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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] [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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2
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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2024; 40:759-776. [PMID: 37898991 PMCID: PMC11178748 DOI: 10.1007/s12264-023-01124-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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3
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Kladova OA, Tyugashev TE, Yakimov DV, Mikushina ES, Novopashina DS, Kuznetsov NA, Kuznetsova AA. The Impact of SNP-Induced Amino Acid Substitutions L19P and G66R in the dRP-Lyase Domain of Human DNA Polymerase β on Enzyme Activities. Int J Mol Sci 2024; 25:4182. [PMID: 38673769 PMCID: PMC11050361 DOI: 10.3390/ijms25084182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Base excision repair (BER), which involves the sequential activity of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases, is one of the enzymatic systems that preserve the integrity of the genome. Normal BER is effective, but due to single-nucleotide polymorphisms (SNPs), the enzymes themselves-whose main function is to identify and eliminate damaged bases-can undergo amino acid changes. One of the enzymes in BER is DNA polymerase β (Polβ), whose function is to fill gaps in DNA. SNPs can significantly affect the catalytic activity of an enzyme by causing an amino acid substitution. In this work, pre-steady-state kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring variants of Polβ that have the substitutions L19P and G66R in the dRP-lyase domain. Despite the substantial distance between the dRP-lyase domain and the nucleotidyltransferase active site, it was found that the capacity to form a complex with DNA and with an incoming dNTP is significantly altered by these substitutions. Therefore, the lower activity of the tested polymorphic variants may be associated with a greater number of unrepaired DNA lesions.
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Affiliation(s)
- Olga A. Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
| | - Timofey E. Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
| | - Denis V. Yakimov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena S. Mikushina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
| | - Daria S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Aleksandra A. Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
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4
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Spingler B. Crystal structure of the nucleoside 2'-de-oxy-guanosine dimethyl sulfoxide disolvate. Acta Crystallogr E Crystallogr Commun 2023; 79:852-855. [PMID: 37693671 PMCID: PMC10483554 DOI: 10.1107/s2056989023007405] [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: 06/13/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023]
Abstract
The title com-pound, C10H13N5O4·2C2H6OS, which is of inter-est with respect to its biological activity, at 183 K has ortho-rhom-bic (P212121) crystal symmetry. The structure displays a network of inter-molecular N-H⋯N, N-H⋯O and O-H⋯O hydrogen bonds. 2'-De-oxy-guanosine mol-ecules are linked to each other and to the two dimethyl sulfoxide solvent mol-ecules by hydrogen bonding.
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Affiliation(s)
- Bernhard Spingler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
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5
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Leng T, Guo Z, Sang Z, Xin Q, Chen F. Effect of COVID-19 on sperm parameters: pathologic alterations and underlying mechanisms. J Assist Reprod Genet 2023:10.1007/s10815-023-02795-y. [PMID: 37115332 PMCID: PMC10140716 DOI: 10.1007/s10815-023-02795-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
The rapid outbreak of the coronavirus disease 2019 (COVID-19) pandemic has brought challenges to different medical fields, especially reproductive health. To date, most studies on the effects of COVID-19 on male reproduction have some limitations. In addition, there is little research on the mechanisms underlying by which severe acute respiratory syndrome coronavirus 2 infection affects semen quality. Here, we revealed the possible impact of COVID-19 on sperm parameters and the potential mechanisms. At present, it is still controversial whether COVID-19-induced fever adversely affects sperm parameters. Severe acute respiratory syndrome coronavirus 2 can induce up-regulation of pro-inflammatory cytokine, which leads to the destruction of blood-testis barrier and impairment of spermatogenesis. Moreover, severe viral infection of the respiratory system could induce systemic oxidative stress. Sperm are highly vulnerable to it due to their limited levels of antioxidant defense, unsophisticated DNA damage detection and repair mechanisms. Our review prompt medical staff and patients to consciously check the reproductive function of COVID-19 male patients. Moreover, opening our prospective beyond the direct infection could be the key to better understand the COVID-19 short and long-term effects and provide a new idea for future treatment of patients with reproductive function injury.
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Affiliation(s)
- Taiyang Leng
- Department of Physiology, Jining Medical University, 133 Hehua Rd, Jining, 272067, China
| | - Zhihui Guo
- Department of Physiology, Jining Medical University, 133 Hehua Rd, Jining, 272067, China
| | - Ziling Sang
- Department of Physiology, Jining Medical University, 133 Hehua Rd, Jining, 272067, China
| | - Qing Xin
- Department of Physiology, Jining Medical University, 133 Hehua Rd, Jining, 272067, China
| | - Fei Chen
- Department of Physiology, Jining Medical University, 133 Hehua Rd, Jining, 272067, China.
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6
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Tang T, Chen Y, Du Y, Yao B, Liu M. Effects of functional modules and bacterial clusters response on transmission performance of antibiotic resistance genes under antibiotic stress during anaerobic digestion of livestock wastewater. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129870. [PMID: 36063716 DOI: 10.1016/j.jhazmat.2022.129870] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/06/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
The formation and transmission of antibiotic resistance genes (ARGs) have attracted increasing attention. It is unclear whether the internal mechanisms by which antibiotics affect horizontal gene transfer (HGT) of ARGs during anaerobic digestion (AD) were influenced by dose and type. We investigated the effects of two major antibiotics (oxytetracycline, OTC, and sulfamethoxazole, SMX) on ARGs during AD according to antibiotic concentration in livestock wastewater influent. The low-dose antibiotic (0.5 mg/L) increased ROS and SOS responses, promoting the formation of ARGs. Meanwhile, low-dose antibiotics could also promote the spread of ARGs by promoting pili, communication responses, and the type IV secretion system (T4SS). However, different types and doses of antibiotics would lead to changes in the above functional modules and then affect the enrichment of ARGs. With the increasing dose of SMX, the advantages of pili and communication responses would gradually change. In the OTC system, low-dose has the strongest promoting ability in both pili and communication responses. Similarly, an increase in the dose of SMX would change T4SS from facilitation to inhibition, while OTC completely inhibits T4SS. Microbial and network analysis also revealed that low-dose antibiotics were more favorable for the growth of host bacteria.
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Affiliation(s)
- Taotao Tang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ying Chen
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ye Du
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Bing Yao
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Min Liu
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China.
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7
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Abstract
DNA damage by chemicals, radiation, or oxidative stress leads to a mutational spectrum, which is complex because it is determined in part by lesion structure, the DNA sequence context of the lesion, lesion repair kinetics, and the type of cells in which the lesion is replicated. Accumulation of mutations may give rise to genetic diseases such as cancer and therefore understanding the process underlying mutagenesis is of immense importance to preserve human health. Chemical or physical agents that cause cancer often leave their mutational fingerprints, which can be used to back-calculate the molecular events that led to disease. To make a clear link between DNA lesion structure and the mutations a given lesion induces, the field of single-lesion mutagenesis was developed. In the last three decades this area of research has seen much growth in several directions, which we attempt to describe in this Perspective.
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Affiliation(s)
- Ashis K Basu
- Department of Chemistry, The University of Connecticut Storrs, Storrs, Connecticut 06269, United States
| | - John M Essigmann
- Departments of Chemistry, Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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8
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Patlán-Vázquez AG, Ayala-García VM, Vallin C, Cortés J, Vásquez-Morales SG, Robleto EA, Nudler E, Pedraza-Reyes M. Dynamics of Mismatch and Alternative Excision-Dependent Repair in Replicating Bacillus subtilis DNA Examined Under Conditions of Neutral Selection. Front Microbiol 2022; 13:866089. [PMID: 35847079 PMCID: PMC9280176 DOI: 10.3389/fmicb.2022.866089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Spontaneous DNA deamination is a potential source of transition mutations. In Bacillus subtilis, EndoV, a component of the alternative excision repair pathway (AER), counteracts the mutagenicity of base deamination-induced mispairs. Here, we report that the mismatch repair (MMR) system, MutSL, prevents the harmful effects of HNO2, a deaminating agent of Cytosine (C), Adenine (A), and Guanine (G). Using Maximum Depth Sequencing (MDS), which measures mutagenesis under conditions of neutral selection, in B. subtilis strains proficient or deficient in MutSL and/or EndoV, revealed asymmetric and heterogeneous patterns of mutations in both DNA template strands. While the lagging template strand showed a higher frequency of C → T substitutions; G → A mutations, occurred more frequently in the leading template strand in different genetic backgrounds. In summary, our results unveiled a role for MutSL in preventing the deleterious effects of base deamination and uncovered differential patterns of base deamination processing by the AER and MMR systems that are influenced by the sequence context and the replicating DNA strand.
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Affiliation(s)
- Adriana G. Patlán-Vázquez
- Division of Natural and Exact Sciences, Department of Biology, University of Guanajuato, Guanajuato, Mexico
| | | | - Carmen Vallin
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Jonathan Cortés
- Biological Research Center, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Suria G. Vásquez-Morales
- Division of Natural and Exact Sciences, Department of Biology, University of Guanajuato, Guanajuato, Mexico
| | - Eduardo A. Robleto
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Evgeny Nudler
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, United States
| | - Mario Pedraza-Reyes
- Division of Natural and Exact Sciences, Department of Biology, University of Guanajuato, Guanajuato, Mexico
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9
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Role of Mitochondrial Dynamics in Cocaine's Neurotoxicity. Int J Mol Sci 2022; 23:ijms23105418. [PMID: 35628228 PMCID: PMC9145816 DOI: 10.3390/ijms23105418] [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: 04/20/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 01/25/2023] Open
Abstract
The dynamic balance of mitochondrial fission and fusion maintains mitochondrial homeostasis and optimal function. It is indispensable for cells such as neurons, which rely on the finely tuned mitochondria to carry out their normal physiological activities. The potent psychostimulant cocaine impairs mitochondria as one way it exerts its neurotoxicity, wherein the disturbances in mitochondrial dynamics have been suggested to play an essential role. In this review, we summarize the neurotoxicity of cocaine and the role of mitochondrial dynamics in cellular physiology. Subsequently, we introduce current findings that link disturbed neuronal mitochondrial dynamics with cocaine exposure. Finally, the possible role and potential therapeutic value of mitochondrial dynamics in cocaine neurotoxicity are discussed.
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10
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Sun S, Brazhnik K, Lee M, Maslov AY, Zhang Y, Huang Z, Klugman S, Park BH, Vijg J, Montagna C. Single-cell analysis of somatic mutation burden in mammary epithelial cells of pathogenic BRCA1/2 mutation carriers. J Clin Invest 2022; 132:148113. [PMID: 35025760 PMCID: PMC8884908 DOI: 10.1172/jci148113] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 01/11/2022] [Indexed: 12/04/2022] Open
Abstract
Inherited germline mutations in the breast cancer gene 1 (BRCA1) or BRCA2 genes (herein BRCA1/2) greatly increase the risk of breast and ovarian cancer, presumably by elevating somatic mutational errors as a consequence of deficient DNA repair. However, this has never been directly demonstrated by a comprehensive analysis of the somatic mutational landscape of primary, noncancer, mammary epithelial cells of women diagnosed with pathogenic BRCA1/2 germline mutations. Here, we used an accurate, single-cell whole-genome sequencing approach to first show that telomerized primary mammary epithelial cells heterozygous for a highly penetrant BRCA1 variant displayed a robustly elevated mutation frequency as compared with their isogenic control cells. We then demonstrated a small but statistically significant increase in mutation frequency in mammary epithelial cells isolated from the breast of BRCA1/2 mutation carriers as compared with those obtained from age-matched controls with no genetically increased risk for breast cancer.
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Affiliation(s)
- Shixiang Sun
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States of America
| | - Kristina Brazhnik
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States of America
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States of America
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States of America
| | - Yi Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States of America
| | - Zhenqiu Huang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States of America
| | - Susan Klugman
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, United States of America
| | - Ben H Park
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States of America
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States of America
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States of America
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11
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Hyun SH, Bhilare KD, In G, Park CK, Kim JH. Effects of Panax ginseng and ginsenosides on oxidative stress and cardiovascular diseases: pharmacological and therapeutic roles. J Ginseng Res 2022; 46:33-38. [PMID: 35058725 PMCID: PMC8753520 DOI: 10.1016/j.jgr.2021.07.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/21/2021] [Indexed: 01/04/2023] Open
Abstract
Traditionally, Asian ginseng or Korean ginseng, Panax ginseng has long been used in Korea and China to treat various diseases. The main active components of Panax ginseng is ginsenoside, which is known to have various pharmacological treatment effects such as antioxidant, vascular easing, anti-allergic, anti-inflammatory, anti-diabetes, and anticancer. Most reactive oxygen species (ROS) cause chronic diseases such as myocardial symptoms and cause fatal oxidative damage to cell membrane lipids and proteins. Therefore, many studies that inhibit the production of oxidative stress have been conducted in various fields of physiology, pathophysiology, medicine and health, and disease. Recently, ginseng or ginsenosides have been known to act as antioxidants in vitro and in vivo results, which have a beneficial effect on preventing cardiovascular disease. The current review aims to provide mechanisms and inform precious information on the effects of ginseng and ginsenosides on the prevention of oxidative stress and cardiovascular disease in animals and clinical trials.
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Affiliation(s)
- Sun Hee Hyun
- Laboratory of Efficacy Research, Korea Ginseng Corporation, Daejeon, Republic of Korea
| | - Kiran D. Bhilare
- College of Veterinary Medicine, Biosafety Research Institute, Jeonbuk National University, Jeollabuk-do, Republic of Korea
| | - Gyo In
- Laboratory of Efficacy Research, Korea Ginseng Corporation, Daejeon, Republic of Korea
| | - Chae-Kyu Park
- Laboratory of Efficacy Research, Korea Ginseng Corporation, Daejeon, Republic of Korea
- Corresponding author. College of Veterinary Medicine, Biosafety Research Institute, Chonbuk National University, Jeollabuk-do, Republic of Korea.
| | - Jong-Hoon Kim
- College of Veterinary Medicine, Biosafety Research Institute, Jeonbuk National University, Jeollabuk-do, Republic of Korea
- Corresponding author. Laboratory of Efficacy Research, Korea Ginseng Corporation, 30, Gajeong-ro, Shinseong-dong, Yuseong-gu, Daejeon, 34128, Republic of Korea.
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12
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Agapov A, Olina A, Kulbachinskiy A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3018-3041. [PMID: 35323981 PMCID: PMC8989532 DOI: 10.1093/nar/gkac174] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular DNA is continuously transcribed into RNA by multisubunit RNA polymerases (RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the activities of cellular enzymes, reactions with endogenous and exogenous chemicals or irradiation. Here, we review available data on translesion RNA synthesis by multisubunit RNAPs from various domains of life, define common principles and variations in DNA damage sensing by RNAP, and consider existing controversies in the field of translesion transcription. Depending on the type of DNA lesion, it may be correctly bypassed by RNAP, or lead to transcriptional mutagenesis, or result in transcription stalling. Various lesions can affect the loading of the templating base into the active site of RNAP, or interfere with nucleotide binding and incorporation into RNA, or impair RNAP translocation. Stalled RNAP acts as a sensor of DNA damage during transcription-coupled repair. The outcome of DNA lesion recognition by RNAP depends on the interplay between multiple transcription and repair factors, which can stimulate RNAP bypass or increase RNAP stalling, and plays the central role in maintaining the DNA integrity. Unveiling the mechanisms of translesion transcription in various systems is thus instrumental for understanding molecular pathways underlying gene regulation and genome stability.
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Affiliation(s)
- Aleksei Agapov
- Correspondence may also be addressed to Aleksei Agapov. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute” Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- To whom correspondence should be addressed. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
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13
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Nachtergael A, Lanterbecq D, Spanoghe M, Belayew A, Duez P. Effects of Chemopreventive Natural Compounds on the Accuracy of 8-oxo-7,8-dihydro-2'-deoxyguanosine Translesion Synthesis. PLANTA MEDICA 2021; 87:868-878. [PMID: 34237787 DOI: 10.1055/a-1527-1435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Translesion synthesis is a DNA damage tolerance mechanism that relies on a series of specialized DNA polymerases able to bypass a lesion on a DNA template strand during replication or post-repair synthesis. Specialized translesion synthesis DNA polymerases pursue replication by inserting a base opposite to this lesion, correctly or incorrectly depending on the lesion nature, involved DNA polymerase(s), sequence context, and still unknown factors. To measure the correct or mutagenic outcome of 8-oxo-7,8-dihydro-2'-deoxyguanosine bypass by translesion synthesis, a primer-extension assay was performed in vitro on a template DNA bearing this lesion in the presence of nuclear proteins extracted from human intestinal epithelial cells (FHs 74 Int cell line); the reaction products were analyzed by both denaturing capillary electrophoresis (to measure the yield of translesion elongation) and pyrosequencing (to determine the identity of the nucleotide inserted in front of the lesion). The influence of 14 natural polyphenols on the correct or mutagenic outcome of translesion synthesis through 8-oxo-7,8-dihydro-2'-deoxyguanosine was then evaluated in 2 experimental conditions by adding the polyphenol either (i) to the reaction mix during the primer extension assay; or (ii) to the culture medium, 24 h before cell harvest and nuclear proteins extraction. Most of the tested polyphenols significantly influenced the outcome of translesion synthesis, either through an error-free (apigenin, baicalein, sakuranetin, and myricetin) or a mutagenic pathway (epicatechin, chalcone, genistein, magnolol, and honokiol).
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Affiliation(s)
- Amandine Nachtergael
- Unit of Therapeutic Chemistry and Pharmacognosy, Research Institute for Health Sciences and Technology, University of Mons (UMONS), Mons, Belgium
| | - Déborah Lanterbecq
- Laboratory of Biotechnology and Applied Biology, Haute Ecole Provinciale de Hainaut CONDORCET, Ath, Belgium
| | - Martin Spanoghe
- Laboratory of Biotechnology and Applied Biology, Haute Ecole Provinciale de Hainaut CONDORCET, Ath, Belgium
| | - Alexandra Belayew
- Department of Metabolic and Molecular Biochemistry, Research Institute for Health Sciences and Technology, University of Mons (UMONS), Mons, Belgium
| | - Pierre Duez
- Unit of Therapeutic Chemistry and Pharmacognosy, Research Institute for Health Sciences and Technology, University of Mons (UMONS), Mons, Belgium
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14
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Huang R, Chen H, Liang J, Li Y, Yang J, Luo C, Tang Y, Ding Y, Liu X, Yuan Q, Yu H, Ye Y, Xu W, Xie X. Dual Role of Reactive Oxygen Species and their Application in Cancer Therapy. J Cancer 2021; 12:5543-5561. [PMID: 34405016 PMCID: PMC8364652 DOI: 10.7150/jca.54699] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 06/30/2021] [Indexed: 12/17/2022] Open
Abstract
Reactive oxygen species (ROS) play a dual role in the initiation, development, suppression, and treatment of cancer. Excess ROS can induce nuclear DNA, leading to cancer initiation. Not only that, but ROS also inhibit T cells and natural killer cells and promote the recruitment and M2 polarization of macrophages; consequently, cancer cells escape immune surveillance and immune defense. Furthermore, ROS promote tumor invasion and metastasis by triggering epithelial-mesenchymal transition in tumor cells. Interestingly, massive accumulation of ROS inhibits tumor growth in two ways: (1) by blocking cancer cell proliferation by suppressing the proliferation signaling pathway, cell cycle, and the biosynthesis of nucleotides and ATP and (2) by inducing cancer cell death via activating endoplasmic reticulum stress-, mitochondrial-, and P53- apoptotic pathways and the ferroptosis pathway. Unfortunately, cancer cells can adapt to ROS via a self-adaption system. This review highlighted the bidirectional regulation of ROS in cancer. The study further discussed the application of massively accumulated ROS in cancer treatment. Of note, the dual role of ROS in cancer and the self-adaptive ability of cancer cells should be taken into consideration for cancer prevention.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Xiang Xie
- Public Center of Experimental Technology, The school of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan Province, 646000, China
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15
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Experimental evolution of extremophile resistance to ionizing radiation. Trends Genet 2021; 37:830-845. [PMID: 34088512 DOI: 10.1016/j.tig.2021.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/22/2022]
Abstract
A growing number of known species possess a remarkable characteristic - extreme resistance to the effects of ionizing radiation (IR). This review examines our current understanding of how organisms can adapt to and survive exposure to IR, one of the most toxic stressors known. The study of natural extremophiles such as Deinococcus radiodurans has revealed much. However, the evolution of Deinococcus was not driven by IR. Another approach, pioneered by Evelyn Witkin in 1946, is to utilize experimental evolution. Contributions to the IR-resistance phenotype affect multiple aspects of cell physiology, including DNA repair, removal of reactive oxygen species, the structure and packaging of DNA and the cell itself, and repair of iron-sulfur centers. Based on progress to date, we overview the diversity of mechanisms that can contribute to biological IR resistance arising as a result of either natural or experimental evolution.
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16
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Selveshwari S, Lele K, Dey S. Genomic signatures of UV resistance evolution in
Escherichia coli
depend on the growth phase during exposure. J Evol Biol 2021; 34:953-967. [DOI: 10.1111/jeb.13764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/27/2020] [Accepted: 01/13/2021] [Indexed: 11/28/2022]
Affiliation(s)
- S Selveshwari
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
| | - Kasturi Lele
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
| | - Sutirth Dey
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
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17
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Herek JS, Vargas L, Rinas Trindade SA, Rutkoski CF, Macagnan N, Hartmann PA, Hartmann MT. Genotoxic effects of glyphosate on Physalaemus tadpoles. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 81:103516. [PMID: 33080355 DOI: 10.1016/j.etap.2020.103516] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/01/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
Genotoxicity studies have revealed that pesticides bind to genetic material in non-target vertebrates, thereby impairing the genetic integrity of these animals. The main objective of this study was to determine the genotoxic damage in erythrocytes of two native South American amphibian Physalaemus cuvieri and Physalaemus gracilis, both species exposed to a glyphosate-based herbicide. We evaluated the presence of micronuclei (MN) and erythrocyte nuclear abnormalities (ENA) as biomarkers for potential genotoxic compounds. Tadpoles were exposed to doses permitted by Brazilian legislation and concentrations found naturally in Brazilian and Argentinian waters (500, 700 and 1000 μg/L). Glyphosate-based herbicide caused micronuclei formation and several types of erythrocyte nuclear abnormalities in both Physalaemus species. The total frequency of MN and ENA demonstrated the occurrence of cell damage at all tested concentrations. Glyphosate herbicide can be considered a genotoxic that may impact the genetic integrity of native populations of P. cuvieri and P. gracilis.
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Affiliation(s)
- Jéssica Samara Herek
- Laboratory of Ecology and Conservation, Federal University of Fronteira Sul, Erechim Campus, Brazil, ERS 135 - Km 72, nº 200, Erechim, RS, Brazil.
| | - Luana Vargas
- Laboratory of Ecology and Conservation, Federal University of Fronteira Sul, Erechim Campus, Brazil, ERS 135 - Km 72, nº 200, Erechim, RS, Brazil.
| | - Suélen Andressa Rinas Trindade
- Laboratory of Ecology and Conservation, Federal University of Fronteira Sul, Erechim Campus, Brazil, ERS 135 - Km 72, nº 200, Erechim, RS, Brazil.
| | - Camila Fatima Rutkoski
- Laboratory of Ecology and Conservation, Federal University of Fronteira Sul, Erechim Campus, Brazil, ERS 135 - Km 72, nº 200, Erechim, RS, Brazil.
| | - Natani Macagnan
- Laboratory of Ecology and Conservation, Federal University of Fronteira Sul, Erechim Campus, Brazil, ERS 135 - Km 72, nº 200, Erechim, RS, Brazil.
| | - Paulo Afonso Hartmann
- Laboratory of Ecology and Conservation, Federal University of Fronteira Sul, Erechim Campus, Brazil, ERS 135 - Km 72, nº 200, Erechim, RS, Brazil.
| | - Marilia Teresinha Hartmann
- Laboratory of Ecology and Conservation, Federal University of Fronteira Sul, Erechim Campus, Brazil, ERS 135 - Km 72, nº 200, Erechim, RS, Brazil.
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18
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Free Radicals as a Double-Edged Sword: The Cancer Preventive and Therapeutic Roles of Curcumin. Molecules 2020; 25:molecules25225390. [PMID: 33217990 PMCID: PMC7698794 DOI: 10.3390/molecules25225390] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 01/07/2023] Open
Abstract
Free radicals, generally composed of reactive oxygen species (ROS) and reactive nitrogen species (RNS), are generated in the body by various endogenous and exogenous systems. The overproduction of free radicals is known to cause several chronic diseases including cancer. However, increased production of free radicals by chemotherapeutic drugs is also associated with apoptosis in cancer cells, indicating the dual nature of free radicals. Among various natural compounds, curcumin manifests as an antioxidant in normal cells that helps in the prevention of carcinogenesis. It also acts as a prooxidant in cancer cells and is associated with inducing apoptosis. Curcumin quenches free radicals, induces antioxidant enzymes (catalase, superoxide dismutase, glutathione peroxidase), and upregulates antioxidative protein markers-Nrf2 and HO-1 that lead to the suppression of cellular oxidative stress. In cancer cells, curcumin aggressively increases ROS that results in DNA damage and subsequently cancer cell death. It also sensitizes drug-resistant cancer cells and increases the anticancer effects of chemotherapeutic drugs. Thus, curcumin shows beneficial effects in prevention, treatment and chemosensitization of cancer cells. In this review, we will discuss the dual role of free radicals as well as the chemopreventive and chemotherapeutic effects of curcumin and its analogues against cancer.
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19
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Zhang X, Li L. The Significance of 8-oxoGsn in Aging-Related Diseases. Aging Dis 2020; 11:1329-1338. [PMID: 33014540 PMCID: PMC7505272 DOI: 10.14336/ad.2019.1021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/21/2019] [Indexed: 01/10/2023] Open
Abstract
Aging is a common risk factor for the occurrence and development of many diseases, such as Parkinson’s disease, Alzheimer’s disease, diabetes, hypertension, atherosclerosis and coronary heart disease, and cancer, among others, and is a key problem threatening the health and life expectancy of the elderly. Oxidative damage is an important mechanism involved in aging. The latest discovery pertaining to oxidative damage is that 8-oxoGsn (8-oxo-7,8-dihydroguanosine), an oxidative damage product of RNA, can represent the level of oxidative stress. The significance of RNA oxidative damage to aging has not been fully explained, but the relationship between the accumulation of 8-oxoGsn, a marker of RNA oxidative damage, and the occurrence of diseases has been confirmed in many aging-related diseases. Studying the aging mechanism, monitoring the aging level of the body and exploring the corresponding countermeasures are of great significance for achieving healthy aging and promoting public health and social development. This article reviews the progress of research on 8-oxoGsn in aging-related diseases.
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Affiliation(s)
- Xinmu Zhang
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Lin Li
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Beijing, China
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20
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Bruckbauer ST, Minkoff BB, Yu D, Cryns VL, Cox MM, Sussman MR. Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli. Mol Cell Proteomics 2020; 19:1375-1395. [PMID: 32536603 PMCID: PMC8015010 DOI: 10.1074/mcp.ra120.002092] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/10/2020] [Indexed: 12/12/2022] Open
Abstract
Recent work has begun to investigate the role of protein damage in cell death because of ionizing radiation (IR) exposure, but none have been performed on a proteome-wide basis, nor have they utilized MS (MS) to determine chemical identity of the amino acid side chain alteration. Here, we use Escherichia coli to perform the first MS analysis of IR-treated intact cells on a proteome scale. From quintuplicate IR-treated (1000 Gy) and untreated replicates, we successfully quantified 13,262 peptides mapping to 1938 unique proteins. Statistically significant, but low in magnitude (<2-fold), IR-induced changes in peptide abundance were observed in 12% of all peptides detected, although oxidative alterations were rare. Hydroxylation (+15.99 Da) was the most prevalent covalent adduct detected. In parallel with these studies on E. coli, identical experiments with the IR-resistant bacterium, Deinococcus radiodurans, revealed orders of magnitude less effect of IR on the proteome. In E. coli, the most significant target of IR by a wide margin was glyceraldehyde 3'-phosphate dehydrogenase (GAPDH), in which the thiol side chain of the catalytic Cys residue was oxidized to sulfonic acid. The same modification was detected in IR-treated human breast carcinoma cells. Sensitivity of GAPDH to reactive oxygen species (ROS) has been described previously in microbes and here, we present GAPDH as an immediate, primary target of IR-induced oxidation across all domains of life.
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Affiliation(s)
- Steven T Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin B Minkoff
- Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Deyang Yu
- Department of Medicine, University of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin, USA
| | - Vincent L Cryns
- Department of Medicine, University of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
| | - Michael R Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.
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21
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Kim H, Kim JS, Kim Y, Jeong Y, Kim JE, Paek NS, Kang CH. Antioxidant and Probiotic Properties of Lactobacilli and Bifidobacteria of Human Origins. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0147-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Kitamura Y, Suzuki T, Kohara A, Saeki KI. Hepatocarcinogen 4-methylquinoline induced G:C to C:G transversions in the cII gene in the liver of lambda/lacZ transgenic mice (Muta™Mouse). Mutat Res 2020; 821:111709. [PMID: 32497932 DOI: 10.1016/j.mrfmmm.2020.111709] [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: 01/15/2020] [Revised: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 11/19/2022]
Abstract
We have previously reported that quinoline increased the mutation frequency of the cII gene in the liver of lambda/lacZ transgenic mice (Muta™Mouse), and G:C to C:G transversions were the molecular signature of quinoline-induced mutations. 4-Methylquinoline (4-MeQ) has the highest mutagenicity among quinoline and isomeric methylquinolines according to the Ames test using Salmonella typhimurium TA 100, in the presence of rat liver microsomal enzymes. In this report, we examined the effect of 4-MeQ on mutagenesis in the lambda cII gene in the liver of the Muta™Mouse, and we analyzed the sequences of the mutated genes. The mutation frequency of the liver cII gene was seven times higher in 4-MeQ-treated mice than in control mice. Sequence analysis revealed that 4-MeQ primarily induced G:C to C:G transversions (37 of 45). The specificities of 4-MeQ for target organ and mutation pattern were very consistent with those of quinoline. Thus, we showed that 4-MeQ was also genotoxic in the liver of the Muta™Mouse, and as with quinoline, the G:C to C:G transversion was the molecular signature of the 4-MeQ-induced mutations.
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Affiliation(s)
- Yuki Kitamura
- College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
| | - Takayoshi Suzuki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Japan
| | - Arihiro Kohara
- JCRB Cell Bank, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Ken-Ichi Saeki
- College of Pharmacy, Kinjo Gakuin University, Nagoya, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.
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23
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Lawless C, Greaves L, Reeve AK, Turnbull DM, Vincent AE. The rise and rise of mitochondrial DNA mutations. Open Biol 2020; 10:200061. [PMID: 32428418 PMCID: PMC7276526 DOI: 10.1098/rsob.200061] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/23/2020] [Indexed: 12/24/2022] Open
Abstract
How mitochondrial DNA mutations clonally expand in an individual cell is a question that has perplexed mitochondrial biologists for decades. A growing body of literature indicates that mitochondrial DNA mutations play a major role in ageing, metabolic diseases, neurodegenerative diseases, neuromuscular disorders and cancers. Importantly, this process of clonal expansion occurs for both inherited and somatic mitochondrial DNA mutations. To complicate matters further there are fundamental differences between mitochondrial DNA point mutations and deletions, and between mitotic and post-mitotic cells, that impact this pathogenic process. These differences, along with the challenges of investigating a longitudinal process occurring over decades in humans, have so far hindered progress towards understanding clonal expansion. Here we summarize our current understanding of the clonal expansion of mitochondrial DNA mutations in different tissues and highlight key unanswered questions. We then discuss the various existing biological models, along with their advantages and disadvantages. Finally, we explore what has been achieved with mathematical modelling so far and suggest future work to advance this important area of research.
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Affiliation(s)
| | | | | | - Doug M. Turnbull
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE2 4HH, UK
| | - Amy E. Vincent
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE2 4HH, UK
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24
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Yamabe S, Tsuchida N, Yamazaki S. DFT Study of the Hydroxyl Radical Addition to 2'-Deoxyguanosine and the Guanine Base in Four Double-Stranded B-Form Dimers. J Phys Chem B 2020; 124:1374-1382. [PMID: 32011138 DOI: 10.1021/acs.jpcb.9b10330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory (DFT) calculations of reactions between 2'-deoxyguanosine (dR-Gua) and hydroxyl radical (HO•) with water molecules (H2O)n, n = 0, 1, and 2, were carried out. The HO• addition to three carbon sites, C(4), C(5), and C(8), and the subsequent ring cleavage of the three HO adducts were investigated. The addition to C(5) is of the smallest activation energy according to the largest lobe of the dR-Gua highest occupied molecular orbital (HOMO) at C(5). However, its adduct has small stability, and the C(8) adduct has the largest one. The C(8) adduct and the ring-opened amide have similar stability, which would lead to the apparent small yield of the former. Calculations were also performed on HO• additions to the C(4) and C(8) sites of the guanine moiety of four dimer sequence models of B-form DNA with nucleotide moieties (a) 5'-GA-3', (b) 5'-GG-3', (c) 5'-GT-3', and (d) 5'-GC-3'. For instance, the (a) 5'-GA-3' model has a molecular formula C39H50N15Na2O21P2. The HO• attack to C(4) is ruled out owing to the reinforced deformation of the parallel stacking of base pairs. The clear selectivity that the (b) 5'-GG-3' sequence is most reactive was found with the inclusion of the water dimer.
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Affiliation(s)
- Shinichi Yamabe
- Department of Chemistry , Nara University of Education , Takabatake-cho , Nara 630-8528 , Japan
| | - Noriko Tsuchida
- Department of Liberal Arts, Faculty of Medicine , Saitama Medical University , 38 Morohongo , Moroyama-machi, Iruma-gun, Saitama 350-0495 , Japan
| | - Shoko Yamazaki
- Department of Chemistry , Nara University of Education , Takabatake-cho , Nara 630-8528 , Japan
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25
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Brazhnik K, Sun S, Alani O, Kinkhabwala M, Wolkoff AW, Maslov AY, Dong X, Vijg J. Single-cell analysis reveals different age-related somatic mutation profiles between stem and differentiated cells in human liver. SCIENCE ADVANCES 2020; 6:eaax2659. [PMID: 32064334 PMCID: PMC6994209 DOI: 10.1126/sciadv.aax2659] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Accumulating somatic mutations have been implicated in age-related cellular degeneration and death. Because of their random nature and low abundance, somatic mutations are difficult to detect except in single cells or clonal cell lineages. Here, we show that in single hepatocytes from human liver, an organ exposed to high levels of genotoxic stress, somatic mutation frequencies are high and increase substantially with age. Considerably lower mutation frequencies were observed in liver stem cells (LSCs) and organoids derived from them. Mutational spectra in hepatocytes showed signatures of oxidative stress that were different in old age and in LSCs. A considerable number of mutations were found in functional parts of the liver genome, suggesting that somatic mutagenesis could causally contribute to the age-related functional decline and increased incidence of disease of human liver. These results underscore the importance of stem cells in maintaining genome sequence integrity in aging somatic tissues.
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Affiliation(s)
- K. Brazhnik
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - S. Sun
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - O. Alani
- Division of Transplant Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - M. Kinkhabwala
- Division of Transplant Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - A. W. Wolkoff
- Marion Bessin Liver Research Center, Division of Hepatology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - A. Y. Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - X. Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - J. Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Center for Single-Cell Omics in Aging and Disease, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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26
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Whitehall JC, Greaves LC. Aberrant mitochondrial function in ageing and cancer. Biogerontology 2019; 21:445-459. [PMID: 31802313 PMCID: PMC7347693 DOI: 10.1007/s10522-019-09853-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/23/2019] [Indexed: 12/12/2022]
Abstract
Alterations in mitochondrial metabolism have been described as one of the major hallmarks of both ageing cells and cancer. Age is the biggest risk factor for the development of a significant number of cancer types and this therefore raises the question of whether there is a link between age-related mitochondrial dysfunction and the advantageous changes in mitochondrial metabolism prevalent in cancer cells. A common underlying feature of both ageing and cancer cells is the presence of somatic mutations of the mitochondrial genome (mtDNA) which we postulate may drive compensatory alterations in mitochondrial metabolism that are advantageous for tumour growth. In this review, we discuss basic mitochondrial functions, mechanisms of mtDNA mutagenesis and their metabolic consequences, and review the evidence for and against a role for mtDNA mutations in cancer development.
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Affiliation(s)
- Julia C Whitehall
- The Medical School, Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Laura C Greaves
- The Medical School, Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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27
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Alsulami RN, Sallans L, Khisamutdinov EF, Pandey U, Glusac K, Wilson RM. Oxidation of nucleic acids: Chemistry of pyrene quinone (PQ 1) and development of dihydrodioxins (DHD 2) as DNA photooxidizing agents. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2018.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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28
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Dietel AK, Merker H, Kaltenpoth M, Kost C. Selective advantages favour high genomic AT-contents in intracellular elements. PLoS Genet 2019; 15:e1007778. [PMID: 31034469 PMCID: PMC6519830 DOI: 10.1371/journal.pgen.1007778] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 05/15/2019] [Accepted: 03/27/2019] [Indexed: 12/27/2022] Open
Abstract
Extrachromosomal genetic elements such as bacterial endosymbionts and plasmids generally exhibit AT-contents that are increased relative to their hosts’ DNA. The AT-bias of endosymbiotic genomes is commonly explained by neutral evolutionary processes such as a mutational bias towards increased A+T. Here we show experimentally that an increased AT-content of host-dependent elements can be selectively favoured. Manipulating the nucleotide composition of bacterial cells by introducing A+T-rich or G+C-rich plasmids, we demonstrate that cells containing GC-rich plasmids are less fit than cells containing AT-rich plasmids. Moreover, the cost of GC-rich elements could be compensated by providing precursors of G+C, but not of A+T, thus linking the observed fitness effects to the cytoplasmic availability of nucleotides. Accordingly, introducing AT-rich and GC-rich plasmids into other bacterial species with different genomic GC-contents revealed that the costs of G+C-rich plasmids decreased with an increasing GC-content of their host’s genomic DNA. Taken together, our work identifies selection as a strong evolutionary force that drives the genomes of intracellular genetic elements toward higher A+T contents. Genomes of endosymbiotic bacteria are commonly more AT-rich than the ones of their free-living relatives. Interestingly, genomes of other intracellular elements like plasmids or bacteriophages also tend to be richer in AT than the genomes of their hosts. The AT-bias of endosymbiotic genomes is commonly explained by neutral evolutionary processes. However, since A+T nucleotides are both more abundant and energetically less expensive than G+C nucleotides, an alternative explanation is that selective advantages drive the nucleotide composition of intracellular elements. Here we provide strong experimental evidence that intracellular elements, whose genome is more AT-rich than the genome of the host, are selectively favoured on the host level. Thus, our results emphasize the importance of selection for shaping the DNA base composition of extrachromosomal genetic elements.
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Affiliation(s)
- Anne-Kathrin Dietel
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Holger Merker
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Martin Kaltenpoth
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
- * E-mail: (MK); (CK)
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
- * E-mail: (MK); (CK)
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29
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Isotope-dilution mass spectrometry for exact quantification of noncanonical DNA nucleosides. Nat Protoc 2019; 14:283-312. [PMID: 30559375 DOI: 10.1038/s41596-018-0094-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA contains not only canonical nucleotides but also a variety of modifications of the bases. In particular, cytosine and adenine are frequently modified. Determination of the exact quantity of these noncanonical bases can contribute to the characterization of the state of a biological system, e.g., determination of disease or developmental processes, and is therefore extremely important. Here, we present a workflow that includes detailed description of critical sample preparation steps and important aspects of mass spectrometry analysis and validation. In this protocol, extraction and digestion of DNA by an optimized spin-column and enzyme-based method are described. Isotopically labeled standards are added in the course of DNA digestion, which allows exact quantification by isotope dilution mass spectrometry. To overcome the major bottleneck of such analyses, we developed a short (~14-min-per-sample) ultra-HPLC (UHPLC) and triple quadrupole mass spectrometric (QQQ-MS) method. Easy calculation of the modification abundance in the genome is possible with the provided evaluation sheets. Compared to alternative methods, the quantification procedure presented here allows rapid, ultrasensitive (low femtomole range) and highly reproducible quantification of different nucleosides in parallel. Including sample preparation and evaluation, quantification of DNA modifications can be achieved in less than a week.
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Bruckbauer ST, Trimarco JD, Martin J, Bushnell B, Senn KA, Schackwitz W, Lipzen A, Blow M, Wood EA, Culberson WS, Pennacchio C, Cox MM. Experimental Evolution of Extreme Resistance to Ionizing Radiation in Escherichia coli after 50 Cycles of Selection. J Bacteriol 2019; 201:e00784-18. [PMID: 30692176 PMCID: PMC6436341 DOI: 10.1128/jb.00784-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/24/2019] [Indexed: 02/06/2023] Open
Abstract
In previous work (D. R. Harris et al., J Bacteriol 191:5240-5252, 2009, https://doi.org/10.1128/JB.00502-09; B. T. Byrne et al., Elife 3:e01322, 2014, https://doi.org/10.7554/eLife.01322), we demonstrated that Escherichia coli could acquire substantial levels of resistance to ionizing radiation (IR) via directed evolution. Major phenotypic contributions involved adaptation of organic systems for DNA repair. We have now undertaken an extended effort to generate E. coli populations that are as resistant to IR as Deinococcus radiodurans After an initial 50 cycles of selection using high-energy electron beam IR, four replicate populations exhibit major increases in IR resistance but have not yet reached IR resistance equivalent to D. radiodurans Regular deep sequencing reveals complex evolutionary patterns with abundant clonal interference. Prominent IR resistance mechanisms involve novel adaptations to DNA repair systems and alterations in RNA polymerase. Adaptation is highly specialized to resist IR exposure, since isolates from the evolved populations exhibit highly variable patterns of resistance to other forms of DNA damage. Sequenced isolates from the populations possess between 184 and 280 mutations. IR resistance in one isolate, IR9-50-1, is derived largely from four novel mutations affecting DNA and RNA metabolism: RecD A90E, RecN K429Q, and RpoB S72N/RpoC K1172I. Additional mechanisms of IR resistance are evident.IMPORTANCE Some bacterial species exhibit astonishing resistance to ionizing radiation, with Deinococcus radiodurans being the archetype. As natural IR sources rarely exceed mGy levels, the capacity of Deinococcus to survive 5,000 Gy has been attributed to desiccation resistance. To understand the molecular basis of true extreme IR resistance, we are using experimental evolution to generate strains of Escherichia coli with IR resistance levels comparable to Deinococcus Experimental evolution has previously generated moderate radioresistance for multiple bacterial species. However, these efforts could not take advantage of modern genomic sequencing technologies. In this report, we examine four replicate bacterial populations after 50 selection cycles. Genomic sequencing allows us to follow the genesis of mutations in populations throughout selection. Novel mutations affecting genes encoding DNA repair proteins and RNA polymerase enhance radioresistance. However, more contributors are apparent.
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Affiliation(s)
- Steven T Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joseph D Trimarco
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Duke Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joel Martin
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Brian Bushnell
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Katherine A Senn
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Anna Lipzen
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Matthew Blow
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Wesley S Culberson
- Department of Medical Physics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Dai L, Xia J, Sahin O, Zhang Q. Identification of a nth-Like Gene Encoding an Endonuclease III in Campylobacter jejuni. Front Microbiol 2019; 10:698. [PMID: 31024487 PMCID: PMC6467930 DOI: 10.3389/fmicb.2019.00698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/20/2019] [Indexed: 01/31/2023] Open
Abstract
Campylobacter jejuni is a leading cause of foodborne illnesses worldwide. As a microaerobic pathogen, C. jejuni is subjected to DNA damages caused by various stresses such as reactive oxygen species (ROS) and UV radiations. The base excision repair (BER) system plays an important role in preventing mutations associated with oxidative DNA damage, but the system remains poorly characterized in Campylobacter. In this study, a BER homolog encoded by cj0595c (named nth) in C. jejuni was analyzed for endonuclease III activity and for its role in maintaining genomic stability. It was found that inactivation of nth resulted in elevated frequencies of spontaneous fluoroquinolone-resistant (FQR) and oxidative stress resistant (OXR) mutants, compared with the wild-type strain in C. jejuni. Sequencing analysis of the FQR and OXR mutants revealed that the elevated mutation rates were associated with C → T or G → A transition in gyrA (FQR mutants) or perR (for OXR mutants). In an in vitro assay, a purified recombinant C. jejuni Nth protein demonstrated endonuclease III activity that recognized and excised the thymine glycol (Tg) base from a double stranded DNA. These findings indicate that Nth functions as a BER repair enzyme in C. jejuni and is important for the repair of DNA damage, protecting the bacteria from stresses encountered within a host and in the environment.
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Affiliation(s)
- Lei Dai
- Departments of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Jing Xia
- Departments of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Orhan Sahin
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Qijing Zhang
- Departments of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
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Okumura K, Nishihara S, Inoue YH. Genetic identification and characterization of three genes that prevent accumulation of oxidative DNA damage in Drosophila adult tissues. DNA Repair (Amst) 2019; 78:7-19. [PMID: 30947023 DOI: 10.1016/j.dnarep.2019.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 01/29/2023]
Abstract
Reactive oxygen species generated in the process of energy production represent a major cause of oxidative DNA damage. Production of the oxidized guanine base, 8-oxo-guanine (8-oxoG), results in mismatched pairing with adenine and subsequently leads to G:C to T:A transversions after DNA replication. Our previous study demonstrated that Drosophila CG1795 encodes an ortholog of Ogg1, which is essential for the elimination of 8-oxoG. Moreover, the Drosophila ribosomal protein S3 (RpS3) possesses N-glycosylase activity that eliminates 8-oxoG in vitro. In this study, we show that RpS3 heterozygotes hyper-accumulate 8-oxoG in midgut cell nuclei after oxidant feeding, suggesting thatRpS3 is required for the elimination of 8-oxoG in Drosophila adults. We further showed that several muscle-aging phenotypes were significantly accelerated in RpS3 heterozygotes. Ogg1 is localized in the nucleus, while RpS3 is in the cytoplasm, closely associated with endoplasmic reticulum networks. Results of genetic analyses also suggest that these two proteins operate similarly but independently in the elimination of oxidized guanine bases from genomic DNA. Next, we obtained genetic evidence suggesting that CG42813 functions as the Drosophila ortholog of mammalian Mth1 in the elimination of oxidized dGTP (8-oxo-dGTP) from the nucleotide pool. Depletion of this gene significantly increased the number of DNA damage foci in the nuclei of Drosophila midgut cells. Furthermore, several aging-related phenotypes such as age-dependent loss of adult locomotor activities and accumulation of polyubiquitylated proteins in adult muscles were also significantly accelerated in CG42813-depleted flies. Lastly, we investigated the phenotype of adults depleted of CG9272, which encodes a protein with homology to mammalian Nth1 that is essential for the elimination of oxidized thymine. Excessive accumulation of oxidized bases was observed in the epithelial cell nuclei after oxidant feeding. In conclusion, three genes that prevent accumulation of oxidative DNA damage were identified in Drosophila.
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Affiliation(s)
- Kazuko Okumura
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-0962, Japan
| | - Shunta Nishihara
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-0962, Japan
| | - Yoshihiro H Inoue
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-0962, Japan.
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Kobets T, Iatropoulos MJ, Williams GM. Mechanisms of DNA-reactive and epigenetic chemical carcinogens: applications to carcinogenicity testing and risk assessment. Toxicol Res (Camb) 2019; 8:123-145. [PMID: 30997017 PMCID: PMC6417487 DOI: 10.1039/c8tx00250a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/18/2018] [Indexed: 01/03/2023] Open
Abstract
Chemicals with carcinogenic activity in either animals or humans produce increases in neoplasia through diverse mechanisms. One mechanism is reaction with nuclear DNA. Other mechanisms consist of epigenetic effects involving either modifications of regulatory macromolecules or perturbation of cellular regulatory processes. The basis for distinguishing between carcinogens that have either DNA reactivity or an epigenetic activity as their primary mechanism of action is detailed in this review. In addition, important applications of information on these mechanisms of action to carcinogenicity testing and human risk assessment are discussed.
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Affiliation(s)
- Tetyana Kobets
- Department of Pathology , New York Medical College , Valhalla , NY 10595 , USA . ; ; Tel: +1 914-594-3105
| | - Michael J Iatropoulos
- Department of Pathology , New York Medical College , Valhalla , NY 10595 , USA . ; ; Tel: +1 914-594-3105
| | - Gary M Williams
- Department of Pathology , New York Medical College , Valhalla , NY 10595 , USA . ; ; Tel: +1 914-594-3105
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Review of the evidence for thresholds for DNA-Reactive and epigenetic experimental chemical carcinogens. Chem Biol Interact 2019; 301:88-111. [DOI: 10.1016/j.cbi.2018.11.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/06/2018] [Accepted: 11/22/2018] [Indexed: 01/01/2023]
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Ameziane El Hassani R, Buffet C, Leboulleux S, Dupuy C. Oxidative stress in thyroid carcinomas: biological and clinical significance. Endocr Relat Cancer 2019; 26:R131-R143. [PMID: 30615595 DOI: 10.1530/erc-18-0476] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 12/16/2022]
Abstract
At physiological concentrations, reactive oxygen species (ROS), including superoxide anions and H2O2, are considered as second messengers that play key roles in cellular functions, such as proliferation, gene expression, host defence and hormone synthesis. However, when they are at supraphysiological levels, ROS are considered potent DNA-damaging agents. Their increase induces oxidative stress, which can initiate and maintain genomic instability. The thyroid gland represents a good model for studying the impact of oxidative stress on genomic instability. Indeed, one particularity of this organ is that follicular thyroid cells synthesise thyroid hormones through a complex mechanism that requires H2O2. Because of their detection in thyroid adenomas and in early cell transformation, both oxidative stress and DNA damage are believed to be neoplasia-preceding events in thyroid cells. Oxidative DNA damage is, in addition, detected in the advanced stages of thyroid cancer, suggesting that oxidative lesions of DNA also contribute to the maintenance of genomic instability during the subsequent phases of tumourigenesis. Finally, ionizing radiation and the mutation of oncogenes, such as RAS and BRAF, play a key role in thyroid carcinogenesis through separate and unique mechanisms: they upregulate the expression of two distinct 'professional' ROS-generating systems, the NADPH oxidases DUOX1 and NOX4, which cause DNA damage that may promote chromosomal instability, tumourigenesis and dedifferentiation.
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Affiliation(s)
- Rabii Ameziane El Hassani
- Laboratory of Biology of Human Pathologies 'BioPatH', Faculty of Sciences, Mohammed V University of Rabat, Rabat, Morocco
| | - Camille Buffet
- UMR 8200 CNRS, Gustave Roussy and Paris Sud University, Villejuif, France
| | - Sophie Leboulleux
- Department of Nuclear Medicine and Endocrine Oncology, Gustave Roussy and Paris Sud University, Villejuif, France
| | - Corinne Dupuy
- UMR 8200 CNRS, Gustave Roussy and Paris Sud University, Villejuif, France
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36
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Chocron ES, Munkácsy E, Pickering AM. Cause or casualty: The role of mitochondrial DNA in aging and age-associated disease. Biochim Biophys Acta Mol Basis Dis 2019; 1865:285-297. [PMID: 30419337 PMCID: PMC6310633 DOI: 10.1016/j.bbadis.2018.09.035] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/20/2018] [Accepted: 09/04/2018] [Indexed: 12/19/2022]
Abstract
The mitochondrial genome (mtDNA) represents a tiny fraction of the whole genome, comprising just 16.6 kilobases encoding 37 genes involved in oxidative phosphorylation and the mitochondrial translation machinery. Despite its small size, much interest has developed in recent years regarding the role of mtDNA as a determinant of both aging and age-associated diseases. A number of studies have presented compelling evidence for key roles of mtDNA in age-related pathology, although many are correlative rather than demonstrating cause. In this review we will evaluate the evidence supporting and opposing a role for mtDNA in age-associated functional declines and diseases. We provide an overview of mtDNA biology, damage and repair as well as the influence of mitochondrial haplogroups, epigenetics and maternal inheritance in aging and longevity.
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Affiliation(s)
- E Sandra Chocron
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA
| | - Erin Munkácsy
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA
| | - Andrew M Pickering
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA; Department of Molecular Medicine, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA.
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37
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Jelinkova S, Fojtik P, Kohutova A, Vilotic A, Marková L, Pesl M, Jurakova T, Kruta M, Vrbsky J, Gaillyova R, Valášková I, Frák I, Lacampagne A, Forte G, Dvorak P, Meli AC, Rotrekl V. Dystrophin Deficiency Leads to Genomic Instability in Human Pluripotent Stem Cells via NO Synthase-Induced Oxidative Stress. Cells 2019; 8:cells8010053. [PMID: 30650618 PMCID: PMC6356905 DOI: 10.3390/cells8010053] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/29/2018] [Accepted: 01/11/2019] [Indexed: 11/16/2022] Open
Abstract
Recent data on Duchenne muscular dystrophy (DMD) show myocyte progenitor's involvement in the disease pathology often leading to the DMD patient's death. The molecular mechanism underlying stem cell impairment in DMD has not been described. We created dystrophin-deficient human pluripotent stem cell (hPSC) lines by reprogramming cells from two DMD patients, and also by introducing dystrophin mutation into human embryonic stem cells via CRISPR/Cas9. While dystrophin is expressed in healthy hPSC, its deficiency in DMD hPSC lines induces the release of reactive oxygen species (ROS) through dysregulated activity of all three isoforms of nitric oxide synthase (further abrev. as, NOS). NOS-induced ROS release leads to DNA damage and genomic instability in DMD hPSC. We were able to reduce both the ROS release as well as DNA damage to the level of wild-type hPSC by inhibiting NOS activity.
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Affiliation(s)
- Sarka Jelinkova
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
| | - Petr Fojtik
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Aneta Kohutova
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
| | - Aleksandra Vilotic
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Lenka Marková
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Martin Pesl
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
- 1st department of Internal Medicine-Cardioangiology, Faculty of Medicine, Masaryk University, 602 00 Brno, Czech Republic.
| | - Tereza Jurakova
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Miriama Kruta
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Jan Vrbsky
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
| | - Renata Gaillyova
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- Department of Clinical Genetics, University hospital Brno, 613 00 Brno, Czech Republic.
| | - Iveta Valášková
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- Department of Clinical Genetics, University hospital Brno, 613 00 Brno, Czech Republic.
| | - Ivan Frák
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Alain Lacampagne
- PhyMedExp, INSERM, University of Montpellier, CNRS, 342 95 Montpellier CEDEX 5, France.
| | - Giancarlo Forte
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
| | - Petr Dvorak
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
| | - Albano C Meli
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- PhyMedExp, INSERM, University of Montpellier, CNRS, 342 95 Montpellier CEDEX 5, France.
| | - Vladimir Rotrekl
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
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Piecing Together How Peroxiredoxins Maintain Genomic Stability. Antioxidants (Basel) 2018; 7:antiox7120177. [PMID: 30486489 PMCID: PMC6316004 DOI: 10.3390/antiox7120177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022] Open
Abstract
Peroxiredoxins, a highly conserved family of thiol oxidoreductases, play a key role in oxidant detoxification by partnering with the thioredoxin system to protect against oxidative stress. In addition to their peroxidase activity, certain types of peroxiredoxins possess other biochemical activities, including assistance in preventing protein aggregation upon exposure to high levels of oxidants (molecular chaperone activity), and the transduction of redox signals to downstream proteins (redox switch activity). Mice lacking the peroxiredoxin Prdx1 exhibit an increased incidence of tumor formation, whereas baker's yeast (Saccharomyces cerevisiae) lacking the orthologous peroxiredoxin Tsa1 exhibit a mutator phenotype. Collectively, these findings suggest a potential link between peroxiredoxins, control of genomic stability, and cancer etiology. Here, we examine the potential mechanisms through which Tsa1 lowers mutation rates, taking into account its diverse biochemical roles in oxidant defense, protein homeostasis, and redox signaling as well as its interplay with thioredoxin and thioredoxin substrates, including ribonucleotide reductase. More work is needed to clarify the nuanced mechanism(s) through which this highly conserved peroxidase influences genome stability, and to determine if this mechanism is similar across a range of species.
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Valenzuela‐García LI, Ayala‐García VM, Regalado‐García AG, Setlow P, Pedraza‐Reyes M. Transcriptional coupling (Mfd) and DNA damage scanning (DisA) coordinate excision repair events for efficient Bacillus subtilis spore outgrowth. Microbiologyopen 2018; 7:e00593. [PMID: 29536659 PMCID: PMC6182552 DOI: 10.1002/mbo3.593] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/06/2018] [Indexed: 01/16/2023] Open
Abstract
The absence of base excision repair (BER) proteins involved in processing ROS-promoted genetic insults activates a DNA damage scanning (DisA)-dependent checkpoint event in outgrowing Bacillus subtilis spores. Here, we report that genetic disabling of transcription-coupled repair (TCR) or nucleotide excision repair (NER) pathways severely affected outgrowth of ΔdisA spores, and much more so than the effects of these mutations on log phase growth. This defect delayed the first division of spore's nucleoid suggesting that unrepaired lesions affected transcription and/or replication during outgrowth. Accordingly, return to life of spores deficient in DisA/Mfd or DisA/UvrA was severely affected by a ROS-inducer or a replication blocking agent, hydrogen peroxide and 4-nitroquinoline-oxide, respectively. Mutation frequencies to rifampin resistance (Rifr ) revealed that DisA allowed faithful NER-dependent DNA repair but activated error-prone repair in TCR-deficient outgrowing spores. Sequencing analysis of rpoB from spontaneous Rifr colonies revealed that mutations resulting from base deamination predominated in outgrowing wild-type spores. Interestingly, a wide range of base substitutions promoted by oxidized DNA bases were detected in ΔdisA and Δmfd outgrown spores. Overall, our results suggest that Mfd and DisA coordinate excision repair events in spore outgrowth to eliminate DNA lesions that interfere with replication and transcription during this developmental period.
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Affiliation(s)
| | | | | | - Peter Setlow
- Department of Molecular Biology and BiophysicsUConn HealthFarmingtonCTUSA
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40
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Zsurka G, Peeva V, Kotlyar A, Kunz WS. Is There Still Any Role for Oxidative Stress in Mitochondrial DNA-Dependent Aging? Genes (Basel) 2018; 9:genes9040175. [PMID: 29561808 PMCID: PMC5924517 DOI: 10.3390/genes9040175] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/09/2018] [Accepted: 03/16/2018] [Indexed: 11/21/2022] Open
Abstract
Recent deep sequencing data has provided compelling evidence that the spectrum of somatic point mutations in mitochondrial DNA (mtDNA) in aging tissues lacks G > T transversion mutations. This fact cannot, however, be used as an argument for the missing contribution of reactive oxygen species (ROS) to mitochondria-related aging because it is probably caused by the nucleotide selectivity of mitochondrial DNA polymerase γ (POLG). In contrast to point mutations, the age-dependent accumulation of mitochondrial DNA deletions is, in light of recent experimental data, still explainable by the segregation of mutant molecules generated by the direct mutagenic effects of ROS (in particular, of HO· radicals formed from H2O2 by a Fenton reaction). The source of ROS remains controversial, because the mitochondrial contribution to tissue ROS production is probably lower than previously thought. Importantly, in the discussion about the potential role of oxidative stress in mitochondria-dependent aging, ROS generated by inflammation-linked processes and the distribution of free iron also require careful consideration.
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Affiliation(s)
- Gábor Zsurka
- Institute of Experimental Epileptology and Neurocognition, University Bonn Medical Center, 53105 Bonn, Germany.
- Department of Epileptology, University Bonn Medical Center, 53105 Bonn, Germany.
| | - Viktoriya Peeva
- Institute of Experimental Epileptology and Neurocognition, University Bonn Medical Center, 53105 Bonn, Germany.
| | - Alexander Kotlyar
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Wolfram S Kunz
- Institute of Experimental Epileptology and Neurocognition, University Bonn Medical Center, 53105 Bonn, Germany.
- Department of Epileptology, University Bonn Medical Center, 53105 Bonn, Germany.
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41
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Anichini C, Lotti F, Longini M, Felici C, Proietti F, Buonocore G. Antioxidant Strategies in Genetic Syndromes with High Neoplastic Risk in Infant Age. TUMORI JOURNAL 2018. [DOI: 10.1177/1778.19256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Cecilia Anichini
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Federica Lotti
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Mariangela Longini
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Cosetta Felici
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Fabrizio Proietti
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Giuseppe Buonocore
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
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42
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Tajai P, Fedeles BI, Suriyo T, Navasumrit P, Kanitwithayanun J, Essigmann JM, Satayavivad J. An engineered cell line lacking OGG1 and MUTYH glycosylases implicates the accumulation of genomic 8-oxoguanine as the basis for paraquat mutagenicity. Free Radic Biol Med 2018; 116:64-72. [PMID: 29289706 PMCID: PMC5902796 DOI: 10.1016/j.freeradbiomed.2017.12.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/13/2017] [Accepted: 12/27/2017] [Indexed: 12/14/2022]
Abstract
Paraquat (1,1'-dimethyl, 4,4'-bipyridinium dichloride; PQ), a widely used herbicide, is toxic to mammals through ingestion, inhalation and skin contact. Epidemiological data suggest that PQ is also mutagenic and carcinogenic, especially in high doses. The toxic and mutagenic properties of PQ are attributed to the ability of the molecule to redox-cycle, which generates reactive oxygen species (ROS) and subsequent oxidative stress. ROS also cause oxidative DNA damage such as 8-oxoguanine (8OG), a mutagenic base that, when replicated, causes G to T transversion mutations. The present study employed the CHO-derived cell line AS52 to quantify the mutagenic properties of low doses of PQ. By containing a functional, chromosomally-integrated copy of the bacterial gpt gene, AS52 cells a facile system for evaluating the mutagenic properties of genotoxicants. To bolster the sensitivity of this system for detecting mutagenesis of weak mutagens like PQ, and to provide a tool for mechanistic evaluation of the mutagenic process, we constructed a new AS52-derived cell line defective for 8OG DNA repair. Specifically, we employed CRISPR-Cas9 technology to knock out 8-oxoguanine DNA glycosylase (OGG1) and MUTYH glycosylase, two key enzymes involved in the base excision repair of 8OG. The double knock-out (DKO) AS52 cells were found to be more sensitive to PQ toxicity than the parental (WT) AS52 cell line. They experienced higher levels of ROS, which translated into more DNA double-strand breaks, which explained the PQ toxicity. The increased ROS levels also led to more 8OG genomic accumulation, and a higher level of mutations in the DKO cells, suggesting that PQ mutagenesis is mediated primarily by 8OG genomic accumulation. Consistent with this view, antioxidant co-treatment lowered induced cellular ROS and PQ-induced mutagenesis. Taken together, our data demonstrate the strong protective role of OGG1 and MUTYH against PQ-induced mutagenesis. Moreover, our experiments establish the engineered OGG1-/-MUTYH-/- AS52 cell line and associated methods as a versatile cellular system for studying in quantitative terms the mutagenesis of other agents, environmental or endogenous, that induce oxidative stress.
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Affiliation(s)
- Preechaya Tajai
- Graduate Program in Environmental Toxicology, Chulabhorn Graduate Institute, Bangkok 10210, Thailand; Departments of Biological Engineering and Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bogdan I Fedeles
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tawit Suriyo
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, Ministry of Education, Bangkok 10210, Thailand
| | - Panida Navasumrit
- Graduate Program in Environmental Toxicology, Chulabhorn Graduate Institute, Bangkok 10210, Thailand; Laboratory of Environmental Toxicology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Jantamas Kanitwithayanun
- Graduate Program in Environmental Toxicology, Chulabhorn Graduate Institute, Bangkok 10210, Thailand; Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - John M Essigmann
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Jutamaad Satayavivad
- Graduate Program in Environmental Toxicology, Chulabhorn Graduate Institute, Bangkok 10210, Thailand; Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, Ministry of Education, Bangkok 10210, Thailand.
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Yang Y, Yang W, Su H, Fang W, Chen X. Mechanistic insights into the photogeneration and quenching of guanine radical cation via one-electron oxidation of G-quadruplex DNA. Phys Chem Chem Phys 2018; 20:13598-13606. [DOI: 10.1039/c8cp01718b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Selectivity of activation site for the photogeneration and quenching of guanine radical cation was elucidated by the analysis of the relaxation paths of one-electron oxidation of G-quadruplex DNA.
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Affiliation(s)
- Yumei Yang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
| | - Wenjing Yang
- College of Material Science & Engineering
- Taiyuan University of Technology
- People's Republic of China
| | - Hongmei Su
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
| | - Xuebo Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
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Zhang J, Guo F, Wei J, Xian M, Tang S, Zhao Y, Liu M, Song L, Geng Y, Yang H, Ding C, Huang L. An integrated approach to identify critical transcription factors in the protection against hydrogen peroxide-induced oxidative stress by Danhong injection. Free Radic Biol Med 2017; 112:480-493. [PMID: 28822748 DOI: 10.1016/j.freeradbiomed.2017.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/07/2017] [Accepted: 07/04/2017] [Indexed: 12/18/2022]
Abstract
Oxidative stress plays a vital role in many pathological processes of the cardiovascular diseases. However, the underlying mechanism remains unclear, especially on a transcription factor (TF) level. In this study, a new method, concatenated tandem array of consensus transcription factor response elements (catTFREs), and an Illumina-based RNA-seq technology were integrated to systematically investigate the role of TFs in hydrogen peroxide (H2O2)-induced oxidative stress in cardiomyocytes; the damage was then rescued by Danhong injection (DHI), a Chinese standardized product approved for cardiovascular diseases treatment. The overall gene expression revealed cell apoptosis and DNA repair were vital for cardiomyocytes in resisting oxidative stress. By comprehensively integrating the transcription activity of TFs and their downstream target genes, an important TFs-target network were constructed and 13 TFs were identified as critical TFs in DHI-mediated protection in H2O2-induced oxidative stress. By using the integrated approach, seven TFs of these 13 TFs were also identified in melatonin-mediated protection in H2O2-induced damage. Furthermore, the transcription activity of DNA-(apurinic or apyrimidinic site) lyase (Apex1), Myocyte-specific enhancer factor 2D (Mef2d) and Pre B-cell leukemia transcription factor 3 (Pbx3) was further verified in pluripotent stem cell-derived cardiomyocytes. This research offers a new understanding of cardiomyocytes in response to H2O2-induced oxidative stress and reveals additional potential therapeutic targets. The combination of two parallel omics datasets (corresponding to the transcriptome and proteome) can reduce the noise in high-throughput data and reveal the fundamental changes of the biological process, making it suitable and reliable for investigation of critical targets in many other complicated pathological processes.
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Affiliation(s)
- Jingjing Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Feifei Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Junying Wei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Minghua Xian
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shihuan Tang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ye Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Ya Geng
- School of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Hongjun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Chen Ding
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China; State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China.
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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Zhang J, Geng Y, Guo F, Zhang F, Liu M, Song L, Ma Y, Li D, Zhang Y, Xu H, Yang H. Screening and identification of critical transcription factors involved in the protection of cardiomyocytes against hydrogen peroxide-induced damage by Yixin-shu. Sci Rep 2017; 7:13867. [PMID: 29066842 PMCID: PMC5655617 DOI: 10.1038/s41598-017-10131-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/04/2017] [Indexed: 01/12/2023] Open
Abstract
Oxidative stress initiates harmful cellular responses, such as DNA damage and protein denaturation, triggering a series of cardiovascular disorders. Systematic investigations of the transcription factors (TFs) involved in oxidative stress can help reveal the underlying molecular mechanisms and facilitate the discovery of effective therapeutic targets in related diseases. In this study, an integrated strategy which integrated RNA-seq-based transcriptomics techniques and a newly developed concatenated tandem array of consensus TF response elements (catTFREs)-based proteomics approach and then combined with a network pharmacology analysis, was developed and this integrated strategy was used to investigate critical TFs in the protection of Yixin-shu (YXS), a standardized medical product used for ischaemic heart disease, against hydrogen peroxide (H2O2)-induced damage in cardiomyocytes. Importantly, YXS initiated biological process such as anti-apoptosis and DNA repair to protect cardiomyocytes from H2O2-induced damage. By using the integrated strategy, DNA-(apurinic or apyrimidinic site) lyase (Apex1), pre B-cell leukemia transcription factor 3 (Pbx3), and five other TFs with their functions involved in anti-oxidation, anti-apoptosis and DNA repair were identified. This study offers a new understanding of the mechanism underlying YXS-mediated protection against H2O2-induced oxidative stress in cardiomyocytes and reveals novel targets for oxidative stress-related diseases.
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Affiliation(s)
- Jingjing Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ya Geng
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Feifei Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Fangbo Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Yuexiang Ma
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Defeng Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yi Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Haiyu Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Hongjun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Xiao Y, Liu Q, Tang X, Yang Z, Wu L, He Y. Mirror-Image Thymidine Discriminates against Incorporation of Deoxyribonucleotide Triphosphate into DNA and Repairs Itself by DNA Polymerases. Bioconjug Chem 2017; 28:2125-2134. [PMID: 28686433 DOI: 10.1021/acs.bioconjchem.7b00301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA polymerases are known to recognize preferably d-nucleotides over l-nucleotides during DNA synthesis. Here, we report that several general DNA polymerases catalyze polymerization reactions of nucleotides directed by the DNA template containing an l-thymidine (l-T). The results display that the 5'-3' primer extension of natural nucleotides get to the end at chiral modification site with Taq and Phanta Max DNA polymerases, but the primer extension proceeds to the end of the template catalyzed by Deep Vent (exo-), Vent (exo-), and Therminator DNA polymerases. Furthermore, templating l-nucleoside displays a lag in the deoxyribonucleotide triphosphate (dNTP) incorporation rates relative to natural template by kinetics analysis, and polymerase chain reactions were inhibited with the DNA template containing two or three consecutive l-Ts. Most interestingly, no single base mutation or mismatch mixture corresponding to the location of l-T in the template was found, which is physiologically significant because they provide a theoretical basis on the involvement of DNA polymerase in the effective repair of l-T that may lead to cytotoxicity.
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Affiliation(s)
- Yating Xiao
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Qingju Liu
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Li Wu
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Yujian He
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
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Activation of Dun1 in response to nuclear DNA instability accounts for the increase in mitochondrial point mutations in Rad27/FEN1 deficient S. cerevisiae. PLoS One 2017; 12:e0180153. [PMID: 28678842 PMCID: PMC5497989 DOI: 10.1371/journal.pone.0180153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/09/2017] [Indexed: 11/25/2022] Open
Abstract
Rad27/FEN1 nuclease that plays important roles in the maintenance of DNA stability in the nucleus has recently been shown to reside in mitochondria. Accordingly, it has been established that Rad27 deficiency causes increased mutagenesis, but decreased microsatellite instability and homologous recombination in mitochondria. Our current analysis of mutations leading to erythromycin resistance indicates that only some of them arise in mitochondrial DNA and that the GC→AT transition is a hallmark of the mitochondrial mutagenesis in rad27 null background. We also show that the mitochondrial mutator phenotype resulting from Rad27 deficiency entirely depends on the DNA damage checkpoint kinase Dun1. DUN1 inactivation suppresses the mitochondrial mutator phenotype caused by Rad27 deficiency and this suppression is eliminated at least in part by subsequent deletion of SML1 encoding a repressor of ribonucleotide reductase. We conclude that Rad27 deficiency causes a mitochondrial mutator phenotype via activation of DNA damage checkpoint kinase Dun1 and that a Dun1-mediated increase of dNTP pools contributes to this phenomenon. These results point to the nuclear DNA instability as the source of mitochondrial mutagenesis. Consistently, we show that mitochondrial mutations occurring more frequently in yeast devoid of Rrm3, a DNA helicase involved in rDNA replication, are also dependent on Dun1. In addition, we have established that overproduction of Exo1, which suppresses DNA damage sensitivity and replication stress in nuclei of Rad27 deficient cells, but does not enter mitochondria, suppresses the mitochondrial mutagenesis. Exo1 overproduction restores also a great part of allelic recombination and microsatellite instability in mitochondria of Rad27 deficient cells. In contrast, the overproduction of Exo1 does not influence mitochondrial direct-repeat mediated deletions in rad27 null background, pointing to this homologous recombination pathway as the direct target of Rad27 activity in mitochondria.
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Mismatch Repair of DNA Replication Errors Contributes to Microevolution in the Pathogenic Fungus Cryptococcus neoformans. mBio 2017; 8:mBio.00595-17. [PMID: 28559486 PMCID: PMC5449657 DOI: 10.1128/mbio.00595-17] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The ability to adapt to a changing environment provides a selective advantage to microorganisms. In the case of many pathogens, a large change in their environment occurs when they move from a natural setting to a setting within a human host and then during the course of disease development to various locations within that host. Two clinical isolates of the human fungal pathogen Cryptococcus neoformans were identified from a collection of environmental and clinical strains that exhibited a mutator phenotype, which is a phenotype which provides the ability to change rapidly due to the accumulation of DNA mutations at high frequency. Whole-genome analysis of these strains revealed mutations in MSH2 of the mismatch repair pathway, and complementation confirmed that these mutations are responsible for the mutator phenotype. Comparison of mutation frequencies in deletion strains of eight mismatch repair pathway genes in C. neoformans showed that the loss of three of them, MSH2, MLH1, and PMS1, results in an increase in mutation rates. Increased mutation rates enable rapid microevolution to occur in these strains, generating phenotypic variations in traits associated with the ability to grow in vivo, in addition to allowing rapid generation of resistance to antifungal agents. Mutation of PMS1 reduced virulence, whereas mutation of MSH2 or MLH1 had no effect on the level of virulence. These findings thus support the hypothesis that this pathogenic fungus can take advantage of a mutator phenotype in order to cause disease but that it can do so only in specific pathways that lead to a mutator trait without a significant tradeoff in fitness. Fungi account for a large number of infections that are extremely difficult to treat; superficial fungal infections affect approximately 1.7 billion (25%) of the general population worldwide, and systemic fungal diseases result in an unacceptably high mortality rate. How fungi adapt to their hosts is not fully understood. This research investigated the role of changes to DNA sequences in adaption to the host environment and the ability to cause disease in Cryptococcus neoformans, one of the world’s most common and most deadly fungal pathogens. The study results showed that microevolutionary rates are enhanced in either clinical isolates or in gene deletion strains with msh2 mutations. This gene has similar functions in regulating the rapid emergence of antifungal drug resistance in a distant fungal relative of C. neoformans, the pathogen Candida glabrata. Thus, microevolution resulting from enhanced mutation rates may be a common contributor to fungal pathogenesis.
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Electronic cigarette aerosols suppress cellular antioxidant defenses and induce significant oxidative DNA damage. PLoS One 2017; 12:e0177780. [PMID: 28542301 PMCID: PMC5436899 DOI: 10.1371/journal.pone.0177780] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 05/03/2017] [Indexed: 01/30/2023] Open
Abstract
Background Electronic cigarette (EC) aerosols contain unique compounds in addition to toxicants and carcinogens traditionally found in tobacco smoke. Studies are warranted to understand the public health risks of ECs. Objective The aim of this study was to determine the genotoxicity and the mechanisms induced by EC aerosol extracts on human oral and lung epithelial cells. Methods Cells were exposed to EC aerosol or mainstream smoke extracts and DNA damage was measured using the primer anchored DNA damage detection assay (q-PADDA) and 8-oxo-dG ELISA assay. Cell viability, reactive oxygen species (ROS) and total antioxidant capacity (TAC) were measured using standard methods. mRNA and protein expression were evaluated by RT-PCR and western blot, respectively. Results EC aerosol extracts induced DNA damage in a dose-dependent manner, but independently of nicotine concentration. Overall, EC aerosol extracts induced significantly less DNA damage than mainstream smoke extracts, as measured by q-PADDA. However, the levels of oxidative DNA damage, as indicated by the presence of 8-oxo-dG, a highly mutagenic DNA lesion, were similar or slightly higher after exposure to EC aerosol compared to mainstream smoke extracts. Mechanistically, while exposure to EC extracts significantly increased ROS, it decreased TAC as well as the expression of 8-oxoguanine DNA glycosylase (OGG1), an enzyme essential for the removal of oxidative DNA damage. Conclusions Exposure to EC aerosol extracts suppressed the cellular antioxidant defenses and led to significant DNA damage. These findings emphasize the urgent need to investigate the potential long-term cancer risk of exposure to EC aerosol for vapers and the general public.
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