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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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Guo X, Chen X, Wang J, Liu Z, Gaile D, Wu H, Yu G, Mao G, Yang Z, Di Z, Guo X, Cao L, Chang P, Kang B, Chen J, Gao W, Ren X. Multi-generational impacts of arsenic exposure on genome-wide DNA methylation and the implications for arsenic-induced skin lesions. ENVIRONMENT INTERNATIONAL 2018; 119:250-263. [PMID: 29982128 PMCID: PMC6143427 DOI: 10.1016/j.envint.2018.06.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 05/19/2023]
Abstract
As a nonmutagenic human carcinogen, arsenic (As)'s carcinogenic activity is likely the result of epigenetic changes, particularly alterations in DNA methylation. While increasing studies indicate a potentially important role for timing of As exposure on DNA methylation patterns and the subsequent differential risks for As toxicity and carcinogenesis, there is a lack of research that tackles these critical questions, particularly in human based populations. Here we reported a family-based study including three generations, in which each generation living in the same household had a distinctive timing of As exposure: in adulthood, in utero and during early childhood, and in germlines exposure for grandparents, parents, and grandchildren, respectively. We generated genome-wide DNA methylation data for 18 As-exposed families, nine control families, as well as 18 arsenical skin lesion patients. Our analysis showed that As exposure may leave detectable DNA methylation changes even though exposure occurred decades ago, and the most significant changes of global DNA methylation were observed among patients afflicted with arsenical skin lesions. As exposure across generations shared common differentially methylated DNA loci and regions (744 DML and 15 DMRs) despite the distinctive exposure timing in each generation. Importantly, based on these DML, clustering analysis grouped skin lesion patients together with grandparents in exposed families in the same cluster, separated from grandparents in control families. Further analysis identified a number of DML and several molecular pathways that were significantly distinguished between controls, exposed populations, as well as skin lesion patients. Finally, our exploratory analysis suggested that some of these DML altered by As exposure, may have the potential to be inherited affecting not only those directly exposed but also later generations. Together, our results suggest that common DML and/or DMRs associated with an increased risk for disease development could be identified regardless of when exposure to As occurred during their life span, and thus may be able to serve as biomarkers for identifying individuals at risk for As-induced skin lesions and possible cancers.
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Affiliation(s)
- Xiaojuan Guo
- School of Public Health, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China; School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xushen Chen
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Jie Wang
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Zhiyue Liu
- School of Public Health, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Daniel Gaile
- Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Hongmei Wu
- School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Guan Yu
- Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Guangyun Mao
- School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zuopeng Yang
- Center for Disease Control and Prevention, Wuyuan County, Inner Mongolia, China
| | - Zhen Di
- Center for Disease Control and Prevention, Hangjinhouqi County, Inner Mongolia, China
| | - Xiuqing Guo
- School of Public Health, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Li Cao
- School of Public Health, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Peiye Chang
- School of Public Health, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Binxian Kang
- Center for Disease Control and Prevention, Wuyuan County, Inner Mongolia, China
| | - Jinyu Chen
- Center for Disease Control and Prevention, Wuyuan County, Inner Mongolia, China
| | - Wen Gao
- Center for Disease Control and Prevention, Wuyuan County, Inner Mongolia, China
| | - Xuefeng Ren
- School of Public Health, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China; Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA.
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Fiziev P, Ernst J. ChromTime: modeling spatio-temporal dynamics of chromatin marks. Genome Biol 2018; 19:109. [PMID: 30097049 PMCID: PMC6085762 DOI: 10.1186/s13059-018-1485-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 07/17/2018] [Indexed: 11/17/2022] Open
Abstract
To model spatial changes of chromatin mark peaks over time we develop and apply ChromTime, a computational method that predicts peaks to be either expanding, contracting, or holding steady between time points. Predicted expanding and contracting peaks can mark regulatory regions associated with transcription factor binding and gene expression changes. Spatial dynamics of peaks provide information about gene expression changes beyond localized signal density changes. ChromTime detects asymmetric expansions and contractions, which for some marks associate with the direction of transcription. ChromTime facilitates the analysis of time course chromatin data in a range of biological systems.
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Affiliation(s)
- Petko Fiziev
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, Los Angeles, CA, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, Los Angeles, CA, USA. .,Computer Science Department, University of California, Los Angeles, CA, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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Ge Y, Zhu J, Wang X, Zheng N, Tu C, Qu J, Ren X. Mapping dynamic histone modification patterns during arsenic-induced malignant transformation of human bladder cells. Toxicol Appl Pharmacol 2018; 355:164-173. [PMID: 29966674 DOI: 10.1016/j.taap.2018.06.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/14/2018] [Accepted: 06/28/2018] [Indexed: 01/17/2023]
Abstract
Arsenic is a known potent risk factor for bladder cancer. Increasing evidence suggests that epigenetic alterations, e.g., DNA methylation and histones posttranslational modifications (PTMs), contribute to arsenic carcinogenesis. Our previous studies have demonstrated that exposure of human urothelial cells (UROtsa cells) to monomethylarsonous acid (MMAIII), one of arsenic active metabolites, changes the histone acetylation marks across the genome that are correlated with MMAIII-induced UROtsa cell malignant transformation. In the current study, we employed a high-resolution and high-throughput liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify and quantitatively measure various PTM patterns during the MMAIII-induced malignant transformation. Our data showed that MMAIII exposure caused a time-dependent increase in histone H3 acetylation on lysine K4, K9, K14, K18, K23, and K27, but a decrease in acetylation on lysine K5, K8, K12, and K16 of histone H4. Consistent with this observation, H3K18ac was increased while H4K8ac was decreased in the leukocytes collected from people exposed to high concentrations of arsenic compared to those exposed to low concentrations. MMAIII was also able to alter histone methylation patterns: MMAIII transformed cells experienced a loss of H3K4me1, and an increase in H3K9me1 and H3K27me1. Collectively, our data shows that arsenic exposure causes dynamic changes in histone acetylation and methylation patterns during arsenic-induced cancer development. Exploring the genomic location of the altered histone marks and the resulting aberrant expression of genes will be of importance in deciphering the mechanism of arsenic-induced carcinogenesis.
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Affiliation(s)
- Yichen Ge
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, The State University of New York, Buffalo, NY 14214, USA
| | - Jinqiu Zhu
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, The State University of New York, Buffalo, NY 14214, USA
| | - Xue Wang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, The State University of New York, Buffalo, NY 14214, USA
| | - Nina Zheng
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, The State University of New York, Buffalo, NY 14214, USA
| | - Chengjian Tu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, The State University of New York, Buffalo, NY 14214, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, The State University of New York, Buffalo, NY 14214, USA
| | - Xuefeng Ren
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, The State University of New York, Buffalo, NY 14214, USA; Department of Pharmacology and Toxicology, School of Biomedical Sciences, The State University of New York, Buffalo, NY 14214, USA.
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