1
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Wei Y, Guo X, Li L, Xue W, Wang L, Chen C, Sun S, Yang Y, Yao W, Wang W, Zhao J, Duan X. The role of N6-methyladenosine methylation in PAHs-induced cancers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:118078-118101. [PMID: 37924411 DOI: 10.1007/s11356-023-30710-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), which are a wide range of environmental toxicants, may act on humans through inhalation, ingestion, and skin contact, resulting in a range of toxic reactions. Epidemiological studies showed that long-term exposure to PAHs in the occupational and living environment results in a substantial rise in the incidence rate of many cancers in the population, so the prevention and treatment of these diseases have become a major worldwide public health problem. N6-methyladenosine (m6A) modification greatly affects the metabolism of RNA and is implicated in the etiopathogenesis of many kinds of diseases. In addition, m6A-binding proteins have an important role in disease development. The abnormal expression of these can cause the malignant proliferation, migration, invasion, and metastasis of cancers. Furthermore, a growing number of studies revealed that environmental toxicants are one of the cancer risk factors and are related to m6A modifications. Exposure to environmental toxicants can alter the methylation level of m6A and the expression of the m6A-binding protein, thus promoting the occurrence and development of cancers through diverse mechanisms. m6A may serve as a biomarker for early environmental exposure. Through the study of m6A, we can find the health injury early, thus providing a new sight for preventing and curing environmental health-related diseases.
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Affiliation(s)
- Yujie Wei
- National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe Road, Erqi District, Zhengzhou, 450052, Henan, China
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaona Guo
- Medical School, Huanghe Science and Technology University, Zhengzhou, Henan, China
| | - Lifeng Li
- National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Wenhua Xue
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Longhao Wang
- National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Chengxin Chen
- National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe Road, Erqi District, Zhengzhou, 450052, Henan, China
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shilong Sun
- National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe Road, Erqi District, Zhengzhou, 450052, Henan, China
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yaqi Yang
- National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Wu Yao
- Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Wei Wang
- Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Zhao
- National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe Road, Erqi District, Zhengzhou, 450052, Henan, China
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaoran Duan
- National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe Road, Erqi District, Zhengzhou, 450052, Henan, China.
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
- Medical School, Huanghe Science and Technology University, Zhengzhou, Henan, China.
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2
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Chen Y, Arlt VM, Stürzenbaum SR. MosSCI-mediated exogenous gene expression is modulated by genomic positioning. Biotechnol J 2023; 18:e2300062. [PMID: 37177911 DOI: 10.1002/biot.202300062] [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: 02/07/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/15/2023]
Abstract
Although the Mos1-mediated single-copy insertion (MosSCI) technique has been widely used to generate stable transgenic Caenorhabditis elegans strains, the link between stability of expression and integration site still needs to be explored. Here, experimental evidence is provided that transgenes are not able to match the level of transcription of their native counterpart, and that insertions at certain locations can result in an external stress-mediated increase in expression. Insertion site ttTi5605 on chromosome II was shown to be a superior location, at least when introducing reproduction related genes. Thus, this study provides a reference for the selection of an optimal site for MosSCI which provides acceptable expression performance whilst minimizing undesirable secondary effects.
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Affiliation(s)
- Yuzhi Chen
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Volker M Arlt
- Toxicology Department, GAB Consulting GmbH, Heidelberg, Germany
| | - Stephen R Stürzenbaum
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
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3
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Nanosafety: An Evolving Concept to Bring the Safest Possible Nanomaterials to Society and Environment. NANOMATERIALS 2022; 12:nano12111810. [PMID: 35683670 PMCID: PMC9181910 DOI: 10.3390/nano12111810] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2022]
Abstract
The use of nanomaterials has been increasing in recent times, and they are widely used in industries such as cosmetics, drugs, food, water treatment, and agriculture. The rapid development of new nanomaterials demands a set of approaches to evaluate the potential toxicity and risks related to them. In this regard, nanosafety has been using and adapting already existing methods (toxicological approach), but the unique characteristics of nanomaterials demand new approaches (nanotoxicology) to fully understand the potential toxicity, immunotoxicity, and (epi)genotoxicity. In addition, new technologies, such as organs-on-chips and sophisticated sensors, are under development and/or adaptation. All the information generated is used to develop new in silico approaches trying to predict the potential effects of newly developed materials. The overall evaluation of nanomaterials from their production to their final disposal chain is completed using the life cycle assessment (LCA), which is becoming an important element of nanosafety considering sustainability and environmental impact. In this review, we give an overview of all these elements of nanosafety.
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4
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Ohmori K, Kamei A, Watanabe Y, Abe K. Gene Expression over Time during Cell Transformation Due to Non-Genotoxic Carcinogen Treatment of Bhas 42 Cells. Int J Mol Sci 2022; 23:ijms23063216. [PMID: 35328637 PMCID: PMC8954493 DOI: 10.3390/ijms23063216] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 02/05/2023] Open
Abstract
The Bhas 42 cell transformation assay (Bhas 42 CTA) is the first Organization for Economic Cooperation and Development (OECD)-certificated method used as a specific tool for the detection of the cell-transformation potential of tumor-promoting compounds, including non-genotoxic carcinogens (NGTxCs), as separate from genotoxic carcinogens. This assay offers the great advantage of enabling the phenotypic detection of oncotransformation. A key benefit of using the Bhas 42 CTA in the study of the cell-transformation mechanisms of tumor-promoting compounds, including non-genotoxic carcinogens, is that the cell-transformation potential of the chemical can be detected directly without treatment with a tumor-initiating compound since Bhas 42 cell line was established by transfecting the v-Ha-ras gene into a mouse fibroblast cloned cell line. Here, we analyzed the gene expression over time, using DNA microarrays, in Bhas 42 cells treated with the tumor-promoting compound 12-O-tetradecanoylphorbol-13-acetate (TPA), and NGTxC, with a total of three repeat experiments. This is the first paper to report on gene expression over time during the process of cell transformation with only a tumor-promoting compound. Pathways that were activated or inactivated during the process of cell transformation in the Bhas 42 cells treated with TPA were related not only directly to RAS but also to various pathways in the hallmarks of cancer.
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Affiliation(s)
- Kiyomi Ohmori
- Chemical Division, Kanagawa Prefectural Institute of Public Health, Chigasaki 2530087, Japan
- Research Initiatives and Promotion Organization, Yokohama National University, Yokohama 2408501, Japan
- Correspondence: or ; Tel./Fax: +81-046-783-4400 or +81-045-339-4448
| | - Asuka Kamei
- Group for Food Functionality Assessment, Kanagawa Institute of Industrial Science and Technology, Kawasaki 2100821, Japan; (A.K.); (K.A.)
| | - Yuki Watanabe
- Health and Anti-Aging Project, Kanagawa Academy of Science and Technology, Kawasaki 2130012, Japan;
| | - Keiko Abe
- Group for Food Functionality Assessment, Kanagawa Institute of Industrial Science and Technology, Kawasaki 2100821, Japan; (A.K.); (K.A.)
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 1138657, Japan
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5
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Prasad R, Yen TJ, Bellacosa A. Active DNA demethylation-The epigenetic gatekeeper of development, immunity, and cancer. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 2:e10033. [PMID: 36618446 PMCID: PMC9744510 DOI: 10.1002/ggn2.10033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 01/11/2023]
Abstract
DNA methylation is a critical process in the regulation of gene expression with dramatic effects in development and continually expanding roles in oncogenesis. 5-Methylcytosine was once considered to be an inherited and stably repressive epigenetic mark, which can be only removed by passive dilution during multiple rounds of DNA replication. However, in the past two decades, physiologically controlled DNA demethylation and deamination processes have been identified, thereby revealing the function of cytosine methylation as a highly regulated and complex state-not simply a static, inherited signature or binary on-off switch. Alongside these fundamental discoveries, clinical studies over the past decade have revealed the dramatic consequences of aberrant DNA demethylation. In this review we discuss DNA demethylation and deamination in the context of 5-methylcytosine as critical processes for physiological and physiopathological transitions within three states-development, immune maturation, and oncogenic transformation; and we describe the expanding role of DNA demethylating drugs as therapeutic agents in cancer.
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Affiliation(s)
- Rahul Prasad
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Timothy J. Yen
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
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6
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Heusinkveld H, Braakhuis H, Gommans R, Botham P, Corvaro M, van der Laan JW, Lewis D, Madia F, Manou I, Schorsch F, Wolterink G, Woutersen R, Corvi R, Mehta J, Luijten M. Towards a mechanism-based approach for the prediction of nongenotoxic carcinogenic potential of agrochemicals. Crit Rev Toxicol 2020; 50:725-739. [DOI: 10.1080/10408444.2020.1841732] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Harm Heusinkveld
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Hedwig Braakhuis
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Robin Gommans
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | | | | | | | - Federica Madia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Irene Manou
- European Partnership for Alternative Approaches to Animal Testing (EPAA), Brussels, Belgium
| | | | - Gerrit Wolterink
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ruud Woutersen
- TNO Quality of Life, Zeist, and Wageningen University & Research, Wageningen, the Netherlands
| | - Raffaella Corvi
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | - Mirjam Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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7
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Schwartz TS. The Promises and the Challenges of Integrating Multi-Omics and Systems Biology in Comparative Stress Biology. Integr Comp Biol 2020; 60:89-97. [PMID: 32386307 DOI: 10.1093/icb/icaa026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Comparative stress biology is inherently a systems biology approach with the goal of integrating the molecular, cellular, and physiological responses with fitness outcomes. In this way, the systems biology approach is expected to provide a holistic understanding of how different stressors result in different fitness outcomes, and how different individuals (or populations or species) respond to stressors differently. In this perceptive article, I focus on the use of multiple types of -omics data in stress biology. Targeting students and those researchers who are considering integrating -omics approaches in their comparative stress biology studies, I discuss the promise of the integration of these measures for furthering our holistic understanding of how organisms respond to different stressors. I also discuss the logistical and conceptual challenges encountered when working with -omics data and the current hurdles to fully utilize these data in studies of stress biology in non-model organisms.
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Affiliation(s)
- Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
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8
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Mosedale M, Watkins PB. Understanding Idiosyncratic Toxicity: Lessons Learned from Drug-Induced Liver Injury. J Med Chem 2020; 63:6436-6461. [PMID: 32037821 DOI: 10.1021/acs.jmedchem.9b01297] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Idiosyncratic adverse drug reactions (IADRs) encompass a diverse group of toxicities that can vary by drug and patient. The complex and unpredictable nature of IADRs combined with the fact that they are rare makes them particularly difficult to predict, diagnose, and treat. Common clinical characteristics, the identification of human leukocyte antigen risk alleles, and drug-induced proliferation of lymphocytes isolated from patients support a role for the adaptive immune system in the pathogenesis of IADRs. Significant evidence also suggests a requirement for direct, drug-induced stress, neoantigen formation, and stimulation of an innate response, which can be influenced by properties intrinsic to both the drug and the patient. This Perspective will provide an overview of the clinical profile, mechanisms, and risk factors underlying IADRs as well as new approaches to study these reactions, focusing on idiosyncratic drug-induced liver injury.
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Affiliation(s)
- Merrie Mosedale
- Institute for Drug Safety Sciences and Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599, United States
| | - Paul B Watkins
- Institute for Drug Safety Sciences and Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599, United States
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9
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Vitobello A, Perner J, Beil J, Zhu J, Del Río-Espínola A, Morawiec L, Westphal M, Dubost V, Altorfer M, Naumann U, Mueller A, Kapur K, Borowsky M, Henderson C, Wolf CR, Schwarz M, Moggs J, Terranova R. Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion. Life Sci Alliance 2019; 2:e201900461. [PMID: 31615920 PMCID: PMC6795216 DOI: 10.26508/lsa.201900461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 12/27/2022] Open
Abstract
Liver cancer susceptibility varies amongst humans and between experimental animal models because of multiple genetic and epigenetic factors. The molecular characterization of such susceptibilities has the potential to enhance cancer risk assessment of xenobiotic exposures and disease prevention strategies. Here, using DNase I hypersensitivity mapping coupled with transcriptomic profiling, we investigate perturbations in cis-acting gene regulatory elements associated with the early stages of phenobarbital (PB)-mediated liver tumor promotion in susceptible versus resistant mouse strains (B6C3F1 versus C57BL/6J). Integrated computational analyses of strain-selective changes in liver chromatin accessibility underlying PB response reveal differential epigenetic regulation of molecular pathways associated with PB-mediated tumor promotion, including Wnt/β-catenin signaling. Complementary transcription factor motif analyses reveal mouse strain-selective gene regulatory networks and a novel role for Stat, Smad, and Fox transcription factors in the early stages of PB-mediated tumor promotion. Mapping perturbations in cis-acting gene regulatory elements provides novel insights into the molecular basis for susceptibility to xenobiotic-induced rodent liver tumor promotion and has the potential to enhance mechanism-based cancer risk assessments of xenobiotic exposures.
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Affiliation(s)
- Antonio Vitobello
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
- Inserm, Unité Mixte de Recherche (UMR) 1231, Université de Bourgogne-Franche Comté, Dijon, France
| | - Juliane Perner
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Johanna Beil
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | | | | | - Laurent Morawiec
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | | | - Valérie Dubost
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Marc Altorfer
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Ulrike Naumann
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Arne Mueller
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Karen Kapur
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | | | - Colin Henderson
- School of Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Innovative Medicines Initiative MARCAR Consortium (http://www.imi-marcar.eu/index.php)
| | - C Roland Wolf
- School of Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Innovative Medicines Initiative MARCAR Consortium (http://www.imi-marcar.eu/index.php)
| | - Michael Schwarz
- Department of Toxicology, University of Tübingen, Tübingen, Germany
- Innovative Medicines Initiative MARCAR Consortium (http://www.imi-marcar.eu/index.php)
| | - Jonathan Moggs
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
- Innovative Medicines Initiative MARCAR Consortium (http://www.imi-marcar.eu/index.php)
| | - Rémi Terranova
- Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
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10
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Rampersaud A, Lodato NJ, Shin A, Waxman DJ. Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR. Toxicol Sci 2019; 171:315-338. [PMID: 31236583 PMCID: PMC6760311 DOI: 10.1093/toxsci/kfz148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
CAR (Nr1i3), a liver nuclear receptor and xenobiotic sensor, induces drug, steroid and lipid metabolism and dysregulates genes linked to hepatocellular carcinogenesis, but its impact on the liver epigenome is poorly understood. TCPOBOP, a halogenated xenochemical and highly specific CAR agonist ligand, induces localized chromatin opening or closing at several thousand mouse liver genomic regions, discovered as differential DNase-hypersensitive sites (ΔDHS). Active enhancer and promoter histone marks induced by TCPOBOP were enriched at opening DHS and TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen at opening DHS and their inducible drug/lipid metabolism gene targets, and at many constitutively open DHS located nearby. TCPOBOP-responsive cell cycle and DNA replication genes co-dependent on MET/EGFR signaling for induction were also enriched for CAR binding. A subset of opening DHS and many closing DHS mapping to TCPOBOP-responsive target genes did not bind CAR, indicating an indirect mechanism for their changes in chromatin accessibility. TCPOBOP-responsive DHS were also enriched for induced binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched factors that may contribute to liver-specific transcriptional responses to TCPOBOP exposure. These studies elucidate the enhancer landscape of TCPOBOP-exposed liver and the widespread epigenetic changes that are induced by both direct and indirect mechanisms linked to CAR activation. The global maps of thousands of environmental chemical-induced epigenetic changes described here constitute a rich resource for further research on xenochemical effects on liver chromatin states and the epigenome.
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Affiliation(s)
- Andy Rampersaud
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
| | - Nicholas J Lodato
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
| | - Aram Shin
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
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11
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Lodato NJ, Rampersaud A, Waxman DJ. Impact of CAR Agonist Ligand TCPOBOP on Mouse Liver Chromatin Accessibility. Toxicol Sci 2019; 164:115-128. [PMID: 29617930 DOI: 10.1093/toxsci/kfy070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Activation of the nuclear receptor and transcription factor CAR (Nr1i3) by its specific agonist ligand TCPOBOP (1, 4-bis[2-(3, 5-dichloropyridyloxy)]benzene) dysregulates hundreds of genes in mouse liver and is linked to male-biased hepatocarcinogenesis. To elucidate the genomic organization of CAR-induced gene responses, we investigated the distribution of TCPOBOP-responsive RefSeq coding and long noncoding RNA (lncRNA) genes across the megabase-scale topologically associating domains (TADs) that segment the genome, and which provide a structural framework that functionally constrains enhancer-promoter interactions. We show that a subset of TCPOBOP-responsive genes cluster within TADs, and that TCPOBOP-induced genes and TCPOBOP-repressed genes are often found in different TADs. Further, using DNase-seq and DNase hypersensitivity site (DHS) analysis, we identified several thousand genomic regions (ΔDHS) where short-term exposure to TCPOBOP induces localized changes (increases or decreases) in mouse liver chromatin accessibility, many of which cluster in TADs together with TCPOBOP-responsive genes. Sites of chromatin opening were highly enriched nearby genes induced by TCPOBOP and chromatin closing was highly enriched nearby genes repressed by TCPOBOP, consistent with TCPOBOP-responsive ΔDHS serving as enhancers and promoters that positively regulate CAR-responsive genes. Gene expression changes lagged behind chromatin opening or closing for a subset of TCPOBOP-responsive ΔDHS. ΔDHS that were specifically responsive to TCPOBOP in male liver were significantly enriched for genomic regions with a basal male bias in chromatin accessibility; however, the male-biased response of hepatocellular carcinoma-related genes to TCPOBOP was not associated with a correspondingly male-biased ΔDHS response. These studies elucidate the genome-wide organization of CAR-responsive genes and of the thousands of associated genomic sites where TCPOBOP exposure induces both rapid and persistent changes in chromatin accessibility.
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Affiliation(s)
- Nicholas J Lodato
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
| | - Andy Rampersaud
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
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12
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Lewis L, Borowa-Mazgaj B, de Conti A, Chappell GA, Luo YS, Bodnar W, Konganti K, Wright FA, Threadgill DW, Chiu WA, Pogribny IP, Rusyn I. Population-Based Analysis of DNA Damage and Epigenetic Effects of 1,3-Butadiene in the Mouse. Chem Res Toxicol 2019; 32:887-898. [PMID: 30990016 DOI: 10.1021/acs.chemrestox.9b00035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metabolism of 1,3-butadiene, a known human and rodent carcinogen, results in formation of reactive epoxides, a key event in its carcinogenicity. Although mice exposed to 1,3-butadiene present DNA adducts in all tested tissues, carcinogenicity is limited to liver, lung, and lymphoid tissues. Previous studies demonstrated that strain- and tissue-specific epigenetic effects in response to 1,3-butadiene exposure may influence susceptibly to DNA damage and serve as a potential mechanism of tissue-specific carcinogenicity. This study aimed to investigate interindividual variability in the effects of 1,3-butadiene using a population-based mouse model. Male mice from 20 Collaborative Cross strains were exposed to 0 or 635 ppm 1,3-butadiene by inhalation (6 h/day, 5 days/week) for 2 weeks. We evaluated DNA damage and epigenetic effects in target (lung and liver) and nontarget (kidney) tissues of 1,3-butadiene-induced carcinogenesis. DNA damage was assessed by measuring N-7-(2,3,4-trihydroxybut-1-yl)-guanine (THB-Gua) adducts. To investigate global histone modification alterations, we evaluated the trimethylation and acetylation of histones H3 and H4 across tissues. Changes in global cytosine DNA methylation were evaluated from the levels of methylation of LINE-1 and SINE B1 retrotransposons. We quantified the degree of variation across strains, deriving a chemical-specific human variability factor to address population variability in carcinogenic risk, which is largely ignored in current cancer risk assessment practice. Quantitative trait locus mapping identified four candidate genes related to chromatin remodeling whose variation was associated with interstrain susceptibility. Overall, this study uses 1,3-butadiene to demonstrate how the Collaborative Cross mouse population can be used to identify the mechanisms for and quantify the degree of interindividual variability in tissue-specific effects that are relevant to chemically induced carcinogenesis.
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Affiliation(s)
- Lauren Lewis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences , Texas A&M University , College Station , Texas 77843 , United States
| | - Barbara Borowa-Mazgaj
- Division of Biochemical Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas 72079 , United States
| | - Aline de Conti
- Division of Biochemical Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas 72079 , United States
| | - Grace A Chappell
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences , Texas A&M University , College Station , Texas 77843 , United States
| | - Yu-Syuan Luo
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences , Texas A&M University , College Station , Texas 77843 , United States
| | - Wanda Bodnar
- Department of Environmental Sciences and Engineering , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27516 , United States
| | - Kranti Konganti
- Department of Molecular and Cellular Medicine, College of Medicine , Texas A&M University , College Station , Texas 77843-1114 , United States
| | - Fred A Wright
- Bioinformatics Research Center , North Carolina State University , Raleigh , North Carolina 27695-7566 , United States
| | - David W Threadgill
- Department of Molecular and Cellular Medicine, College of Medicine , Texas A&M University , College Station , Texas 77843-1114 , United States
| | - Weihsueh A Chiu
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences , Texas A&M University , College Station , Texas 77843 , United States
| | - Igor P Pogribny
- Division of Biochemical Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas 72079 , United States
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences , Texas A&M University , College Station , Texas 77843 , United States
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13
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Lewis L, Chappell GA, Kobets T, O'Brian BE, Sangaraju D, Kosyk O, Bodnar W, Tretyakova NY, Pogribny IP, Rusyn I. Sex-specific differences in genotoxic and epigenetic effects of 1,3-butadiene among mouse tissues. Arch Toxicol 2019; 93:791-800. [PMID: 30552462 PMCID: PMC6451682 DOI: 10.1007/s00204-018-2374-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 12/10/2018] [Indexed: 01/31/2023]
Abstract
Exposure to environmental chemicals has been shown to have an impact on the epigenome. One example is a known human carcinogen 1,3-butadiene which acts primarily by a genotoxic mechanism, but also disrupts the chromatin structure by altering patterns of cytosine DNA methylation and histone modifications. Sex-specific differences in 1,3-butadiene-induced genotoxicity and carcinogenicity are well established; however, it remains unknown whether 1,3-butadiene-associated epigenetic alterations are also sex dependent. Therefore, we tested the hypothesis that inhalational exposure to 1,3-butadiene will result in sex-specific epigenetic alterations. DNA damage and epigenetic effects of 1,3-butadiene were evaluated in liver, lung, and kidney tissues of male and female mice of two inbred strains (C57BL/6J and CAST/EiJ). Mice were exposed to 0 or 425 ppm of 1,3-butadiene by inhalation (6 h/day, 5 days/week) for 2 weeks. Strain- and tissue-specific differences in 1,3-butadiene-induced DNA adducts and crosslinks were detected in the liver, lung and kidney; however, significant sex-specific differences in DNA damage were observed in the lung of C57BL/6J mice only. In addition, we assessed expression of the DNA repair genes and observed a marked upregulation of Mgmt in the kidney in female C57BL/6J mice. Sex-specific epigenetic effects of 1,3-butadiene exposure were evident in alterations of cytosine DNA methylation and histone modifications in the liver and lung in both strains. Specifically, we observed a loss of cytosine DNA methylation in the liver and lung of male and female 1,3-butadiene-exposed C57BL/6J mice, whereas hypermethylation was found in the liver and lung in 1,3-butadiene-exposed female CAST/EiJ mice. Our findings suggest that strain- and sex-specific effects of 1,3-butadiene on the epigenome may contribute to the known differences in cancer susceptibility.
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Affiliation(s)
- Lauren Lewis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Grace A Chappell
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Tetyana Kobets
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC, USA
| | - Bridget E O'Brian
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC, USA
| | - Dewakar Sangaraju
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Oksana Kosyk
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC, USA
| | - Wanda Bodnar
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Igor P Pogribny
- Division of Biochemical Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.
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14
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Meehan RR, Thomson JP, Lentini A, Nestor CE, Pennings S. DNA methylation as a genomic marker of exposure to chemical and environmental agents. Curr Opin Chem Biol 2018; 45:48-56. [PMID: 29505975 DOI: 10.1016/j.cbpa.2018.02.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/07/2018] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
Abstract
Recent progress in interpreting comprehensive genetic and epigenetic profiles for human cellular states has contributed new insights into the developmental origins of disease, elucidated novel signalling pathways and enhanced drug discovery programs. A similar comprehensive approach to decoding the epigenetic readouts from chemical challenges in vivo would yield new paradigms for monitoring and assessing environmental exposure in model systems and humans.
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Affiliation(s)
- Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
| | - John P Thomson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Antonio Lentini
- Department of Clinical and Experimental Medicine, Linköping University, Linköping SE 58183, Sweden
| | - Colm E Nestor
- Department of Clinical and Experimental Medicine, Linköping University, Linköping SE 58183, Sweden.
| | - Sari Pennings
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, EH16 4TJ, UK.
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15
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Bhattacharjee P, Paul S, Bhattacharjee S, Giri AK, Bhattacharjee P. Association of H3K79 monomethylation (an epigenetic signature) with arsenic-induced skin lesions. Mutat Res 2017; 807:1-9. [PMID: 29161537 DOI: 10.1016/j.mrfmmm.2017.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022]
Abstract
Arsenic, a non mutagenic carcinogen, poses a profound health risk upon prolonged exposure. The objective of the study was to analyze the post-translational modifications of the major histone H3 and the associated molecular crosstalk to identify the epigenetic signature of arsenic susceptibility. Herein, we identified significant upregulation of H3K79me1, in individuals with arsenic-induced skin lesion (WSL), and H3K79me1 was found to be regulated by the upstream methyltransferase DOT1L. Moreover, the downstream target molecule 53BP1, a tumor suppressor protein that has a docking preference for H3K79me1 at a site of a double-strand break (DSB), was downregulated, indicating greater DNA damage in the WSL group. Western blot data confirmed higher levels of γH2AX, a known marker of DSBs, in group WSL. In vitro dose-response analysis also confirmed the association of the H3K79me1 signature with arsenic toxicity. Taken together, our findings revealed that H3K79me1 and DOT1L could be a novel epigenetic signature of the arsenic-exposed WSL group.
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Affiliation(s)
- Pritha Bhattacharjee
- Department of Zoology and Department of Environmental Science, University of Calcutta, Kolkata 700019, India
| | - Somnath Paul
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | | | - Ashok K Giri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India.
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16
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Thomson JP, Ottaviano R, Buesen R, Moggs JG, Schwarz M, Meehan RR. Defining baseline epigenetic landscapes in the rat liver. Epigenomics 2017; 9:1503-1527. [PMID: 29130343 PMCID: PMC5957268 DOI: 10.2217/epi-2017-0029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Aim Characterization of the hepatic epigenome following exposure to chemicals and therapeutic drugs provides novel insights into toxicological and pharmacological mechanisms, however appreciation of genome-wide inter- and intra-strain baseline epigenetic variation, particularly in under-characterized species such as the rat is limited. Material & methods To enhance the utility of epigenomic endpoints safety assessment, we map both DNA modifications (5-methyl-cytosine and 5-hydroxymethyl-cytosine) and enhancer related chromatin marks (H3K4me1 and H3K27ac) across multiple male and female rat livers for two important outbred laboratory rat strains (Sprague–Dawley and Wistar). Results & conclusion Integration of DNA modification, enhancer chromatin marks and gene expression profiles reveals clear gender-specific chromatin states at genes which exhibit gender-specific transcription. Taken together this work provides a valuable baseline liver epigenome resource for rat strains that are commonly used in chemical and pharmaceutical safety assessment.
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Affiliation(s)
- John P Thomson
- MRC Human Genetics Unit, Genome Regulation, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Raffaele Ottaviano
- MRC Human Genetics Unit, Genome Regulation, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Roland Buesen
- BASF SE, Experimental Toxicology & Ecology, 67056 Ludwigshafen, Germany
| | - Jonathan G Moggs
- Preclinical Safety, Translational Medicine, Novartis Institutes for BioMedical Research, CH-4057 Basel, Switzerland
| | - Michael Schwarz
- Department of Toxicology, Institute of Experimental & Clinical Pharmacology & Toxicology, University of Tübingen, 72074 Tübingen, Germany
| | - Richard R Meehan
- MRC Human Genetics Unit, Genome Regulation, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
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17
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Wolters JEJ, van Breda SGJ, Caiment F, Claessen SM, de Kok TMCM, Kleinjans JCS. Nuclear and Mitochondrial DNA Methylation Patterns Induced by Valproic Acid in Human Hepatocytes. Chem Res Toxicol 2017; 30:1847-1854. [PMID: 28853863 PMCID: PMC5645762 DOI: 10.1021/acs.chemrestox.7b00171] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Valproic
acid (VPA) is one of the most widely prescribed antiepileptic
drugs in the world. Despite its pharmacological importance, it may
cause liver toxicity and steatosis through mitochondrial dysfunction.
The aim of this study is to further investigate VPA-induced mechanisms
of steatosis by analyzing changes in patterns of methylation in nuclear
DNA (nDNA) and mitochondrial DNA (mtDNA). Therefore, primary human
hepatocytes (PHHs) were exposed to an incubation concentration of
VPA that was shown to cause steatosis without inducing overt cytotoxicity.
VPA was administered daily for 5 days, and this was followed by a
3 day washout (WO). Methylated DNA regions (DMRs) were identified
by using the methylated DNA immunoprecipitation–sequencing
(MeDIP-seq) method. The nDNA DMRs after VPA treatment could indeed
be classified into oxidative stress- and steatosis-related pathways.
In particular, networks of the steatosis-related gene EP300 provided novel insight into the mechanisms of toxicity induced by
VPA treatment. Furthermore, we suggest that VPA induces a crosstalk
between nDNA hypermethylation and mtDNA hypomethylation that plays
a role in oxidative stress and steatosis development. Although most
VPA-induced methylation patterns appeared reversible upon terminating
VPA treatment, 31 nDNA DMRs (including 5 zinc finger protein genes)
remained persistent after the WO period. Overall, we have shown that
MeDIP-seq analysis is highly informative in disclosing novel mechanisms
of VPA-induced toxicity in PHHs. Our results thus provide a prototype
for the novel generation of interesting methylation biomarkers for
repeated dose liver toxicity in vitro.
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Affiliation(s)
- Jarno E J Wolters
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Simone G J van Breda
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Sandra M Claessen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
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18
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Joseph P. Transcriptomics in toxicology. Food Chem Toxicol 2017; 109:650-662. [PMID: 28720289 DOI: 10.1016/j.fct.2017.07.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 12/11/2022]
Abstract
Xenobiotics, of which many are toxic, may enter the human body through multiple routes. Excessive human exposure to xenobiotics may exceed the body's capacity to defend against the xenobiotic-induced toxicity and result in potentially fatal adverse health effects. Prevention of the adverse health effects, potentially associated with human exposure to the xenobiotics, may be achieved by detecting the toxic effects at an early, reversible and, therefore, preventable stage. Additionally, an understanding of the molecular mechanisms underlying the toxicity may be helpful in preventing and/or managing the ensuing adverse health effects. Human exposures to a large number of xenobiotics are associated with hepatotoxicity or pulmonary toxicity. Global gene expression changes taking place in biological systems, in response to exposure to xenobiotics, may represent the early and mechanistically relevant cellular events contributing to the onset and progression of xenobiotic-induced adverse health outcomes. Hepatotoxicity and pulmonary toxicity resulting from exposure to xenobiotics are discussed as specific examples to demonstrate the potential application of transcriptomics or global gene expression analysis in the prevention of adverse health effects associated with exposure to xenobiotics.
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Affiliation(s)
- Pius Joseph
- Molecular Carcinogenesis Laboratory, Toxicology and Molecular Biology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA.
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19
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Dearfield KL, Gollapudi BB, Bemis JC, Benz RD, Douglas GR, Elespuru RK, Johnson GE, Kirkland DJ, LeBaron MJ, Li AP, Marchetti F, Pottenger LH, Rorije E, Tanir JY, Thybaud V, van Benthem J, Yauk CL, Zeiger E, Luijten M. Next generation testing strategy for assessment of genomic damage: A conceptual framework and considerations. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:264-283. [PMID: 27650663 DOI: 10.1002/em.22045] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/08/2016] [Indexed: 06/06/2023]
Abstract
For several decades, regulatory testing schemes for genetic damage have been standardized where the tests being utilized examined mutations and structural and numerical chromosomal damage. This has served the genetic toxicity community well when most of the substances being tested were amenable to such assays. The outcome from this testing is usually a dichotomous (yes/no) evaluation of test results, and in many instances, the information is only used to determine whether a substance has carcinogenic potential or not. Over the same time period, mechanisms and modes of action (MOAs) that elucidate a wider range of genomic damage involved in many adverse health outcomes have been recognized. In addition, a paradigm shift in applied genetic toxicology is moving the field toward a more quantitative dose-response analysis and point-of-departure (PoD) determination with a focus on risks to exposed humans. This is directing emphasis on genomic damage that is likely to induce changes associated with a variety of adverse health outcomes. This paradigm shift is moving the testing emphasis for genetic damage from a hazard identification only evaluation to a more comprehensive risk assessment approach that provides more insightful information for decision makers regarding the potential risk of genetic damage to exposed humans. To enable this broader context for examining genetic damage, a next generation testing strategy needs to take into account a broader, more flexible approach to testing, and ultimately modeling, of genomic damage as it relates to human exposure. This is consistent with the larger risk assessment context being used in regulatory decision making. As presented here, this flexible approach for examining genomic damage focuses on testing for relevant genomic effects that can be, as best as possible, associated with an adverse health effect. The most desired linkage for risk to humans would be changes in loci associated with human diseases, whether in somatic or germ cells. The outline of a flexible approach and associated considerations are presented in a series of nine steps, some of which can occur in parallel, which was developed through a collaborative effort by leading genetic toxicologists from academia, government, and industry through the International Life Sciences Institute (ILSI) Health and Environmental Sciences Institute (HESI) Genetic Toxicology Technical Committee (GTTC). The ultimate goal is to provide quantitative data to model the potential risk levels of substances, which induce genomic damage contributing to human adverse health outcomes. Any good risk assessment begins with asking the appropriate risk management questions in a planning and scoping effort. This step sets up the problem to be addressed (e.g., broadly, does genomic damage need to be addressed, and if so, how to proceed). The next two steps assemble what is known about the problem by building a knowledge base about the substance of concern and developing a rational biological argument for why testing for genomic damage is needed or not. By focusing on the risk management problem and potential genomic damage of concern, the next step of assay(s) selection takes place. The work-up of the problem during the earlier steps provides the insight to which assays would most likely produce the most meaningful data. This discussion does not detail the wide range of genomic damage tests available, but points to types of testing systems that can be very useful. Once the assays are performed and analyzed, the relevant data sets are selected for modeling potential risk. From this point on, the data are evaluated and modeled as they are for any other toxicology endpoint. Any observed genomic damage/effects (or genetic event(s)) can be modeled via a dose-response analysis and determination of an estimated PoD. When a quantitative risk analysis is needed for decision making, a parallel exposure assessment effort is performed (exposure assessment is not detailed here as this is not the focus of this discussion; guidelines for this assessment exist elsewhere). Then the PoD for genomic damage is used with the exposure information to develop risk estimations (e.g., using reference dose (RfD), margin of exposure (MOE) approaches) in a risk characterization and presented to risk managers for informing decision making. This approach is applicable now for incorporating genomic damage results into the decision-making process for assessing potential adverse outcomes in chemically exposed humans and is consistent with the ILSI HESI Risk Assessment in the 21st Century (RISK21) roadmap. This applies to any substance to which humans are exposed, including pharmaceuticals, agricultural products, food additives, and other chemicals. It is time for regulatory bodies to incorporate the broader knowledge and insights provided by genomic damage results into the assessments of risk to more fully understand the potential of adverse outcomes in chemically exposed humans, thus improving the assessment of risk due to genomic damage. The historical use of genomic damage data as a yes/no gateway for possible cancer risk has been too narrowly focused in risk assessment. The recent advances in assaying for and understanding genomic damage, including eventually epigenetic alterations, obviously add a greater wealth of information for determining potential risk to humans. Regulatory bodies need to embrace this paradigm shift from hazard identification to quantitative analysis and to incorporate the wider range of genomic damage in their assessments of risk to humans. The quantitative analyses and methodologies discussed here can be readily applied to genomic damage testing results now. Indeed, with the passage of the recent update to the Toxic Substances Control Act (TSCA) in the US, the new generation testing strategy for genomic damage described here provides a regulatory agency (here the US Environmental Protection Agency (EPA), but suitable for others) a golden opportunity to reexamine the way it addresses risk-based genomic damage testing (including hazard identification and exposure). Environ. Mol. Mutagen. 58:264-283, 2017. © 2016 The Authors. Environmental and Molecular Mutagenesis Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Kerry L Dearfield
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, District of Columbia
| | - B Bhaskar Gollapudi
- Exponent® Inc, Center for Toxicology and Mechanistic Biology, Midland, Michigan
| | | | | | - George R Douglas
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Rosalie K Elespuru
- U.S. Food and Drug Administration, CDRH/OSEL DBCMS, Silver Spring, Maryland
| | - George E Johnson
- Institute of Life Science, College of Medicine, Swansea University, Swansea, SA2 8PP, United Kingdom
| | | | - Matthew J LeBaron
- The Dow Chemical Company, Molecular, Cellular, and Biochemical Toxicology, Midland, Michigan
| | - Albert P Li
- In Vitro ADMET Laboratories LLC, Columbia, Maryland
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Lynn H Pottenger
- Formerly of The Dow Chemical Company, Toxicology & Environmental Research and Consulting now with Olin Corporation, Midland, Michigan
| | - Emiel Rorije
- National Institute for Public Health and the Environment (RIVM), Center for Safety of Substances and Products, Bilthoven, 3720 BA, The Netherlands
| | - Jennifer Y Tanir
- ILSI Health and Environmental Sciences Institute (HESI), Washington, District of Columbia
| | - Veronique Thybaud
- Sanofi, Drug Disposition, Safety and Animal Research, Vitry-sur-Seine, France
| | - Jan van Benthem
- National Institute for Public Health and the Environment (RIVM), Center for Health Protection, Bilthoven, 3720 BA, The Netherlands
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Errol Zeiger
- Errol Zeiger Consulting, Chapel Hill, North Carolina
| | - Mirjam Luijten
- National Institute for Public Health and the Environment (RIVM), Center for Health Protection, Bilthoven, 3720 BA, The Netherlands
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20
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Miousse IR, Murphy LA, Lin H, Schisler MR, Sun J, Chalbot MCG, Sura R, Johnson K, LeBaron MJ, Kavouras IG, Schnackenberg LK, Beger RD, Rasoulpour RJ, Koturbash I. Dose-response analysis of epigenetic, metabolic, and apical endpoints after short-term exposure to experimental hepatotoxicants. Food Chem Toxicol 2017; 109:690-702. [PMID: 28495587 DOI: 10.1016/j.fct.2017.05.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 12/16/2022]
Abstract
Identification of sensitive and novel biomarkers or endpoints associated with toxicity and carcinogenesis is of a high priority. There is increasing interest in the incorporation of epigenetic and metabolic biomarkers to complement apical data; however, a number of questions, including the tissue specificity, dose-response patterns, early detection of those endpoints, and the added value need to be addressed. In this study, we investigated the dose-response relationship between apical, epigenetic, and metabolomics endpoints following short-term exposure to experimental hepatotoxicants, clofibrate (CF) and phenobarbital (PB). Male F344 rats were exposed to PB (0, 5, 25, and 100 mg/kg/day) or CF (0, 10, 50, and 250 mg/kg/day) for seven days. Exposure to PB or CF resulted in dose-dependent increases in relative liver weights, hepatocellular hypertrophy and proliferation, and increases in Cyp2b1 and Cyp4a1 transcripts. These changes were associated with altered histone modifications within the regulatory units of cytochrome genes, LINE-1 DNA hypomethylation, and altered microRNA profiles. Metabolomics data indicated alterations in the metabolism of bile acids. This study provides the first comprehensive analysis of the apical, epigenetic and metabolic alterations, and suggests that the latter two occur within or near the dose response curve of apical endpoint alterations following exposure to experimental hepatotoxicants.
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Affiliation(s)
- Isabelle R Miousse
- Department of Environmental and Occupational Health, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
| | - Lynea A Murphy
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Haixia Lin
- Department of Environmental and Occupational Health, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
| | - Melissa R Schisler
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Jinchun Sun
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Marie-Cecile G Chalbot
- Department of Environmental Health Sciences, Ryals School of Public Health, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35246, USA.
| | - Radhakrishna Sura
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Kamin Johnson
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Matthew J LeBaron
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Ilias G Kavouras
- Department of Environmental Health Sciences, Ryals School of Public Health, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35246, USA.
| | - Laura K Schnackenberg
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Reza J Rasoulpour
- Toxicology and Environmental Research & Consulting, The Dow Chemical Company, Midland, MI, USA.
| | - Igor Koturbash
- Department of Environmental and Occupational Health, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
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21
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Goodman JI. Incorporation of an Epigenetic Evaluation into Safety Assessment: What we First Need to Know. CURRENT OPINION IN TOXICOLOGY 2017; 3:20-24. [PMID: 30740577 DOI: 10.1016/j.cotox.2017.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The rapidly evolving field of epigenetic regulation of gene expression is having an impact across the spectrum of biomedical research. Toxicologists have embraced this area as evidenced by their increasing focus on discerning potential epigenetic mechanisms underlying mechanisms by which chemical and physical agents might cause toxicity. It is not surprising that an interest in epigenetic mechanisms of toxicity would lead to a desire to incorporate an epigenetic component into safety assessment. However, premature movement in this direction carries the risk of imposing more confusion than light. This commentary provides an overview of epigenetics, with an emphasis on how the various epigenetic parameters are integrated, as a basis for understanding the complexity behind the desire to include epigenetic evaluations in safety evaluations. Basically, we have much more to learn before turning the goal into a reality. However, considerable progress has been made with regard to using epigenetic profiles as signatures of xenobiotic exposure.
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Affiliation(s)
- Jay I Goodman
- Michigan State University Department of Pharmacology and Toxicology East Lansing, Michigan 48824 USA
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22
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Mosedale M, Watkins PB. Drug-induced liver injury: Advances in mechanistic understanding that will inform risk management. Clin Pharmacol Ther 2017; 101:469-480. [PMID: 27861792 DOI: 10.1002/cpt.564] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 10/26/2016] [Accepted: 11/06/2016] [Indexed: 12/11/2022]
Abstract
Drug-induced liver injury (DILI) is a major public health problem. Intrinsic (dose-dependent) DILI associated with acetaminophen overdose is the number one cause of acute liver failure in the US. However, the most problematic type of DILI impacting drug development is idiosyncratic, occurring only very rarely among treated patients and often only after several weeks or months of treatment with the offending drug. Recent advances in our understanding of the pathogenesis of DILI suggest that three mechanisms may underlie most hepatocyte effects in response to both intrinsic and idiosyncratic DILI drugs: mitochondrial dysfunction, oxidative stress, and alterations in bile acid homeostasis. However, in some cases hepatocyte stress promotes an immune response that results in clinically important idiosyncratic DILI. This review discusses recent advances in our understanding of the pathogenesis of both intrinsic and idiosyncratic DILI as well as emerging tools and techniques that will likely improve DILI risk identification and management.
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Affiliation(s)
- M Mosedale
- Institute for Drug Safety Sciences, University of North Carolina at Chapel Hill, Research Triangle Park, North Carolina, USA; Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - P B Watkins
- Institute for Drug Safety Sciences, University of North Carolina at Chapel Hill, Research Triangle Park, North Carolina, USA; Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
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23
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Thomson JP, Meehan RR. The application of genome-wide 5-hydroxymethylcytosine studies in cancer research. Epigenomics 2016; 9:77-91. [PMID: 27936926 DOI: 10.2217/epi-2016-0122] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Early detection and characterization of molecular events associated with tumorgenesis remain high priorities. Genome-wide epigenetic assays are promising diagnostic tools, as aberrant epigenetic events are frequent and often cancer specific. The deposition and analysis of multiple patient-derived cancer epigenomic profiles contributes to our appreciation of the underlying biology; aiding the detection of novel identifiers for cancer subtypes. Modifying enzymes and co-factors regulating these epigenetic marks are frequently mutated in cancers, and as epigenetic modifications themselves are reversible, this makes their study very attractive with respect to pharmaceutical intervention. Here we focus on the novel modified base, 5-hydoxymethylcytosine, and discuss how genome-wide 5-hydoxymethylcytosine profiling expedites our molecular understanding of cancer, serves as a lineage tracer, classifies the mode of action of potentially carcinogenic agents and clarifies the roles of potential novel cancer drug targets; thus assisting the development of new diagnostic/prognostic tools.
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Affiliation(s)
- John P Thomson
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
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24
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Luijten M, Olthof ED, Hakkert BC, Rorije E, van der Laan JW, Woutersen RA, van Benthem J. An integrative test strategy for cancer hazard identification. Crit Rev Toxicol 2016; 46:615-39. [PMID: 27142259 DOI: 10.3109/10408444.2016.1171294] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Assessment of genotoxic and carcinogenic potential is considered one of the basic requirements when evaluating possible human health risks associated with exposure to chemicals. Test strategies currently in place focus primarily on identifying genotoxic potential due to the strong association between the accumulation of genetic damage and cancer. Using genotoxicity assays to predict carcinogenic potential has the significant drawback that risks from non-genotoxic carcinogens remain largely undetected unless carcinogenicity studies are performed. Furthermore, test systems already developed to reduce animal use are not easily accepted and implemented by either industries or regulators. This manuscript reviews the test methods for cancer hazard identification that have been adopted by the regulatory authorities, and discusses the most promising alternative methods that have been developed to date. Based on these findings, a generally applicable tiered test strategy is proposed that can be considered capable of detecting both genotoxic as well as non-genotoxic carcinogens and will improve understanding of the underlying mode of action. Finally, strengths and weaknesses of this new integrative test strategy for cancer hazard identification are presented.
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Affiliation(s)
- Mirjam Luijten
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , the Netherlands
| | - Evelyn D Olthof
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , the Netherlands
| | - Betty C Hakkert
- b Centre for Safety of Substances and Products, National Institute for Public Health and the Environment (RIVM) , Bilthoven , the Netherlands
| | - Emiel Rorije
- b Centre for Safety of Substances and Products, National Institute for Public Health and the Environment (RIVM) , Bilthoven , the Netherlands
| | | | - Ruud A Woutersen
- d Netherlands Organization for Applied Scientific Research (TNO) , Zeist , the Netherlands
| | - Jan van Benthem
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , the Netherlands
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25
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Biotin-mediated epigenetic modifications: Potential defense against the carcinogenicity of benzo[a]pyrene. Toxicol Lett 2016; 241:216-24. [DOI: 10.1016/j.toxlet.2015.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/03/2015] [Accepted: 11/08/2015] [Indexed: 12/16/2022]
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26
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Sancak D, Ozden S. Global histone modifications in Fumonisin B1 exposure in rat kidney epithelial cells. Toxicol In Vitro 2015. [PMID: 26208285 DOI: 10.1016/j.tiv.2015.07.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Fumonisin B1 (FB1) is a Fusarium mycotoxin frequently occurring in maize-based food and feed. Although the effects of FB1 on sphingolipid metabolism are clear, little is known about early molecular changes associated with FB1 carcinogenicity. It has been shown that FB1 disrupts DNA methylation and chromatin modifications in HepG2 cells. We investigated dose- and time-dependent effects of FB1 in global histone modifications such as histone H3 lysine 9 di-, trimethylation (H3K9me2/me3), histone H3 lysine 4 trimethylation (H3K4me3), histone H4 lysine 20 trimethylation (H4K20me3), histone H3 lysine 9 acetylation (H3K9ac) and the enzymes involved in these mechanisms in rat kidney epithelial cells (NRK-52E). The increased levels of global H3K9me2/me3 were observed in FB1 treated cells, while the global levels of H4K20me3 and H3K9ac were decreased. FB1 caused some changes on the activities of H3K9 histone methyltransferase (HMT) and histone acetyltransferase (HAT) at high concentrations in NRK-52E cells. Further, the effects of trichostatin A (TSA), a histone deacetylase inhibitor, were investigated in NRK-52E cells. TSA was found to cause an increase on H3K9ac levels as expected. In this study we suggest that FB1 may disrupt epigenetic events by altering global histone modifications, introducing a novel aspect on the potential mechanism of FB1 carcinogenesis.
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Affiliation(s)
- Duygu Sancak
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, 34116 Beyazit, Istanbul, Turkey
| | - Sibel Ozden
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Istanbul University, 34116 Beyazit, Istanbul, Turkey.
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27
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Miousse IR, Currie R, Datta K, Ellinger-Ziegelbauer H, French JE, Harrill AH, Koturbash I, Lawton M, Mann D, Meehan RR, Moggs JG, O'Lone R, Rasoulpour RJ, Pera RAR, Thompson K. Importance of investigating epigenetic alterations for industry and regulators: An appraisal of current efforts by the Health and Environmental Sciences Institute. Toxicology 2015; 335:11-9. [PMID: 26134581 DOI: 10.1016/j.tox.2015.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/15/2015] [Accepted: 06/23/2015] [Indexed: 12/20/2022]
Abstract
Recent technological advances have led to rapid progress in the characterization of epigenetic modifications that control gene expression in a generally heritable way, and are likely involved in defining cellular phenotypes, developmental stages and disease status from one generation to the next. On November 18, 2013, the International Life Sciences Institute (ILSI) Health and Environmental Sciences Institute (HESI) held a symposium entitled "Advances in Assessing Adverse Epigenetic Effects of Drugs and Chemicals" in Washington, D.C. The goal of the symposium was to identify gaps in knowledge and highlight promising areas of progress that represent opportunities to utilize epigenomic profiling for risk assessment of drugs and chemicals. Epigenomic profiling has the potential to provide mechanistic information in toxicological safety assessments; this is especially relevant for the evaluation of carcinogenic or teratogenic potential and also for drugs that directly target epigenetic modifiers, like DNA methyltransferases or histone modifying enzymes. Furthermore, it can serve as an endpoint or marker for hazard characterization in chemical safety assessment. The assessment of epigenetic effects may also be approached with new model systems that could directly assess transgenerational effects or potentially sensitive stem cell populations. These would enhance the range of safety assessment tools for evaluating xenobiotics that perturb the epigenome. Here we provide a brief synopsis of the symposium, update findings since that time and then highlight potential directions for future collaborative efforts to incorporate epigenetic profiling into risk assessment.
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Affiliation(s)
- Isabelle R Miousse
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Richard Currie
- Syngenta Jealotts Hill International Research Centre, Bracknell, Berkshire, UK
| | | | - Heidrun Ellinger-Ziegelbauer
- Toxicology, Bayer Pharma AG, Wuppertal, Germany; Member of the Innovative Medicines Initiative (IMI) BioMARkers & molecular tumor classification for non-genotoxic CARcinogenesis (MARCAR) consortium www.imi-marcar.eu
| | - John E French
- National Institute for Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC, USA
| | - Alison H Harrill
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Derek Mann
- Fibrosis Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Member of the Innovative Medicines Initiative (IMI) BioMARkers & molecular tumor classification for non-genotoxic CARcinogenesis (MARCAR) consortium www.imi-marcar.eu
| | - Jonathan G Moggs
- Discovery and Investigative Safety, Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland; Member of the Innovative Medicines Initiative (IMI) BioMARkers & molecular tumor classification for non-genotoxic CARcinogenesis (MARCAR) consortium www.imi-marcar.eu
| | - Raegan O'Lone
- ILSI Health and Environmental Sciences Institute, Washington, D.C., USA
| | - Reza J Rasoulpour
- Toxicology Environmental Research and Consulting, The Dow Chemical Company, Midland, MI, USA
| | | | - Karol Thompson
- Division of Applied Regulatory Science, OCP, CDER, US FDA, Silver Spring, MD, USA
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28
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Thomson JP, Fawkes A, Ottaviano R, Hunter JM, Shukla R, Mjoseng HK, Clark R, Coutts A, Murphy L, Meehan RR. DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures. Sci Rep 2015; 5:9778. [PMID: 25985418 PMCID: PMC4435000 DOI: 10.1038/srep09778] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/02/2015] [Indexed: 02/02/2023] Open
Abstract
Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; "DIP-SC-seq") on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets.
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Affiliation(s)
- John P Thomson
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Angie Fawkes
- Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Raffaele Ottaviano
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Jennifer M Hunter
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Ruchi Shukla
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Heidi K Mjoseng
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Richard Clark
- Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Audrey Coutts
- Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Lee Murphy
- Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Richard R Meehan
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
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29
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Henderson CJ, Cameron AR, Chatham L, Stanley LA, Wolf CR. Evidence that the capacity of nongenotoxic carcinogens to induce oxidative stress is subject to marked variability. Toxicol Sci 2015; 145:138-48. [PMID: 25690736 PMCID: PMC4833039 DOI: 10.1093/toxsci/kfv039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Many drugs and environmental chemicals which are not directly mutagenic have the capacity to increase the incidence of tumors in the liver and other tissues. For this reason, such compounds are known as nongenotoxic carcinogens. The mechanisms underlying their effects remain unclear; however, their capacity to induce oxidative stress is considered to be a critical step in the carcinogenic process, although the evidence that this is actually the case remains equivocal and sparse. We have exploited a novel heme oxygenase-1 reporter mouse to evaluate the capacity of nongenotoxic carcinogens with different mechanisms of action to induce oxidative stress in the liver in vivo. When these compounds were administered at doses reported to cause liver tumors, marked differences in activation of the reporter were observed. 1,4-Dichlorobenzene and nafenopin were strong inducers of oxidative stress, whereas phenobarbital, piperonyl butoxide, cyproterone acetate, and WY14,643 were, at best, only very weak inducers. In the case of phenobarbital and thioacetamide, the number of LacZ-positive hepatocytes increased with time, and for the latter also with dose. The data obtained demonstrate that although some nongenotoxic carcinogens can induce oxidative stress, it is not a dominant feature of the response to these compounds. Therefore in contrast to the current models, these data suggest that oxidative stress is not a key determinant in the mechanism of nongenotoxic carcinogenesis but may contribute to the effects in a compound-specific manner.
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Affiliation(s)
- Colin J Henderson
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital & Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Amy R Cameron
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital & Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Lynsey Chatham
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital & Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Lesley A Stanley
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital & Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Charles Roland Wolf
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital & Medical School, University of Dundee, Dundee DD1 9SY, UK
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30
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Chappell G, Kobets T, O'Brien B, Tretyakova N, Sangaraju D, Kosyk O, Sexton KG, Bodnar W, Pogribny IP, Rusyn I. Epigenetic events determine tissue-specific toxicity of inhalational exposure to the genotoxic chemical 1,3-butadiene in male C57BL/6J mice. Toxicol Sci 2014; 142:375-84. [PMID: 25237060 PMCID: PMC4250847 DOI: 10.1093/toxsci/kfu191] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
1,3-Butadiene (BD), a widely used industrial chemical and a ubiquitous environmental pollutant, is a known human carcinogen. Although genotoxicity is an established mechanism of the tumorigenicity of BD, epigenetic effects have also been observed in livers of mice exposed to the chemical. To better characterize the diverse molecular mechanisms of BD tumorigenicity, we evaluated genotoxic and epigenotoxic effects of BD exposure in mouse tissues that are target (lung and liver) and non-target (kidney) for BD-induced tumors. We hypothesized that epigenetic alterations may explain, at least in part, the tissue-specific differences in BD tumorigenicity in mice. We evaluated the level of N-7-(2,3,4-trihydroxybut-1-yl)guanine adducts and 1,4-bis-(guan-7-yl)-2,3-butanediol crosslinks, DNA methylation, and histone modifications in male C57BL/6 mice exposed to filtered air or 425 ppm of BD by inhalation (6 h/day, 5 days/week) for 2 weeks. Although DNA damage was observed in all three tissues of BD-exposed mice, variation in epigenetic effects clearly existed between the kidneys, liver, and lungs. Epigenetic alterations indicative of genomic instability, including demethylation of repetitive DNA sequences and alterations in histone-lysine acetylation, were evident in the liver and lung tissues of BD-exposed mice. Changes in DNA methylation were insignificant in the kidneys of treated mice, whereas marks of condensed heterochromatin and transcriptional silencing (histone-lysine trimethylation) were increased. These modifications may represent a potential mechanistic explanation for the lack of tumorigenesis in the kidney. Our results indicate that differential tissue susceptibility to chemical-induced tumorigenesis may be attributed to tissue-specific epigenetic alterations.
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Affiliation(s)
- Grace Chappell
- *Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079 and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Tetyana Kobets
- *Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079 and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455 *Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079 and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Bridget O'Brien
- *Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079 and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Natalia Tretyakova
- *Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079 and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Dewakar Sangaraju
- *Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079 and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Oksana Kosyk
- *Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079 and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Kenneth G Sexton
- *Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079 and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Wanda Bodnar
- *Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079 and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Igor P Pogribny
- *Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079 and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Ivan Rusyn
- *Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079 and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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31
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McCarrey JR. Distinctions between transgenerational and non-transgenerational epimutations. Mol Cell Endocrinol 2014; 398:13-23. [PMID: 25079508 DOI: 10.1016/j.mce.2014.07.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/25/2014] [Accepted: 07/25/2014] [Indexed: 12/22/2022]
Abstract
Recent studies have described numerous environmentally-induced disruptions of the epigenome (epimutations) in mammals. While some of these appear to be corrected by normal germline-specific epigenetic reprogramming and are therefore not transmitted transgenerationally, others are not corrected and are transmitted over multiple subsequent generations. The mechanism(s) that distinguish transgenerational and non-transgenerational epimutations have not been delineated. This review examines several potential molecular and developmental distinctions between transgenerational and non-transgenerational epimutations in the context of the likelihood that any of these may or may not contribute to transgenerational inheritance of epimutations.
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Affiliation(s)
- John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, USA.
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32
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Gu C, Begley TJ, Dedon PC. tRNA modifications regulate translation during cellular stress. FEBS Lett 2014; 588:4287-96. [PMID: 25304425 DOI: 10.1016/j.febslet.2014.09.038] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/29/2014] [Accepted: 09/29/2014] [Indexed: 12/20/2022]
Abstract
The regulation of gene expression in response to stress is an essential cellular protection mechanism. Recent advances in tRNA modification analysis and genome-based codon bias analytics have facilitated studies that lead to a novel model for translational control, with translation elongation dynamically regulated during stress responses. Stress-induced increases in specific anticodon wobble bases are required for the optimal translation of stress response transcripts that are significantly biased in the use of degenerate codons keyed to these modified tRNA bases. These findings led us to introduce the notion of tRNA modification tunable transcripts (MoTTs - transcripts whose translation is regulated by tRNA modifications), which are identifiable using genome-wide codon counting algorithms. In support of this general model of translational control of stress response, studies making use of detailed measures of translation, tRNA methyltransferase mutants, and computational and mass spectrometry approaches reveal that stress reprograms tRNA modifications to translationally regulate MoTTs linked to arginine and leucine codons, which helps cells survive insults by damaging agents. These studies highlight how tRNA methyltransferase activities and MoTTs are key components of the cellular stress response.
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Affiliation(s)
- Chen Gu
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas J Begley
- State University of New York - College of Nanoscale Science and Engineering, Albany, NY, United States; The RNA Institute at the University at Albany, Albany, NY, United States.
| | - Peter C Dedon
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States; Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
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33
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Bacolla A, Cooper DN, Vasquez KM. Mechanisms of base substitution mutagenesis in cancer genomes. Genes (Basel) 2014; 5:108-46. [PMID: 24705290 PMCID: PMC3978516 DOI: 10.3390/genes5010108] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 01/24/2023] Open
Abstract
Cancer genome sequence data provide an invaluable resource for inferring the key mechanisms by which mutations arise in cancer cells, favoring their survival, proliferation and invasiveness. Here we examine recent advances in understanding the molecular mechanisms responsible for the predominant type of genetic alteration found in cancer cells, somatic single base substitutions (SBSs). Cytosine methylation, demethylation and deamination, charge transfer reactions in DNA, DNA replication timing, chromatin status and altered DNA proofreading activities are all now known to contribute to the mechanisms leading to base substitution mutagenesis. We review current hypotheses as to the major processes that give rise to SBSs and evaluate their relative relevance in the light of knowledge acquired from cancer genome sequencing projects and the study of base modifications, DNA repair and lesion bypass. Although gene expression data on APOBEC3B enzymes provide support for a role in cancer mutagenesis through U:G mismatch intermediates, the enzyme preference for single-stranded DNA may limit its activity genome-wide. For SBSs at both CG:CG and YC:GR sites, we outline evidence for a prominent role of damage by charge transfer reactions that follow interactions of the DNA with reactive oxygen species (ROS) and other endogenous or exogenous electron-abstracting molecules.
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Affiliation(s)
- Albino Bacolla
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Karen M Vasquez
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
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34
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Dao T, Cheng RYS, Revelo MP, Mitzner W, Tang W. Hydroxymethylation as a Novel Environmental Biosensor. Curr Environ Health Rep 2014; 1:1-10. [PMID: 24860723 PMCID: PMC4029614 DOI: 10.1007/s40572-013-0005-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Beyond the genome, epigenetics has become a promising approach in understanding the interactions between the gene and the environment. Epigenetic regulation includes DNA methylation, histone modifications, and non-coding RNAs. Among these, DNA methylation, which is the addition of a methyl group to the fifth base of cytosine to produce 5-methylcytosine (5-mC), is most commonly studied. Epigenetic regulation has changed given the discovery of 5-hydroxymethylcytosine (5-hmC), considered the "sixth base", and the nature of TET proteins to catalyze 5-mC oxidation to 5-hmC. 5-hydroxymethylation has been proposed to be a stable intermediate between methylation and demethylation and has raised questions about the functions of 5-hmC in gene regulation in cells, tissues, and organs in response to environmental exposure. Herein, we have provided an introduction to the chemistry of 5-hydroxymethylation, and the techniques for detection of 5-hydroxymethylation. In addition, we have reviewed current reports describing how 5-hmC responds to environmental factors, leading to the development of disease. And finally, we have discussed the potential use of 5-hmC in the study of disease development. All in all, it is our goal to provide innovative and convincing epigenetic studies for understanding the etiology of environmentally-related human disease, and translate these epigenetic findings into lifestyle recommendations and clinical practices to prevent and cure disease.
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Affiliation(s)
- T Dao
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - R Y S Cheng
- Radiation Biology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - M P Revelo
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States
| | - W Mitzner
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Wy Tang
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
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Dedon PC, Begley TJ. A system of RNA modifications and biased codon use controls cellular stress response at the level of translation. Chem Res Toxicol 2014; 27:330-7. [PMID: 24422464 PMCID: PMC3997223 DOI: 10.1021/tx400438d] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cells respond to environmental stressors and xenobiotic exposures using regulatory networks to control gene expression, and there is an emerging appreciation for the role of numerous postsynthetic chemical modifications of DNA, RNA, and proteins in controlling transcription and translation of the stress response. In this Perspective, we present a model for a new network that regulates the cellular response to xenobiotic exposures and other stresses in which stress-induced reprogramming of a system of dozens of post-transcriptional modifications on tRNA (tRNA) promotes selective translation of codon-biased mRNAs for critical response proteins. As a product of novel genomic and bioanalytical technologies, this model has strong parallels with the regulatory networks of DNA methylation in epigenetics and the variety of protein secondary modifications comprising signaling pathways and the histone code. When present at the tRNA wobble position, the modified ribonucleosides enhance the translation of mRNAs in which the cognate codons of the tRNAs are highly over-represented and that represent critical stress response proteins. A parallel system may also downregulate the translation of families of proteins. Notably, dysregulation of the tRNA methyltransferase enzymes in humans has also been implicated in cancer etiology, with demonstrated oncogenic and tumor-suppressive effects.
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Affiliation(s)
- Peter C Dedon
- Department of Biological Engineering, Center for Environmental Health Science, Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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