distribution systems in China were determined using this method. All four nucleotides were detectable in water treatment plant (WTP) influent and effluent, at concentrations of up to 30 ng/L and with occurrence frequency of around 90%. The concentrations of identified nucleotides increased 3-10 times after 10 km of water age in the water distribution system. Biological filters and coagulation increased the concentrations of nucleotides, conversely, active carbon, ozonation, and ultrafiltration membrane removed nucleotides in water. The effects of active carbon and coagulation were further confirmed using laboratory-controlled experiment. In addition, monochlorinated nucleotides were identified as the chlorination products of nucleotides.
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Affiliation(s)
- Yi Fan
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Guangrong Sun
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Han Yeong Kaw
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Wei Wang
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
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16
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Lu K, Hsiao YC, Liu CW, Schoeny R, Gentry R, Starr TB. A Review of Stable Isotope Labeling and Mass Spectrometry Methods to Distinguish Exogenous from Endogenous DNA Adducts and Improve Dose-Response Assessments. Chem Res Toxicol 2021; 35:7-29. [PMID: 34910474 DOI: 10.1021/acs.chemrestox.1c00212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cancer remains the second most frequent cause of death in human populations worldwide, which has been reflected in the emphasis placed on management of risk from environmental chemicals considered to be potential human carcinogens. The formation of DNA adducts has been considered as one of the key events of cancer, and persistence and/or failure of repair of these adducts may lead to mutation, thus initiating cancer. Some chemical carcinogens can produce DNA adducts, and DNA adducts have been used as biomarkers of exposure. However, DNA adducts of various types are also produced endogenously in the course of normal metabolism. Since both endogenous physiological processes and exogenous exposure to xenobiotics can cause DNA adducts, the differentiation of the sources of DNA adducts can be highly informative for cancer risk assessment. This review summarizes a highly applicable methodology, termed stable isotope labeling and mass spectrometry (SILMS), that is superior to previous methods, as it not only provides absolute quantitation of DNA adducts but also differentiates the exogenous and endogenous origins of DNA adducts. SILMS uses stable isotope-labeled substances for exposure, followed by DNA adduct measurement with highly sensitive mass spectrometry. Herein, the utilities and advantage of SILMS have been demonstrated by the rich data sets generated over the last two decades in improving the risk assessment of chemicals with DNA adducts being induced by both endogenous and exogenous sources, such as formaldehyde, vinyl acetate, vinyl chloride, and ethylene oxide.
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Affiliation(s)
- Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Rita Schoeny
- Rita Schoeny LLC, 726 Fifth Street NE, Washington, D.C. 20002, United States
| | - Robinan Gentry
- Ramboll US Consulting, Inc., Monroe, Louisiana 71201, United States
| | - Thomas B Starr
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,TBS Associates, 7500 Rainwater Road, Raleigh, North Carolina 27615, United States
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17
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Chang YJ, Cooke MS, Chen YR, Yang SF, Li PS, Hu CW, Chao MR. Is high resolution a strict requirement for mass spectrometry-based cellular DNA adductomics? CHEMOSPHERE 2021; 274:129991. [PMID: 33979922 PMCID: PMC8119933 DOI: 10.1016/j.chemosphere.2021.129991] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/31/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Exposure to endogenous and exogenous factors can result in the formation of a wide variety of DNA adducts, and these may lead to gene mutations, thereby contributing to the development of cancer. DNA adductomics, a novel tool for exposomics, aims to detect the totality of DNA adducts. Liquid chromatography-high resolution mass spectrometry (LC-HRMS) is the state-of-the-art method for DNA adductomic analysis, although its high cost has limited widespread use. In this study, we compared the analytical performance between HRMS and the more popular/accessible triple-quadrupole MS (QqQ-MS). We initially developed and optimized a hybrid quadrupole-linear ion trap-orbitrap MS (Q-LIT-OT-MS) method, considering the detection of both purine and pyrimidine adducts. LC-Q-LIT-OT-MS and LC-QqQ-MS methods were compared by non-targeted screening of formaldehyde-induced DNA adducts. Using the results from Q-LIT-OT-MS as the gold standard, QqQ-MS successfully detected 12 out of 18 formaldehyde-induced DNA adducts/inter-strand crosslinks (ICLs). QqQ-MS however also produced nine false-positive results owing to the inherent instrumental mass resolution limits. To discriminate the false-positive results from the accurate ones, we firstly introduced a statistical analysis, partial least squares-discriminant analysis, which efficiently excluded the false signals. Six DNA adducts/ICLs were not detected by QqQ-MS, due to insufficient sensitivity. This could be overcome by employing a selected reaction monitoring scan mode with multiple injections. Overall, this study demonstrated that high resolution may not be a strict requirement for MS-based DNA adductomics. LC-QqQ-MS with statistical analysis, could also provide a comparable performance as HRMS for pre-screening purposes.
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Affiliation(s)
- Yuan-Jhe Chang
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung, 402, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, 402, Taiwan
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Shun-Fa Yang
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, 402, Taiwan; Institute of Medicine, Chung Shan Medical University, Taichung, 402, Taiwan
| | - Pei-Shan Li
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung, 402, Taiwan
| | - Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung, 402, Taiwan.
| | - Mu-Rong Chao
- 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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18
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Cheng X, Liu C, Yang Y, Liang L, Chen B, Yu H, Xia J, Liu S, Li Y. Advances in sulfur mustard-induced DNA adducts: Characterization and detection. Toxicol Lett 2021; 344:46-57. [PMID: 33705862 DOI: 10.1016/j.toxlet.2021.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022]
Abstract
Sulfur mustard (SM) is a blister chemical warfare agent with severe cytotoxicity and genotoxicity. It can extensively alkylate important macromolecules in organisms, such as proteins, DNA, and lipids, and produce a series of metabolites, among which the characteristic ones can be used as biomarkers. The exact toxicological mechanisms of SM remain unclear but mainly involve the DNA lesions induced by alkylation and oxidative stress caused by glutathione depletion. Various methods have been used to analyze DNA damage caused by SM. Among these methods, liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology stands out and makes it possible to observe damage in view of biomarkers induced by SM. Sample preparation is critical for detection by LC-MS/MS and mainly includes DNA isolation, adduct hydrolysis, and adduct purification. Moreover, optimization of chromatographic conditions, selection of MS transitions, and quantitative strategies are also essential. SM-DNA adducts are generally considered to be N7-HETEG, O6-HETEG, N7-BisG, and N3-HETEA. This article proposes some other possibilities of SM-DNA adducts for the identification of SM genotoxicity.
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Affiliation(s)
- Xi Cheng
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, PR China; State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Changcai Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Yang Yang
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Longhui Liang
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Bo Chen
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Huilan Yu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Junmei Xia
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Shilei Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China.
| | - Yihe Li
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, PR China.
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19
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Pohanka M. Colorimetric hand-held sensors and biosensors with a small digital camera as signal recorder, a review. REVIEWS IN ANALYTICAL CHEMISTRY 2020; 39:20-30. [DOI: 10.1515/revac-2020-0111] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2025]
Abstract
Abstract
Sensors, biosensors, lateral flow immunoassays, portable thin-layer chromatography and similar devices for hand-held assay are tools suitable for field or out of laboratories assays of various analytes. The assays frequently exert a limit of detection and sensitivity close to more expensive and elaborative analytical methods. In recent years, huge progress has been made in the field of optical instruments where digital cameras or light sensitive chips serve for the measurement of color density. General availability of cameras, a decrease of prices and their integration into wide spectrum phones, tablets and computers give the promise of easy application of analytical methods where such cameras will be employed. This review summarizes research on hand-held assays where small cameras like the ones integrated into smartphones are used. Discussion about such assays, their practical applicability and relevant specifications are also written here.
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Affiliation(s)
- Miroslav Pohanka
- Faculty of Military Health Sciences, University of Defense , Trebesska 1575 , Hradec Kralove CZ-50001 , Czech Republic
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20
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Zhang Z, Zhang Y, Song S, Yin L, Sun D, Gu J. Recent advances in the bioanalytical methods of polyethylene glycols and PEGylated pharmaceuticals. J Sep Sci 2020; 43:1978-1997. [DOI: 10.1002/jssc.201901340] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/15/2020] [Accepted: 02/16/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Zhi Zhang
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
| | - Yuyao Zhang
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
| | - Shiwen Song
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
| | - Lei Yin
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Research Institute of Translational MedicineThe First Bethune Hospital of Jilin University Changchun P. R. China
| | - Dong Sun
- Department of Biopharmacy, College of Life ScienceJilin University Changchun P. R. China
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education”Yantai University Yantai P. R. China
| | - Jingkai Gu
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
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21
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Kahremanoglu K, Temel ER, Korkut TE, Nalbant AA, Azer BB, Durucan C, Volkan M, Boyaci E. Development of a solid-phase microextraction LC-MS/MS method for determination of oxidative stress biomarkers in biofluids. J Sep Sci 2020; 43:1925-1933. [PMID: 32118350 DOI: 10.1002/jssc.202000211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 01/08/2023]
Abstract
Recently the connection between oxidative stress and various diseases, including cancer and Alzheimer's, attracts notice as a pathway suitable for diagnostic purposes. 8-Oxo-deoxyguanosine and 8-oxo-deoxyadenosine produced from the interaction of reactive oxygen species with DNA become prominent as biomarkers. Several methods have been developed for their determination in biofluids, including solid-phase extraction and enzyme-linked immunosorbent assays. However, still, there is a need for reliable and fast analytical methods. In this context, solid-phase microextraction offers many advantages such as flexibility in geometry and applicable sample volume, as well as high adaptability to high-throughput sampling. In this study, a solid-phase microextraction method was developed for the determination of 8-oxo-deoxyguanosine and 8-oxo-deoxyadenosine in biofluids. The extractive phase of solid-phase microextraction consisted of hydrophilic-lipophilic balanced polymeric particles. In order to develop a solid-phase microextraction method suitable for the determination of the analytes in saliva and urine, several parameters, including desorption solvent, desorption time, sample pH, and ionic strength, were scrutinized. Analytical figures of merit indicated that the developed method provides reasonable interday and intraday precisions (<15% in both biofluids) with acceptable accuracy. The method provides a limit of quantification for both biomarkers at 5.0 and 10.0 ng/mL levels in saliva and urine matrices, respectively.
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Affiliation(s)
- Kubra Kahremanoglu
- Department of Chemistry, Middle East Technical University, Ankara, Turkey
| | - Ezgi Rana Temel
- Department of Chemistry, Middle East Technical University, Ankara, Turkey
| | - Tamara Ecem Korkut
- Department of Chemistry, Middle East Technical University, Ankara, Turkey
| | | | - Bersu Baştuğ Azer
- Department of Metallurgical and Materials Engineering, Middle East Technical University, Ankara, Turkey.,BIOMATEN Center of Excellence in Biomaterials and Tissue Engineering, Middle East Technical University, Ankara, Turkey
| | - Caner Durucan
- Department of Metallurgical and Materials Engineering, Middle East Technical University, Ankara, Turkey.,BIOMATEN Center of Excellence in Biomaterials and Tissue Engineering, Middle East Technical University, Ankara, Turkey
| | - Murvet Volkan
- Department of Chemistry, Middle East Technical University, Ankara, Turkey
| | - Ezel Boyaci
- Department of Chemistry, Middle East Technical University, Ankara, Turkey
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