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Nkongolo K, Michael P. Reduced representation bisulfite sequencing (RRBS) analysis reveals variation in distribution and levels of DNA methylation in white birch ( Betula papyrifera) exposed to nickel. Genome 2024. [PMID: 39226484 DOI: 10.1139/gen-2024-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Research in understanding the role of genetics and epigenetics in plant adaptations to environmental stressors such as metals is still in its infancy. The objective of the present study is to assess the effect of nickel on DNA methylation level and distribution in white birch (Betula papyrifera Marshall) using reduced representation bisulfite sequencing (RRBS). The distribution of methylated C sites of each sample revealed that the level of methylation was much higher in CG context varying between 54% and 65%, followed by CHG (24%-31.5%), and then CHH with the methylation rate between 3.3% and 5.2%. The analysis of differentially methylated regions (DMR) revealed that nickel induced both hypermethylation and hypomethylation when compared to water. Detailed analysis showed for the first time that nickel induced a higher level of hypermethylation compared to controls, while potassium triggers a higher level of hypomethylation compared to nickel. Surprisingly, the analysis of the distribution of DMRs revealed that 38%-42% were located in gene bodies, 20%-24% in exon, 19%-20% in intron, 16%-17% in promoters, and 0.03%-0.04% in transcription start site. RRBS was successful in detecting and mapping DMR in plants exposed to nickel.
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Affiliation(s)
- Kabwe Nkongolo
- Biomolecular Sciences Program and School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada
| | - Paul Michael
- Biomolecular Sciences Program and School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada
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2
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Kang YT, Yang WJ, Huang HC, Tang SC, Ko JL. Exposure to nickel chloride induces epigenetic modification on detoxification enzyme glutathione S-transferase M2. ENVIRONMENTAL TOXICOLOGY 2024; 39:1729-1736. [PMID: 38050843 DOI: 10.1002/tox.24055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/23/2023] [Accepted: 11/12/2023] [Indexed: 12/07/2023]
Abstract
Nickel (Ni) is a human carcinogen with genotoxic and epigenotoxic effects. Environmental and occupational exposure to Ni increases the risk of cancer and chronic inflammatory diseases. Our previous findings indicate that Ni alters gene expression through epigenetic regulation, specifically impacting E-cadherin and angiopoietin-like 4 (ANGPTL4), involved in epithelial-mesenchymal transition and migration. GST-M2, a member of the glutathione S-transferase (GST) enzyme family, plays a crucial role in cellular defense against oxidative damage and has been increasingly associated with cancer. GST-M2 overexpression inhibits lung cancer invasion and metastasis in vitro and in vivo. Hypermethylation of its promoter in cancer cells reduces gene expression, correlating with poor prognosis in non-small-cell lung cancer patients. The impact of Ni on GST-M2 remains unclear. We will investigate whether nickel exerts regulatory effects on GST-M2 through epigenetic modifications. Additionally, metformin, an antidiabetic drug, is being studied as a chemopreventive agent against nickel-induced damage. Our findings indicate that nickel chloride (NiCl2 ) exposure, both short-term and long-term, represses GST-M2 expression. However, the expression can be restored by demethylation agent 5-aza-2'-deoxycytidine and metformin. NiCl2 promotes hypermethylation of the GST-M2 promoter, as confirmed by methylation-specific PCR and bisulfite sequencing. Additionally, NiCl2 also influences histone acetylation, and metformin counteracts the suppressive effect of NiCl2 on histone H3 expression. Metformin reestablishes the binding of specificity protein 1 to the GST-M2 promoter, which is otherwise disrupted by NiCl2 . These findings elucidate the mechanism by which Ni reduces GST-M2 expression and transcriptional activity, potentially contributing to Ni-induced lung carcinogenesis.
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Affiliation(s)
- Yu-Ting Kang
- Institute of Medicine, Chung-Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Wan-Jung Yang
- Institute of Medicine, Chung-Shan Medical University, Taichung, Taiwan
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Hsu Chih Huang
- Institute of Medicine, Chung-Shan Medical University, Taichung, Taiwan
- Division of Thoracic Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Sheau-Chung Tang
- Department of Nursing, National Taichung University of Science and Technology, Taichung, Taiwan
| | - Jiunn-Liang Ko
- Institute of Medicine, Chung-Shan Medical University, Taichung, Taiwan
- Department of Medical Oncology and Chest Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
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3
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Gaspar AD, Cuddapah S. Nickel-induced alterations to chromatin structure and function. Toxicol Appl Pharmacol 2022; 457:116317. [PMID: 36400264 PMCID: PMC9722551 DOI: 10.1016/j.taap.2022.116317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
Nickel (Ni), a heavy metal is prevalent in the atmosphere due to both natural and anthropogenic activities. Ni is a carcinogen implicated in the development of lung and nasal cancers in humans. Furthermore, Ni exposure is associated with a number of chronic lung diseases in humans including asthma, chronic bronchitis, emphysema, pulmonary fibrosis, pulmonary edema and chronic obstructive pulmonary disease (COPD). While Ni compounds are weak mutagens, a number of studies have demonstrated the potential of Ni to alter the epigenome, suggesting epigenomic dysregulation as an important underlying cause for its pathogenicity. In the eukaryotic nucleus, the DNA is organized in a three-dimensional (3D) space through assembly of higher order chromatin structures. Such an organization is critically important for transcription and other biological activities. Accumulating evidence suggests that by negatively affecting various cellular regulatory processes, Ni could potentially affect chromatin organization. In this review, we discuss the role of Ni in altering the chromatin architecture, which potentially plays a major role in Ni pathogenicity.
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Affiliation(s)
- Adrian Domnic Gaspar
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Suresh Cuddapah
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA.
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Zhao L, Islam R, Wang Y, Zhang X, Liu LZ. Epigenetic Regulation in Chromium-, Nickel- and Cadmium-Induced Carcinogenesis. Cancers (Basel) 2022; 14:cancers14235768. [PMID: 36497250 PMCID: PMC9737485 DOI: 10.3390/cancers14235768] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022] Open
Abstract
Environmental and occupational exposure to heavy metals, such as hexavalent chromium, nickel, and cadmium, are major health concerns worldwide. Some heavy metals are well-documented human carcinogens. Multiple mechanisms, including DNA damage, dysregulated gene expression, and aberrant cancer-related signaling, have been shown to contribute to metal-induced carcinogenesis. However, the molecular mechanisms accounting for heavy metal-induced carcinogenesis and angiogenesis are still not fully understood. In recent years, an increasing number of studies have indicated that in addition to genotoxicity and genetic mutations, epigenetic mechanisms play critical roles in metal-induced cancers. Epigenetics refers to the reversible modification of genomes without changing DNA sequences; epigenetic modifications generally involve DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs. Epigenetic regulation is essential for maintaining normal gene expression patterns; the disruption of epigenetic modifications may lead to altered cellular function and even malignant transformation. Therefore, aberrant epigenetic modifications are widely involved in metal-induced cancer formation, development, and angiogenesis. Notably, the role of epigenetic mechanisms in heavy metal-induced carcinogenesis and angiogenesis remains largely unknown, and further studies are urgently required. In this review, we highlight the current advances in understanding the roles of epigenetic mechanisms in heavy metal-induced carcinogenesis, cancer progression, and angiogenesis.
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Abstract
BACKGROUND Autoimmune hepatitis has an unknown cause and genetic associations that are not disease-specific or always present. Clarification of its missing causality and heritability could improve prevention and management strategies. AIMS Describe the key epigenetic and genetic mechanisms that could account for missing causality and heritability in autoimmune hepatitis; indicate the prospects of these mechanisms as pivotal factors; and encourage investigations of their pathogenic role and therapeutic potential. METHODS English abstracts were identified in PubMed using multiple key search phases. Several hundred abstracts and 210 full-length articles were reviewed. RESULTS Environmental induction of epigenetic changes is the prime candidate for explaining the missing causality of autoimmune hepatitis. Environmental factors (diet, toxic exposures) can alter chromatin structure and the production of micro-ribonucleic acids that affect gene expression. Epistatic interaction between unsuspected genes is the prime candidate for explaining the missing heritability. The non-additive, interactive effects of multiple genes could enhance their impact on the propensity and phenotype of autoimmune hepatitis. Transgenerational inheritance of acquired epigenetic marks constitutes another mechanism of transmitting parental adaptations that could affect susceptibility. Management strategies could range from lifestyle adjustments and nutritional supplements to precision editing of the epigenetic landscape. CONCLUSIONS Autoimmune hepatitis has a missing causality that might be explained by epigenetic changes induced by environmental factors and a missing heritability that might reflect epistatic gene interactions or transgenerational transmission of acquired epigenetic marks. These unassessed or under-evaluated areas warrant investigation.
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Yuan J, Mo Y, Zhang Y, Zhang Y, Zhang Q. Nickel nanoparticles induce epithelial-mesenchymal transition in human bronchial epithelial cells via the HIF-1α/HDAC3 pathway. Nanotoxicology 2022; 16:695-712. [PMID: 36345150 PMCID: PMC9892310 DOI: 10.1080/17435390.2022.2142169] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
We and others have previously demonstrated that exposure to nickel nanoparticles (Nano-Ni) caused fibrogenic and carcinogenic effects; however, the underlying mechanisms are still not fully understood. This study aimed to investigate the effects of Nano-Ni on epithelial-mesenchymal transition (EMT) in human bronchial epithelial cells (BEAS-2B) and its underlying mechanisms since EMT is involved in both cancer pathogenesis and tissue fibrosis. Our results showed that exposure to Nano-Ni, compared to the control Nano-TiO2, caused a remarkable decrease in the expression of E-cadherin and an increase in the expression of vimentin and α-SMA, indicating an inducible role of Nano-Ni in EMT development in human bronchial epithelial cells. HIF-1α nuclear accumulation, HDAC3 upregulation, and decreased histone acetylation were also observed in the cells exposed to Nano-Ni, but not in those exposed to Nano-TiO2. Pretreatment of the cells with a specific HIF-1α inhibitor, CAY10585, or HIF-1α-specific siRNA transfection prior to Nano-Ni exposure resulted in the restoration of E-cadherin and abolished Nano-Ni-induced upregulation of vimentin and α-SMA, suggesting a crucial role of HIF-1α in Nano-Ni-induced EMT development. CAY10585 pretreatment also attenuated the HDAC3 upregulation and increased histone acetylation. Inhibition of HDAC3 with specific siRNA significantly restrained Nano-Ni-induced reduction in histone acetylation and restored EMT-related protein expression to near control levels. In summary, our findings suggest that exposure to Nano-Ni promotes the development of EMT in human bronchial epithelial cells by decreasing histone acetylation through HIF-1α-mediated HDAC3 upregulation. Our findings may provide information for further understanding of the molecular mechanisms of Nano-Ni-induced fibrosis and carcinogenesis.
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Affiliation(s)
| | | | - Yuanbao Zhang
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray Street, Louisville, KY 40209, USA
| | - Yue Zhang
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray Street, Louisville, KY 40209, USA
| | - Qunwei Zhang
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray Street, Louisville, KY 40209, USA
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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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Zhou C, Liu M, Mei X, Li Q, Zhang W, Deng P, He Z, Xi Y, Tong T, Pi H, Lu Y, Chen C, Zhang L, Yu Z, Zhou Z, He M. Histone hypoacetylation contributes to neurotoxicity induced by chronic nickel exposure in vivo and in vitro. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:147014. [PMID: 34088129 DOI: 10.1016/j.scitotenv.2021.147014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/04/2021] [Accepted: 04/04/2021] [Indexed: 06/12/2023]
Abstract
Nickel (Ni) is a heavy metal that is both an environmental pollutant and a threat to human health. However, the effects of Ni on the central nervous system in susceptible populations have not been well established. In the present study, the neurotoxicity of Ni and its underlying mechanism were investigated in vivo and in vitro. Ni exposure through drinking water (10 mg Ni/L, 12 weeks) caused learning and memory impairment in mice. Reduced dendrite complexity was observed in both Ni-exposed mouse hippocampi and Ni-treated (200 μM, 72 h) primary cultured hippocampal neurons. The levels of histone acetylation, especially at histone H3 lysine 9 (H3K9ac), were reduced in Ni-exposed mouse hippocampi and cultured neurons. RNA sequencing and chromatin immunoprecipitation (ChIP) sequencing analyses revealed that H3K9ac-modulated gene expression were downregulated. Treatment with sodium butyrate, a histone deacetylase inhibitor, attenuated Ni-induced H3K9 hypoacetylation, neural gene downregulation and dendrite complexity reduction in cultured neurons. Sodium butyrate also restored Ni-induced memory impairment in mice. These results indicate that Ni-induced H3K9 hypoacetylation may be a contributor to the neurotoxicity of Ni. The finding that Ni disturbs histone acetylation in the nervous system may provide new insight into the health risk of chronic Ni exposure.
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Affiliation(s)
- Chao Zhou
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China
| | - Mengyu Liu
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China; Department of Medical Laboratory, General Hospital of the Central Theater Command of the Chinese People's Liberation Army, 430070 Wuhan, People's Republic of China
| | - Xiang Mei
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China
| | - Qian Li
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, 400037 Chongqing, People's Republic of China
| | - Wenjuan Zhang
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China
| | - Ping Deng
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China
| | - Zhixin He
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China
| | - Yu Xi
- Department of Environmental Medicine, School of Public Health, Department of Emergency Medicine, First Affiliated Hospital, School of Medicine, Zhejiang University, 310058 Hangzhou, People's Republic of China
| | - Tong Tong
- Department of Environmental Medicine, School of Public Health, Department of Emergency Medicine, First Affiliated Hospital, School of Medicine, Zhejiang University, 310058 Hangzhou, People's Republic of China
| | - Huifeng Pi
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China
| | - Yonghui Lu
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China
| | - Chunhai Chen
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China
| | - Lei Zhang
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China
| | - Zhengping Yu
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China.
| | - Zhou Zhou
- Department of Environmental Medicine, School of Public Health, Department of Emergency Medicine, First Affiliated Hospital, School of Medicine, Zhejiang University, 310058 Hangzhou, People's Republic of China.
| | - Mindi He
- Department of Occupational Health, Army Medical University, 400038 Chongqing, People's Republic of China.
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Ijomone OM, Ijomone OK, Iroegbu JD, Ifenatuoha CW, Olung NF, Aschner M. Epigenetic influence of environmentally neurotoxic metals. Neurotoxicology 2020; 81:51-65. [PMID: 32882300 PMCID: PMC7708394 DOI: 10.1016/j.neuro.2020.08.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 02/08/2023]
Abstract
Continuous globalization and industrialization have ensured metals are an increasing aspect of daily life. Their usefulness in manufacturing has made them vital to national commerce, security and global economy. However, excess exposure to metals, particularly as a result of environmental contamination or occupational exposures, has been detrimental to overall health. Excess exposure to several metals is considered environmental risk in the aetiology of several neurological and neurodegenerative diseases. Metal-induced neurotoxicity has been a major health concern globally with intensive research to unravel the mechanisms associated with it. Recently, greater focus has been directed at epigenetics to better characterize the underlying mechanisms of metal-induced neurotoxicity. Epigenetic changes are those modifications on the DNA that can turn genes on or off without altering the DNA sequence. This review discusses how epigenetic changes such as DNA methylation, post translational histone modification and noncoding RNA-mediated gene silencing mediate the neurotoxic effects of several metals, focusing on manganese, arsenic, nickel, cadmium, lead, and mercury.
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Affiliation(s)
- Omamuyovwi M Ijomone
- The Neuro- Lab, Department of Human Anatomy, School of Health and Health Technology, Federal University of Technology, Akure, Nigeria.
| | - Olayemi K Ijomone
- The Neuro- Lab, Department of Human Anatomy, School of Health and Health Technology, Federal University of Technology, Akure, Nigeria; Department of Anatomy, University of Medical Sciences, Ondo, Nigeria
| | - Joy D Iroegbu
- The Neuro- Lab, Department of Human Anatomy, School of Health and Health Technology, Federal University of Technology, Akure, Nigeria
| | - Chibuzor W Ifenatuoha
- The Neuro- Lab, Department of Human Anatomy, School of Health and Health Technology, Federal University of Technology, Akure, Nigeria
| | - Nzube F Olung
- The Neuro- Lab, Department of Human Anatomy, School of Health and Health Technology, Federal University of Technology, Akure, Nigeria
| | - Michael Aschner
- Departments of Molecular Pharmacology and Neurosciences, Albert Einstein College of Medicine, NY, USA.
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Schrenk D, Bignami M, Bodin L, Chipman JK, del Mazo J, Grasl‐Kraupp B, Hogstrand C, Hoogenboom L(R, Leblanc J, Nebbia CS, Ntzani E, Petersen A, Sand S, Schwerdtle T, Vleminckx C, Wallace H, Guérin T, Massanyi P, Van Loveren H, Baert K, Gergelova P, Nielsen E. Update of the risk assessment of nickel in food and drinking water. EFSA J 2020; 18:e06268. [PMID: 33193868 PMCID: PMC7643711 DOI: 10.2903/j.efsa.2020.6268] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The European Commission asked EFSA to update its previous Opinion on nickel in food and drinking water, taking into account new occurrence data, the updated benchmark dose (BMD) Guidance and newly available scientific information. More than 47,000 analytical results on the occurrence of nickel were used for calculating chronic and acute dietary exposure. An increased incidence of post-implantation loss in rats was identified as the critical effect for the risk characterisation of chronic oral exposure and a BMDL 10 of 1.3 mg Ni/kg body weight (bw) per day was selected as the reference point for the establishment of a tolerable daily intake (TDI) of 13 μg/kg bw. Eczematous flare-up reactions in the skin elicited in nickel-sensitised humans, a condition known as systemic contact dermatitis, was identified as the critical effect for the risk characterisation of acute oral exposure. A BMDL could not be derived, and therefore, the lowest-observed-adverse-effect-level of 4.3 μg Ni/kg bw was selected as the reference point. The margin of exposure (MOE) approach was applied and an MOE of 30 or higher was considered as being indicative of a low health concern. The mean lower bound (LB)/upper bound (UB) chronic dietary exposure was below or at the level of the TDI. The 95th percentile LB/UB chronic dietary exposure was below the TDI in adolescents and in all adult age groups, but generally exceeded the TDI in toddlers and in other children, as well as in infants in some surveys. This may raise a health concern in these young age groups. The MOE values for the mean UB acute dietary exposure and for the 95th percentile UB raises a health concern for nickel-sensitised individuals. The MOE values for an acute scenario regarding consumption of a glass of water on an empty stomach do not raise a health concern.
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Ramazi S, Allahverdi A, Zahiri J. Evaluation of post-translational modifications in histone proteins: A review on histone modification defects in developmental and neurological disorders. J Biosci 2020. [DOI: 10.1007/s12038-020-00099-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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12
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Jose CC, Wang Z, Tanwar VS, Zhang X, Zang C, Cuddapah S. Nickel-induced transcriptional changes persist post exposure through epigenetic reprogramming. Epigenetics Chromatin 2019; 12:75. [PMID: 31856895 PMCID: PMC6921556 DOI: 10.1186/s13072-019-0324-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/09/2019] [Indexed: 12/20/2022] Open
Abstract
Background Nickel is an occupational and environmental toxicant associated with a number of diseases in humans including pulmonary fibrosis, bronchitis and lung and nasal cancers. Our earlier studies showed that the nickel-exposure-induced genome-wide transcriptional changes, which persist even after the termination of exposure may underlie nickel pathogenesis. However, the mechanisms that drive nickel-induced persistent changes to the transcriptome remain elusive. Results To elucidate the mechanisms that underlie nickel-induced long-term transcriptional changes, in this study, we examined the transcriptome and the epigenome of human lung epithelial cells during nickel exposure and after the termination of exposure. We identified two categories of persistently differentially expressed genes: (i) the genes that were differentially expressed during nickel exposure; and (ii) the genes that were differentially expressed only after the termination of exposure. Interestingly, > 85% of the nickel-induced gene expression changes occurred only after the termination of exposure. We also found extensive genome-wide alterations to the activating histone modification, H3K4me3, after the termination of nickel exposure, which coincided with the post-exposure gene expression changes. In addition, we found significant post-exposure alterations to the repressive histone modification, H3K27me3. Conclusion Our results suggest that while modest first wave of transcriptional changes occurred during nickel exposure, extensive transcriptional changes occurred during a second wave of transcription for which removal of nickel ions was essential. By uncovering a new category of transcriptional and epigenetic changes, which occur only after the termination of exposure, this study provides a novel understanding of the long-term deleterious consequences of nickel exposure on human health.
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Affiliation(s)
- Cynthia C Jose
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, 10010, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Vinay Singh Tanwar
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, 10010, USA
| | - Xiaoru Zhang
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, 10010, USA
| | - Chongzhi Zang
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| | - Suresh Cuddapah
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, 10010, USA.
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Son YO. Molecular Mechanisms of Nickel-Induced Carcinogenesis. Endocr Metab Immune Disord Drug Targets 2019; 20:1015-1023. [PMID: 31774048 DOI: 10.2174/1871530319666191125112728] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/11/2019] [Accepted: 03/22/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND The increased use of heavy metal nickel in modern industries results in increased environmental impact. Occupational and environmental exposure to nickel is closely linked to an increased risk of human lung cancer and nasal cancer. OBJECTIVE Unlike other heavy metal carcinogens, nickel has weak mutagenic activity. Carcinogenesis caused by nickel is intensively studied, but the precise mechanism of action is not yet known. RESULTS Epigenetic changes, activation of hypoxia signaling pathways, and generation of reactive oxygen species (ROS) are considered to be the major molecular mechanisms involved in nickelinduced carcinogenesis. CONCLUSION This review provides insights into current research on nickel-induced carcinogenesis and suggests possible effective therapeutic strategies for nickel-induced carcinogenesis.
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Affiliation(s)
- Young-Ok Son
- Department of Animal Biotechnology, Faculty of Biotechnology and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju City, Jeju Special Self-Governing Province, 63243, Korea
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14
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Wang J, Wu Y, Zhang X, Zhang F, Lü D, Shangguan B, Gao Y, Long M. Flow-enhanced priming of hESCs through H2B acetylation and chromatin decondensation. Stem Cell Res Ther 2019; 10:349. [PMID: 31775893 PMCID: PMC6880446 DOI: 10.1186/s13287-019-1454-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Distinct mechanical stimuli are known to manipulate the behaviors of embryonic stem cells (ESCs). Fundamental rationale of how ESCs respond to mechanical forces and the potential biological effects remain elusive. Here we conducted the mechanobiological study for hESCs upon mechanomics analysis to unravel typical mechanosensitive processes on hESC-specific fluid shear. METHODS hESC line H1 was subjected to systematically varied shear flow, and mechanosensitive proteins were obtained by mass spectrometry (MS) analysis. Then, function enrichment analysis was performed to identify the enriched gene sets. Under a steady shear flow of 1.1 Pa for 24 h, protein expressions were further detected using western blotting (WB), quantitative real-time PCR (qPCR), and immunofluorescence (IF) staining. Meanwhile, the cells were treated with 200 nM trichostatin (TSA) for 1 h as positive control to test chromatin decondensation. Actin, DNA, and RNA were then visualized with TRITC-labeled phalloidin, Hoechst 33342, and SYTO® RNASelect™ green fluorescent cell stain (Life Technologies), respectively. In addition, cell stiffness was determined with atomic force microscopy (AFM) and annexin V-PE was used to determine the apoptosis with a flow cytometer (FCM). RESULTS Typical mechanosensitive proteins were unraveled upon mechanomics analysis under fluid shear related to hESCs in vivo. Functional analyses revealed significant alterations in histone acetylation, nuclear size, and cytoskeleton for hESC under shear flow. Shear flow was able to induce H2B acetylation and nuclear spreading by CFL2/F-actin cytoskeletal reorganization. The resulting chromatin decondensation and a larger nucleus readily accommodate signaling molecules and transcription factors. CONCLUSIONS Shear flow regulated chromatin dynamics in hESCs via cytoskeleton and nucleus alterations and consolidated their primed state.
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Affiliation(s)
- Jiawen Wang
- Center for Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yi Wu
- Center for Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Zhang
- Center for Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Fan Zhang
- Center for Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Dongyuan Lü
- Center for Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Bing Shangguan
- Center for Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yuxin Gao
- Center for Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Mian Long
- Center for Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China. .,School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China.
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15
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Chromatin dynamics at the core of kidney fibrosis. Matrix Biol 2018; 68-69:194-229. [DOI: 10.1016/j.matbio.2018.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/16/2018] [Accepted: 02/17/2018] [Indexed: 02/06/2023]
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16
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Gullì M, Marchi L, Fragni R, Buschini A, Visioli G. Epigenetic modifications preserve the hyperaccumulator Noccaea caerulescens from Ni geno-toxicity. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:464-475. [PMID: 29656392 DOI: 10.1002/em.22191] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/09/2018] [Accepted: 03/05/2018] [Indexed: 05/22/2023]
Abstract
The Ni hyperaccumulator Noccaea caerulescens has adapted to live in a naturally stressed environment, evolving a complex pattern of traits to cope with adverse conditions. Evidence is accumulating regarding the important role of epigenetic modifications in regulating plant responses to stress. In this study, we present data from the natural "open-field" adaptation of the Ni hyperaccumulator N. caerulescens to serpentine soil and provide the first evidence of the involvement of epigenetic changes in response to the high Ni content present in plant leaves. The alkaline comet assay revealed the integrity of the nuclei of leaf cells of N. caerulescens grown in a Ni-rich environment, while in the non-tolerant Arabidopsis thaliana exposed to Ni, the nuclei were severely damaged. DNA of N. caerulescens plants grown in situ were considerably hyper-methylated compared to A. thaliana plants exposed to Ni. In addition, qRT-PCR revealed that N. caerulescens MET1, DRM2, and HDA8 genes involved in epigenetic DNA and histone modification were up-regulated in the presence of high Ni content in leaves. Such epigenetic modifications may constitute a defense strategy that prevents genome instability and direct damage to the DNA structure by Ni ion, enabling plants to survive in an extreme environment. Further studies will be necessary to analyze in detail the involvement of DNA methylation and other epigenetic mechanisms in the complex process of metal hyperaccumulation and plants' adaptive response. Environ. Mol. Mutagen. 59:464-475, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma, 43124, Italy
| | - Laura Marchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma, 43124, Italy
| | - Rosaria Fragni
- SSICA, Experimental Station for the Food Preserving Industry, via Tanara 31, Parma, 43100, Italy
| | - Annamaria Buschini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma, 43124, Italy
| | - Giovanna Visioli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma, 43124, Italy
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17
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Laulicht-Glick F, Wu F, Zhang X, Jordan A, Brocato J, Kluz T, Sun H, Costa M. Tungsten exposure causes a selective loss of histone demethylase protein. Mol Carcinog 2017; 56:1778-1788. [PMID: 28218462 DOI: 10.1002/mc.22634] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/08/2017] [Accepted: 02/16/2017] [Indexed: 01/20/2023]
Abstract
In the course of our investigations into the toxicity of tungstate, we discovered that cellular exposure resulted in the loss of the histone demethylase protein. We specifically investigated the loss of two histone demethylase dioxygenases, JARID1A and JMJD1A. Both of these proteins were degraded in the presence of tungstate and this resulted in increased global levels of H3K4me3 and H3K9me2, the substrates of JARID1A and JMJD1A, respectively. Treatment with MG132 completely inhibited the loss of the demethylase proteins induced by tungstate treatment, suggesting that tungstate activated the proteasomal degradation of these proteins. The changes in global histone marks and loss of histone demethylase protein persisted for at least 48 h after removing sodium tungstate from the culture. The increase in global histone methylation remained when cells were cultured in methionine-free media, indicating that the increased histone methylation did not depend upon any de novo methylation process, but rather was due to the loss of the demethylase protein. Similar increases of H3K4me3 and H3K9me2 were observed in the livers of the mice that were acutely exposed to tungstate via their drinking water. Taken together, our results indicated that tungstate exposure specifically reduced histone demethylase JARID1A and JMJD1A via proteasomal degradation, leading to increased histone methylation.
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Affiliation(s)
- Freda Laulicht-Glick
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Feng Wu
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Xiaoru Zhang
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Ashley Jordan
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Jason Brocato
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Thomas Kluz
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Hong Sun
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
| | - Max Costa
- Department of Environmental Medicine, New York University Langone Medical Center, Tuxedo, New York
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18
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Salemi R, Marconi A, Di Salvatore V, Franco S, Rapisarda V, Libra M. Epigenetic alterations and occupational exposure to benzene, fibers, and heavy metals associated with tumor development. Mol Med Rep 2017; 15:3366-3371. [DOI: 10.3892/mmr.2017.6383] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/16/2017] [Indexed: 11/05/2022] Open
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19
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Tessier SN, Luu BE, Smith JC, Storey KB. The role of global histone post-translational modifications during mammalian hibernation. Cryobiology 2017; 75:28-36. [PMID: 28257856 DOI: 10.1016/j.cryobiol.2017.02.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/25/2017] [Accepted: 02/27/2017] [Indexed: 12/22/2022]
Abstract
Mammalian hibernators must cope with hypothermia, ischemia-reperfusion, and finite fuel reserves during days or weeks of continuous torpor. One means of lowering ATP demands during hibernation involves substantial transcriptional controls. The present research analyzed epigenetic regulatory factors as a means of achieving transcriptional control over cycles of torpor-arousal. This study analyzes differential regulation of select histone modifications (e.g. phosphorylation, acetylation, methylation), and identifies post-translational modifications on purified histones using mass spectrometry from thirteen-lined ground squirrels (Ictidomys tridecemlineatus). Post-translational modifications on histone proteins were responsive to torpor-arousal, suggesting a potential mechanism to dynamically alter chromatin structure. Furthermore, proteomic sequencing data of ground squirrel histones identified lysine 19 and 24 acetylation on histone H3, while acetylation sites identified on H2B were lysine 6, 47, 110, and 117. The present study provides a new glimpse into the epigenetic mechanisms which may play a role in transcriptional regulation during mammalian hibernation.
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Affiliation(s)
- Shannon N Tessier
- Department of Surgery & Center for Engineering in Medicine, Massachusetts General Hospital & Harvard Medical School, Charlestown, MA 02129, USA
| | - Bryan E Luu
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Jeffrey C Smith
- Institute of Biochemistry & Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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20
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Chen QY, Brocato J, Laulicht F, Costa M. Mechanisms of Nickel Carcinogenesis. ESSENTIAL AND NON-ESSENTIAL METALS 2017. [DOI: 10.1007/978-3-319-55448-8_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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21
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de Jesus TCL, Nunes VS, Lopes MDC, Martil DE, Iwai LK, Moretti NS, Machado FC, de Lima-Stein ML, Thiemann OH, Elias MC, Janzen C, Schenkman S, da Cunha JPC. Chromatin Proteomics Reveals Variable Histone Modifications during the Life Cycle of Trypanosoma cruzi. J Proteome Res 2016; 15:2039-51. [DOI: 10.1021/acs.jproteome.6b00208] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Teresa Cristina Leandro de Jesus
- Laboratório
Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell
Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
- Departamento
de Física e Informática, Instituto de Física
de São Carlos, Universidade de São Paulo - USP, São Carlos, São Paulo 13563-120, Brazil
| | - Vinícius Santana Nunes
- Departamento
de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Mariana de Camargo Lopes
- Laboratório
Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell
Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Daiana Evelin Martil
- Departamento
de Física e Informática, Instituto de Física
de São Carlos, Universidade de São Paulo - USP, São Carlos, São Paulo 13563-120, Brazil
| | - Leo Kei Iwai
- Laboratório
Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell
Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Nilmar Silvio Moretti
- Departamento
de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Fabrício Castro Machado
- Departamento
de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Mariana L. de Lima-Stein
- Departamento
de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Otavio Henrique Thiemann
- Departamento
de Física e Informática, Instituto de Física
de São Carlos, Universidade de São Paulo - USP, São Carlos, São Paulo 13563-120, Brazil
| | - Maria Carolina Elias
- Laboratório
Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell
Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Christian Janzen
- Department
of Cell and Developmental Biology, Theodor-Boveri-Institute at the
Biocenter, University of Würzburg, 97070 Germany
| | - Sergio Schenkman
- Departamento
de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Laboratório
Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell
Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil
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22
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Lawrence M, Daujat S, Schneider R. Lateral Thinking: How Histone Modifications Regulate Gene Expression. Trends Genet 2015; 32:42-56. [PMID: 26704082 DOI: 10.1016/j.tig.2015.10.007] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 12/21/2022]
Abstract
The DNA of each cell is wrapped around histone octamers, forming so-called 'nucleosomal core particles'. These histone proteins have tails that project from the nucleosome and many residues in these tails can be post-translationally modified, influencing all DNA-based processes, including chromatin compaction, nucleosome dynamics, and transcription. In contrast to those present in histone tails, modifications in the core regions of the histones had remained largely uncharacterised until recently, when some of these modifications began to be analysed in detail. Overall, recent work has shown that histone core modifications can not only directly regulate transcription, but also influence processes such as DNA repair, replication, stemness, and changes in cell state. In this review, we focus on the most recent developments in our understanding of histone modifications, particularly those on the lateral surface of the nucleosome. This region is in direct contact with the DNA and is formed by the histone cores. We suggest that these lateral surface modifications represent a key insight into chromatin regulation in the cell. Therefore, lateral surface modifications form a key area of interest and a focal point of ongoing study in epigenetics.
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23
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Li Z, Chen X, Li S, Wang Z. Effect of nickel chloride on Arabidopsis genomic DNA and methylation of 18S rDNA. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2014.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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24
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Guo X, Zhang Y, Zhang Q, Fa P, Gui Y, Gao G, Cai Z. The regulatory role of nickel on H3K27 demethylase JMJD3 in kidney cancer cells. Toxicol Ind Health 2014; 32:1286-92. [PMID: 25427687 DOI: 10.1177/0748233714552687] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nickel compounds are an important class of environmental pollutants and carcinogens. Chronic exposure to nickel compounds has been connected with increased risks of numerous cancers, including lung and kidney cancers. But the precise mechanism by which nickel compounds exert their carcinogenic properties is not completely understood. In this study, kidney cancer cells namely human embryonic kidney 293-containing SV40 large T-antigen (HEK293T) and 786-0 were incubated with various concentrations of nickel chloride for 24 h before analysing the expression of three histone H3K27 methylation-modifying enzymes and H3K27me3 using quantitative real-time polymerase chain reaction, Western blot and immunofluorescence analyses. Our results showed that incubation of nickel chloride upregulated the expression of H3K27me3 demethylase jumonji domain-containing protein 3 (JMJD3) in kidney cancer cells, which was accompanied by the reduction in the protein level of H3K27me3. Enhanced demethylation of H3K27me3 may represent a novel mechanism underlying the carcinogenicity of nickel compounds.
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Affiliation(s)
- Xiaoqiang Guo
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, Shenzhen, China Laboratory of Molecular Iron Metabolism, College of Life Science, Hebei Normal University, Shijiazhuang, Hebei, China Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yanmin Zhang
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Qiang Zhang
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Pingping Fa
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Yaoting Gui
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Guoquan Gao
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhiming Cai
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, Shenzhen, China
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25
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Epigenetic dysregulation by nickel through repressive chromatin domain disruption. Proc Natl Acad Sci U S A 2014; 111:14631-6. [PMID: 25246589 DOI: 10.1073/pnas.1406923111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Investigations into the genomic landscape of histone modifications in heterochromatic regions have revealed histone H3 lysine 9 dimethylation (H3K9me2) to be important for differentiation and maintaining cell identity. H3K9me2 is associated with gene silencing and is organized into large repressive domains that exist in close proximity to active genes, indicating the importance of maintenance of proper domain structure. Here we show that nickel, a nonmutagenic environmental carcinogen, disrupted H3K9me2 domains, resulting in the spreading of H3K9me2 into active regions, which was associated with gene silencing. We found weak CCCTC-binding factor (CTCF)-binding sites and reduced CTCF binding at the Ni-disrupted H3K9me2 domain boundaries, suggesting a loss of CTCF-mediated insulation function as a potential reason for domain disruption and spreading. We furthermore show that euchromatin islands, local regions of active chromatin within large H3K9me2 domains, can protect genes from H3K9me2-spreading-associated gene silencing. These results have major implications in understanding H3K9me2 dynamics and the consequences of chromatin domain disruption during pathogenesis.
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26
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Brocato J, Costa M. 10th NTES Conference: Nickel and Arsenic Compounds Alter the Epigenome of Peripheral Blood Mononuclear Cells. J Trace Elem Med Biol 2014; 31:209-13. [PMID: 24837610 PMCID: PMC4201979 DOI: 10.1016/j.jtemb.2014.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 03/31/2014] [Accepted: 04/07/2014] [Indexed: 11/18/2022]
Abstract
The mechanisms that underlie metal carcinogenesis are the subject of intense investigation; however, data from in vitro and in vivo studies are starting to piece together a story that implicates epigenetics as a key player. Data from our lab has shown that nickel compounds inhibit dioxygenase enzymes by displacing iron in the active site. Arsenic is hypothesized to inhibit these enzymes by diminishing ascorbate levels--an important co-factor for dioxygenases. Inhibition of histone demethylase dioxygenases can increase histone methylation levels, which also may affect gene expression. Recently, our lab conducted a series of investigations in human subjects exposed to high levels of nickel or arsenic compounds. Global levels of histone modifications in peripheral blood mononuclear cells (PBMCs) from exposed subjects were compared to low environmentally exposed controls. Results showed that nickel increased H3K4me3 and decreased H3K9me2 globally. Arsenic increased H3K9me2 and decreased H3K9ac globally. Other histone modifications affected by arsenic were sex-dependent. Nickel affected the expression of 2756 genes in human PBMCs and many of the genes were involved in immune and carcinogenic pathways. This review will describe data from our lab that demonstrates for the first time that nickel and arsenic compounds affect global levels of histone modifications and gene expression in exposed human populations.
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Affiliation(s)
- Jason Brocato
- Nelson Institute of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, NY 10987, USA
| | - Max Costa
- Nelson Institute of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, NY 10987, USA.
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27
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Dahdouh F, Raane M, Thévenod F, Lee WK. Nickel-induced cell death and survival pathways in cultured renal proximal tubule cells: roles of reactive oxygen species, ceramide and ABCB1. Arch Toxicol 2014; 88:881-92. [DOI: 10.1007/s00204-014-1194-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 01/09/2014] [Indexed: 12/17/2022]
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28
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Environmental chemical stressors as epigenome modifiers: a new horizon in assessment of toxicological effects. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-0007-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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29
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Feng Y, Maity R, Whitelegge JP, Hadjikyriacou A, Li Z, Zurita-Lopez C, Al-Hadid Q, Clark AT, Bedford MT, Masson JY, Clarke SG. Mammalian protein arginine methyltransferase 7 (PRMT7) specifically targets RXR sites in lysine- and arginine-rich regions. J Biol Chem 2013; 288:37010-25. [PMID: 24247247 DOI: 10.1074/jbc.m113.525345] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian protein arginine methyltransferase 7 (PRMT7) has been implicated in roles of transcriptional regulation, DNA damage repair, RNA splicing, cell differentiation, and metastasis. However, the type of reaction that it catalyzes and its substrate specificity remain controversial. In this study, we purified a recombinant mouse PRMT7 expressed in insect cells that demonstrates a robust methyltransferase activity. Using a variety of substrates, we demonstrate that the enzyme only catalyzes the formation of ω-monomethylarginine residues, and we confirm its activity as the prototype type III protein arginine methyltransferase. This enzyme is active on all recombinant human core histones, but histone H2B is a highly preferred substrate. Analysis of the specific methylation sites within intact histone H2B and within H2B and H4 peptides revealed novel post-translational modification sites and a unique specificity of PRMT7 for methylating arginine residues in lysine- and arginine-rich regions. We demonstrate that a prominent substrate recognition motif consists of a pair of arginine residues separated by one residue (RXR motif). These findings will significantly accelerate substrate profile analysis, biological function study, and inhibitor discovery for PRMT7.
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Affiliation(s)
- You Feng
- From the Departments of Chemistry and Biochemistry and
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30
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Sun H, Shamy M, Costa M. Nickel and epigenetic gene silencing. Genes (Basel) 2013; 4:583-95. [PMID: 24705264 PMCID: PMC3927569 DOI: 10.3390/genes4040583] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 10/11/2013] [Accepted: 10/17/2013] [Indexed: 02/07/2023] Open
Abstract
Insoluble nickel compounds are well-established human carcinogens. Occupational exposure to these compounds leads to increased incidence of lung and nasal cancer in nickel refinery workers. Apart from its weak mutagenic activity and hypoxia mimicking effect there is mounting experimental evidence indicating that epigenetic alteration plays an important role in nickel-induced carcinogenesis. Multiple epigenetic mechanisms have been identified to mediate nickel-induced gene silencing. Nickel ion is able to induce heterochromatinization by binding to DNA-histone complexes and initiating chromatin condensation. The enzymes required for establishing or removing epigenetic marks can be targeted by nickel, leading to altered DNA methylation and histone modification landscapes. The current review will focus on the epigenetic changes that contribute to nickel-induced gene silencing.
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Affiliation(s)
- Hong Sun
- Department of Environmental Medicine, NYU School of Medicine, Tuxedo, NY 10987, USA.
| | - Magdy Shamy
- Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Max Costa
- Department of Environmental Medicine, NYU School of Medicine, Tuxedo, NY 10987, USA.
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Peana M, Medici S, Nurchi VM, Crisponi G, Zoroddu MA. Nickel binding sites in histone proteins: Spectroscopic and structural characterization. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Zhang J, Zhou Y, Wu YJ, Li MJ, Wang RJ, Huang SQ, Gao RR, Ma L, Shi HJ, Zhang J. Hyper-methylated miR-203 dysregulates ABL1 and contributes to the nickel-induced tumorigenesis. Toxicol Lett 2013; 223:42-51. [PMID: 23968727 DOI: 10.1016/j.toxlet.2013.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/07/2013] [Accepted: 08/09/2013] [Indexed: 10/26/2022]
Abstract
Nickel compounds have been found to be carcinogenic based upon epidemiological, animal and cell culture studies. Previous studies suggest that epigenetic mechanisms play a role in Nickel-induced carcinogenesis such as DNA methylation and histone modification. In this study, we investigated the role of microRNAs (miRNAs) in nickel-induced carcinogenesis. The expression of several miRNAs which may function as tumor suppressor genes revealed a strong downregulation of miR-203 in Ni3S2-transformed 16HBE cells (NSTCs). Meanwhile, we observed hypermethylation of CpGs in miR-203 promoter and first exon area, and proved that the hyper-methylated miR-203 was involved in the Nickel-induced tumorigenesis. Moreover, we identified that miR-203 may suppress the tumorigenesis at least in part through negatively regulating its target gene ABL1. Our findings indicate that DNA methylation-associated silencing of tumor suppressor miRNAs contributes to the development of Nickel-induced cancer.
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Affiliation(s)
- Jing Zhang
- Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; School of Life Science and Technology, Tongji University, Shanghai 200092, China.
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Abstract
The use of nickel casting alloys for long-term restorations in dentistry has long been controversial. A 'tug-of-war' between economic, engineering and biological considerations is central to this controversy; nickel-casting alloys have low costs and favorable physical properties, but are corrosion-prone in the oral environment. Clinicians and researchers have questioned the safety of nickel-containing dental alloys because several nickel compounds are known to cause adverse biological effects in vivo and in vitro in contexts outside of dentistry. The debate revolves around the extent to which corrosion products from oral restorations cause intraoral or systemic biological problems. Current evidence suggests that nickel alloys may be used successfully and safely in dentistry if clinical risks are taken into account. However, these alloys may cause significant clinical problems, primarily allergenic and inflammatory, if the risks are ignored.
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Affiliation(s)
- John C Wataha
- Department of Restorative Dentistry, University of Washington School of Dentistry, Seattle, WA 98195-7456, USA.
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Zhang J, Zhou Y, Ma L, Huang S, Wang R, Gao R, Wu Y, Shi H, Zhang J. The alteration of miR-222 and its target genes in nickel-induced tumor. Biol Trace Elem Res 2013; 152:267-74. [PMID: 23447020 DOI: 10.1007/s12011-013-9619-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/24/2013] [Indexed: 11/30/2022]
Abstract
Nickel is an important kind of metal and a necessary trace element in people's production and livelihood; it is also a well-confirmed human carcinogen. In the past few years, researchers did a large number of studies about the molecular mechanisms of nickel carcinogenesis, and they focused on activation of proto-oncogenes and inactivation of anti-oncogenes caused by gene point mutation, gene deletion, gene amplification, DNA methylation, chromosome condensation, and so on that were induced by nickel. However, the researches on tumorigenic molecular mechanisms regulated by microRNAs (miRNAs) are rare. In this study, we established nickel-induced tumor by injecting Ni3S2 compounds to Wistar Rattus. By establishing a cDNA library of miRNA from rat muscle tumor tissue induced by Ni3S2, we found that the expression of miR-222 was significantly upregulated in tumor tissue compared with the normal tissue. As we expected, the expression levels of target genes of miR-222, CDKN1B and CDKN1C, were downregulated in the nickel-induced tumor. The same alteration of miR-222 and its target genes was also found in malignant 16HBE cells induced with Ni3S2 compounds. We conclude that miR-222 may promote cell proliferation infinitely during nickel-induced tumorigenesis in part by regulating the expression of its target genes CDKN1B and CDKN1C. Our study elucidated a novel molecular mechanism of nickel-induced tumorigenesis.
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Affiliation(s)
- Jing Zhang
- Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai 200065, China.
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35
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Arita A, Shamy MY, Chervona Y, Clancy HA, Sun H, Hall MN, Qu Q, Gamble MV, Costa M. The effect of exposure to carcinogenic metals on histone tail modifications and gene expression in human subjects. J Trace Elem Med Biol 2012; 26:174-8. [PMID: 22633395 PMCID: PMC3620044 DOI: 10.1016/j.jtemb.2012.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 03/16/2012] [Indexed: 10/28/2022]
Abstract
The precise mechanisms by which nickel and arsenic compounds exert their carcinogenic properties are not completely understood. In recent years, alterations of epigenetic mechanisms have been implicated in the carcinogenesis of compounds of these two metals. In vitro exposure to certain nickel or arsenic compounds induces changes in both DNA methylation patterns, as well as, in the levels of posttranslational modifications of histone tails. Changes in DNA methylation patterns have been reported in human subjects exposed to arsenic. Here we review our recent reports on the alterations in global levels of posttranslational histone modifications in peripheral blood mononuclear cells (PBMCs) of subjects with occupational exposure to nickel and subjects exposed to arsenic in their drinking water. Occupational exposure to nickel was associated with an increase in H3K4me3 and decrease in H3K9me2. A global increase in H3K9me2 and decrease in H3K9ac was found in subjects exposed to arsenic. Additionally, exposure to arsenic resulted in opposite changes in a number of histone modifications in males when compared with females in the arsenic population. The results of these two studies suggest that exposure to nickel or arsenic compounds, and possibly other carcinogenic metal compounds, can induce changes in global levels of posttranslational histone modifications in peripheral blood mononuclear cells.
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Affiliation(s)
- Adriana Arita
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York, USA
| | - Magdy Y. Shamy
- Department of Environmental Sciences, Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yana Chervona
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York, USA
| | - Harriet A. Clancy
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York, USA
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York, USA
| | - Megan N. Hall
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Qingshan Qu
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York, USA
| | - Mary V. Gamble
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York, USA
- Corresponding author: Max Costa; New York University School of Medicine, 57 Old Forge Road, Tuxedo, New York, 10987, USA.
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36
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Dik S, Scheepers PTJ, Godderis L. Effects of environmental stressors on histone modifications and their relevance to carcinogenesis: A systematic review. Crit Rev Toxicol 2012; 42:491-500. [DOI: 10.3109/10408444.2012.684146] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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37
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Hou L, Zhang X, Wang D, Baccarelli A. Environmental chemical exposures and human epigenetics. Int J Epidemiol 2012; 41:79-105. [PMID: 22253299 PMCID: PMC3304523 DOI: 10.1093/ije/dyr154] [Citation(s) in RCA: 279] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2011] [Indexed: 02/06/2023] Open
Abstract
Every year more than 13 million deaths worldwide are due to environmental pollutants, and approximately 24% of diseases are caused by environmental exposures that might be averted through preventive measures. Rapidly growing evidence has linked environmental pollutants with epigenetic variations, including changes in DNA methylation, histone modifications and microRNAs. Environ mental chemicals and epigenetic changes All of these mechanisms are likely to play important roles in disease aetiology, and their modifications due to environmental pollutants might provide further understanding of disease aetiology, as well as biomarkers reflecting exposures to environmental pollutants and/or predicting the risk of future disease. We summarize the findings on epigenetic alterations related to environmental chemical exposures, and propose mechanisms of action by means of which the exposures may cause such epigenetic changes. We discuss opportunities, challenges and future directions for future epidemiology research in environmental epigenomics. Future investigations are needed to solve methodological and practical challenges, including uncertainties about stability over time of epigenomic changes induced by the environment, tissue specificity of epigenetic alterations, validation of laboratory methods, and adaptation of bioinformatic and biostatistical methods to high-throughput epigenomics. In addition, there are numerous reports of epigenetic modifications arising following exposure to environmental toxicants, but most have not been directly linked to disease endpoints. To complete our discussion, we also briefly summarize the diseases that have been linked to environmental chemicals-related epigenetic changes.
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Affiliation(s)
- Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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38
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Chen J, Han J, Wang J. Prevention of cytotoxicity of nickel by quercetin: the role of reactive oxygen species and histone acetylation. Toxicol Ind Health 2012; 29:360-6. [PMID: 22294440 DOI: 10.1177/0748233711433940] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Excessive exposure to nickel may cause health effects on the blood, lung, nose, kidney, reproductive system, skin and the unborn child. In the present study, we found that Ni²⁺ exposure led to a time- and dose-dependent proliferation arrest and death in human leukemia HL-60 cells. In the presence of 1 mM Ni²⁺, reactive oxygen species (ROS) generation (indicated by the level of malondialdehyde) increased to 323% and histone acetylation decreased to 32%. Interestingly, quercetin (QU) dose dependently prevented Ni²⁺-induced cell proliferation arrest and death from 0 to 80 μM but showed similar activity of scavenging ROS at the concentrations of 20, 40 and 80 µM. When the effect of QU on histone acetylation was studied, QU significantly prevented Ni²⁺-induced histone hypoacetylation at 40 or 80 µM. Moreover, increase in histone acetylation by trichostatin A could also significantly enhance the protection effect of QU at 10 or 20 µM but not at higher concentrations. Thus, our results further confirmed the critical role of ROS and histone hypoacetylation in the cytotoxicity of Ni²⁺ exposure and proved that QU is a potentially useful native dietary compound to efficiently prevent Ni²⁺-caused cytotoxicity through both diminishing ROS generation and increasing histone acetylation.
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Affiliation(s)
- Jie Chen
- Department of Hematology, Changhai Hospital, The Second Military Medical University, China
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39
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On the role of low-dose effects and epigenetics in toxicology. EXPERIENTIA SUPPLEMENTUM (2012) 2012; 101:499-550. [PMID: 22945581 DOI: 10.1007/978-3-7643-8340-4_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
For a long time, scientists considered genotoxic effects as the major issue concerning the influence of environmental chemicals on human health. Over the last decades, a new layer superimposed the genome, i.e., the epigenome, tremendously changing this point of view. The term "epigenetics" comprises stable alterations in gene expression potential arising from variations in DNA methylation and a variety of histone modifications, without changing the underlying DNA sequence. Recently, also gene silencing by small noncoding RNAs (ncRNAs), in particular by microRNAs, was included in the list of epigenetic mechanisms. Multiple studies in vivo as well as in vitro have shown that a multitude of different environmental factors are capable of changing the epigenetic pattern as well as miRNA expression in certain cell types, leading to aberrant gene expression profiles in cells and tissues. These changes may have extensive effects concerning the proper gene expression necessary in a specified cell type and can even lead into a state of disease. Especially the roles of epigenetic modifications and miRNA alterations in tumorigenesis have been a major focus in research over the last years. This chapter will give an overview on epigenetic features and on the spectrum of epigenetic changes observed after exposure against environmental chemicals and pollutants.
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40
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Fragou D, Fragou A, Kouidou S, Njau S, Kovatsi L. Epigenetic mechanisms in metal toxicity. Toxicol Mech Methods 2011; 21:343-52. [DOI: 10.3109/15376516.2011.557878] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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41
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Koturbash I, Beland FA, Pogribny IP. Role of epigenetic events in chemical carcinogenesis—a justification for incorporating epigenetic evaluations in cancer risk assessment. Toxicol Mech Methods 2011; 21:289-97. [DOI: 10.3109/15376516.2011.557881] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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42
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Jufvas Å, Strålfors P, Vener AV. Histone variants and their post-translational modifications in primary human fat cells. PLoS One 2011; 6:e15960. [PMID: 21249133 PMCID: PMC3017551 DOI: 10.1371/journal.pone.0015960] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 12/01/2010] [Indexed: 01/12/2023] Open
Abstract
Epigenetic changes related to human disease cannot be fully addressed by studies of cells from cultures or from other mammals. We isolated human fat cells from subcutaneous abdominal fat tissue of female subjects and extracted histones from either purified nuclei or intact cells. Direct acid extraction of whole adipocytes was more efficient, yielding about 100 µg of protein with histone content of 60%-70% from 10 mL of fat cells. Differential proteolysis of the protein extracts by trypsin or ArgC-protease followed by nanoLC/MS/MS with alternating CID/ETD peptide sequencing identified 19 histone variants. Four variants were found at the protein level for the first time; particularly HIST2H4B was identified besides the only H4 isoform earlier known to be expressed in humans. Three of the found H2A potentially organize small nucleosomes in transcriptionally active chromatin, while two H2AFY variants inactivate X chromosome in female cells. HIST1H2BA and three of the identified H1 variants had earlier been described only as oocyte or testis specific histones. H2AFX and H2AFY revealed differential and variable N-terminal processing. Out of 78 histone modifications by acetylation/trimethylation, methylation, dimethylation, phosphorylation and ubiquitination, identified from six subjects, 68 were found for the first time. Only 23 of these modifications were detected in two or more subjects, while all the others were individual specific. The direct acid extraction of adipocytes allows for personal epigenetic analyses of human fat tissue, for profiling of histone modifications related to obesity, diabetes and metabolic syndrome, as well as for selection of individual medical treatments.
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Affiliation(s)
- Åsa Jufvas
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Peter Strålfors
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Alexander V. Vener
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- * E-mail:
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43
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Rabbani-Chadegani III A, Fani N, Abdossamadi S, Shahmir N. Toxic effects of lead and nickel nitrate on rat liver chromatin components. J Biochem Mol Toxicol 2010; 25:127-34. [DOI: 10.1002/jbt.20368] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 06/13/2010] [Accepted: 07/07/2010] [Indexed: 01/28/2023]
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Ziech D, Franco R, Pappa A, Malamou-Mitsi V, Georgakila S, Georgakilas AG, Panayiotidis MI. The role of epigenetics in environmental and occupational carcinogenesis. Chem Biol Interact 2010; 188:340-9. [PMID: 20599843 DOI: 10.1016/j.cbi.2010.06.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 06/20/2010] [Indexed: 02/07/2023]
Abstract
Over the last few years there has been an increasing effort in identifying environmental and occupational carcinogenic agents and linking them to the incidence of a variety of human cancers. The carcinogenic process itself is multistage and rather complex involving several different mechanisms by which various carcinogenic agents exert their effect. Amongst them are epigenetic mechanisms often involving silencing of tumor suppressor genes and/or activation of proto-oncogenes, respectively. These alterations in gene expression are considered critical during carcinogenesis and have been observed in many environmental- and occupational-induced human cancers. Some of the underlying mechanisms proposed to account for such differential gene expression include alterations in DNA methylation and/or histone modifications. Throughout this article, we aim to provide a current account of our understanding on how the epigenetic pathway is involved in contributing to an altered gene expression profile during human carcinogenesis that ultimately will allow us for better cancer diagnostics and therapeutic strategies.
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Affiliation(s)
- Dominique Ziech
- Nevada Center for Ethics and Health Policy, University of Nevada, Reno, 89557, USA
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45
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Nunes AM, Zavitsanos K, Del Conte R, Malandrinos G, Hadjiliadis N. The Possible Role of 94−125 Peptide Fragment of Histone H2B in Nickel-Induced Carcinogenesis. Inorg Chem 2010; 49:5658-68. [DOI: 10.1021/ic1005665] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ana Mónica Nunes
- Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Kimon Zavitsanos
- Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Rebecca Del Conte
- Magnetic Resonance Center, University of Florence, Via L. Sacconi 6, 0019, Sesto Fiorentino, Italy
| | | | - Nick Hadjiliadis
- Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
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46
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Chen H, Giri NC, Zhang R, Yamane K, Zhang Y, Maroney M, Costa M. Nickel ions inhibit histone demethylase JMJD1A and DNA repair enzyme ABH2 by replacing the ferrous iron in the catalytic centers. J Biol Chem 2010; 285:7374-83. [PMID: 20042601 PMCID: PMC2844186 DOI: 10.1074/jbc.m109.058503] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Revised: 12/23/2009] [Indexed: 01/20/2023] Open
Abstract
Iron- and 2-oxoglutarate-dependent dioxygenases are a diverse family of non-heme iron enzymes that catalyze various important oxidations in cells. A key structural motif of these dioxygenases is a facial triad of 2-histidines-1-carboxylate that coordinates the Fe(II) at the catalytic site. Using histone demethylase JMJD1A and DNA repair enzyme ABH2 as examples, we show that this family of dioxygenases is highly sensitive to inhibition by carcinogenic nickel ions. We find that, with iron, the 50% inhibitory concentrations of nickel (IC(50) [Ni(II)]) are 25 microm for JMJD1A and 7.5 microm for ABH2. Without iron, JMJD1A is 10 times more sensitive to nickel inhibition with an IC(50) [Ni(II)] of 2.5 microm, and approximately one molecule of Ni(II) inhibits one molecule of JMJD1A, suggesting that nickel causes inhibition by replacing the iron. Furthermore, nickel-bound JMJD1A is not reactivated by excessive iron even up to a 2 mm concentration. Using x-ray absorption spectroscopy, we demonstrate that nickel binds to the same site in ABH2 as iron, and replacement of the iron by nickel does not prevent the binding of the cofactor 2-oxoglutarate. Finally, we show that nickel ions target and inhibit JMJD1A in intact cells, and disruption of the iron-binding site decreases binding of nickel ions to ABH2 in intact cells. Together, our results reveal that the members of this dioxygenase family are specific targets for nickel ions in cells. Inhibition of these dioxygenases by nickel is likely to have widespread impacts on cells (e.g. impaired epigenetic programs and DNA repair) and may eventually lead to cancer development.
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Affiliation(s)
- Haobin Chen
- From the Department of Environmental Medicine, New York University of School of Medicine, New York, New York 10016
| | - Nitai Charan Giri
- the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01002, and
| | - Ronghe Zhang
- From the Department of Environmental Medicine, New York University of School of Medicine, New York, New York 10016
| | - Kenichi Yamane
- the Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Yi Zhang
- the Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Michael Maroney
- the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01002, and
| | - Max Costa
- From the Department of Environmental Medicine, New York University of School of Medicine, New York, New York 10016
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47
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Nunes AM, Zavitsanos K, Malandrinos G, Hadjiliadis N. Coordination of Cu2+and Ni2+ with the histone model peptide of H2B N-terminal tail (1-31 residues): A spectroscopic study. Dalton Trans 2010; 39:4369-81. [DOI: 10.1039/b927157k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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48
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Kurowska E, Bal W. Recent Advances in Molecular Toxicology of Cadmium and Nickel. ADVANCES IN MOLECULAR TOXICOLOGY 2010. [DOI: 10.1016/s1872-0854(10)04003-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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49
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A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae. BMC Genomics 2009; 10:524. [PMID: 19917080 PMCID: PMC2784802 DOI: 10.1186/1471-2164-10-524] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 11/15/2009] [Indexed: 12/22/2022] Open
Abstract
Background The understanding of the biological function, regulation, and cellular interactions of the yeast genome and proteome, along with the high conservation in gene function found between yeast genes and their human homologues, has allowed for Saccharomyces cerevisiae to be used as a model organism to deduce biological processes in human cells. Here, we have completed a systematic screen of the entire set of 4,733 haploid S. cerevisiae gene deletion strains (the entire set of nonessential genes for this organism) to identify gene products that modulate cellular toxicity to nickel sulfate (NiSO4). Results We have identified 149 genes whose gene deletion causes sensitivity to NiSO4 and 119 genes whose gene deletion confers resistance. Pathways analysis with proteins whose absence renders cells sensitive and resistant to nickel identified a wide range of cellular processes engaged in the toxicity of S. cerevisiae to NiSO4. Functional categories overrepresented with proteins whose absence renders cells sensitive to NiSO4 include homeostasis of protons, cation transport, transport ATPases, endocytosis, siderophore-iron transport, homeostasis of metal ions, and the diphthamide biosynthesis pathway. Functional categories overrepresented with proteins whose absence renders cells resistant to nickel include functioning and transport of the vacuole and lysosome, protein targeting, sorting, and translocation, intra-Golgi transport, regulation of C-compound and carbohydrate metabolism, transcriptional repression, and chromosome segregation/division. Interactome analysis mapped seven nickel toxicity modulating and ten nickel-resistance networks. Additionally, we studied the degree of sensitivity or resistance of the 111 nickel-sensitive and 72 -resistant strains whose gene deletion product has a similar protein in human cells. Conclusion We have undertaken a whole genome approach in order to further understand the mechanism(s) regulating the cell's toxicity to nickel compounds. We have used computational methods to integrate the data and generate global models of the yeast's cellular response to NiSO4. The results of our study shed light on molecular pathways associated with the cellular response of eukaryotic cells to nickel compounds and provide potential implications for further understanding the toxic effects of nickel compounds to human cells.
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50
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Barr FD, Krohmer LJ, Hamilton JW, Sheldon LA. Disruption of histone modification and CARM1 recruitment by arsenic represses transcription at glucocorticoid receptor-regulated promoters. PLoS One 2009; 4:e6766. [PMID: 19707557 PMCID: PMC2727952 DOI: 10.1371/journal.pone.0006766] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 07/31/2009] [Indexed: 11/30/2022] Open
Abstract
Chronic exposure to inorganic arsenic (iAs) found in the environment is one of the most significant and widespread environmental health risks in the U.S. and throughout the world. It is associated with a broad range of health effects from cancer to diabetes as well as reproductive and developmental anomalies. This diversity of diseases can also result from disruption of metabolic and other cellular processes regulated by steroid hormone receptors via aberrant transcriptional regulation. Significantly, exposure to iAs inhibits steroid hormone-mediated gene activation. iAs exposure is associated with disease, but is also used therapeutically to treat specific cancers complicating an understanding of iAs action. Transcriptional activation by steroid hormone receptors is accompanied by changes in histone and non-histone protein post-translational modification (PTM) that result from the enzymatic activity of coactivator and corepressor proteins such as GRIP1 and CARM1. This study addresses how iAs represses steroid receptor-regulated gene transcription. PTMs on histones H3 and H4 at the glucocorticoid receptor (GR)-activated mouse mammary tumor virus (MMTV) promoter were identified by chromatin immunoprecipitation analysis following exposure to steroid hormone±iAs. Histone H3K18 and H3R17 amino acid residues had significantly different patterns of PTMs after treatment with iAs. Promoter interaction of the coactivator CARM1 was disrupted, but the interaction of GRIP1, a p160 coactivator through which CARM1 interacts with a promoter, was intact. Over-expression of CARM1 was able to fully restore and GRIP1 partially restored iAs-repressed transcription indicating that these coactivators are functionally associated with iAs-mediated transcriptional repression. Both are essential for robust transcription at steroid hormone regulated genes and both are associated with disease when inappropriately expressed. We postulate that iAs effects on CARM1 and GRIP1 may underlie some of its therapeutic effects and as well be associated with its toxic effects.
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Affiliation(s)
- Fiona D. Barr
- Department of Physiology, Dartmouth Medical School, Lebanon, New Hampshire
| | - Lori J. Krohmer
- Department of Physiology, Dartmouth Medical School, Lebanon, New Hampshire
| | - Joshua W. Hamilton
- Department of Pharmacology & Toxicology, Dartmouth Medical School, Hanover, New Hampshire
- Center for Environmental Health Sciences, Dartmouth Medical School, Hanover, New Hampshire
| | - Lynn A. Sheldon
- Department of Physiology, Dartmouth Medical School, Lebanon, New Hampshire
- Center for Environmental Health Sciences, Dartmouth Medical School, Hanover, New Hampshire
- * E-mail:
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