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Valente A, Vieira L, Silva MJ, Ventura C. The Effect of Nanomaterials on DNA Methylation: A Review. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1880. [PMID: 37368308 DOI: 10.3390/nano13121880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023]
Abstract
DNA methylation is an epigenetic mechanism that involves the addition of a methyl group to a cytosine residue in CpG dinucleotides, which are particularly abundant in gene promoter regions. Several studies have highlighted the role that modifications of DNA methylation may have on the adverse health effects caused by exposure to environmental toxicants. One group of xenobiotics that is increasingly present in our daily lives are nanomaterials, whose unique physicochemical properties make them interesting for a large number of industrial and biomedical applications. Their widespread use has raised concerns about human exposure, and several toxicological studies have been performed, although the studies focusing on nanomaterials' effect on DNA methylation are still limited. The aim of this review is to investigate the possible impact of nanomaterials on DNA methylation. From the 70 studies found eligible for data analysis, the majority were in vitro, with about half using cell models related to the lungs. Among the in vivo studies, several animal models were used, but most were mice models. Only two studies were performed on human exposed populations. Global DNA methylation analyses was the most frequently applied approach. Although no trend towards hypo- or hyper-methylation could be observed, the importance of this epigenetic mechanism in the molecular response to nanomaterials is evident. Furthermore, methylation analysis of target genes and, particularly, the application of comprehensive DNA methylation analysis techniques, such as genome-wide sequencing, allowed identifying differentially methylated genes after nanomaterial exposure and affected molecular pathways, contributing to the understanding of their possible adverse health effects.
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Affiliation(s)
- Ana Valente
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, I.P. (INSA), Av. Padre Cruz, 1649-016 Lisbon, Portugal
- Department of Animal Biology, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal
| | - Luís Vieira
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, I.P. (INSA), Av. Padre Cruz, 1649-016 Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), NOVA Medical School, NOVA University of Lisbon, 1169-056 Lisbon, Portugal
| | - Maria João Silva
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, I.P. (INSA), Av. Padre Cruz, 1649-016 Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), NOVA Medical School, NOVA University of Lisbon, 1169-056 Lisbon, Portugal
| | - Célia Ventura
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, I.P. (INSA), Av. Padre Cruz, 1649-016 Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), NOVA Medical School, NOVA University of Lisbon, 1169-056 Lisbon, Portugal
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Barguilla I, Maguer-Satta V, Guyot B, Pastor S, Marcos R, Hernández A. In Vitro Approaches to Determine the Potential Carcinogenic Risk of Environmental Pollutants. Int J Mol Sci 2023; 24:ijms24097851. [PMID: 37175558 PMCID: PMC10178670 DOI: 10.3390/ijms24097851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
One important environmental/health challenge is to determine, in a feasible way, the potential carcinogenic risk associated with environmental agents/exposures. Since a significant proportion of tumors have an environmental origin, detecting the potential carcinogenic risk of environmental agents is mandatory, as regulated by national and international agencies. The challenge mainly implies finding a way of how to overcome the inefficiencies of long-term trials with rodents when thousands of agents/exposures need to be tested. To such an end, the use of in vitro cell transformation assays (CTAs) was proposed, but the existing prevalidated CTAs do not cover the complexity associated with carcinogenesis processes and present serious limitations. To overcome such limitations, we propose to use a battery of assays covering most of the hallmarks of the carcinogenesis process. For the first time, we grouped such assays as early, intermediate, or advanced biomarkers which allow for the identification of the cells in the initiation, promotion or aggressive stages of tumorigenesis. Our proposal, as a novelty, points out that using a battery containing assays from all three groups can identify if a certain agent/exposure can pose a carcinogenic risk; furthermore, it can gather mechanistic insights into the mode of the action of a specific carcinogen. This structured battery could be very useful for any type of in vitro study, containing human cell lines aiming to detect the potential carcinogenic risks of environmental agents/exposures. In fact, here, we include examples in which these approaches were successfully applied. Finally, we provide a series of advantages that, we believe, contribute to the suitability of our proposed approach for the evaluation of exposure-induced carcinogenic effects and for the development of an alternative strategy for conducting an exposure risk assessment.
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Affiliation(s)
- Irene Barguilla
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | | | - Boris Guyot
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Susana Pastor
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Ricard Marcos
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Alba Hernández
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
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3
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Belitsky GA, Kirsanov KI, Lesovaya EA, Yakubovskaya MG. Mechanisms of the carcinogenicity of nanomaterials. ADVANCES IN MOLECULAR ONCOLOGY 2022. [DOI: 10.17650/2313-805x-2022-9-4-8-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nanomaterials become more widespread in the different areas of human life, forming the new technosphere philosophy, in particular, new approaches for development and usage of these materials in everyday life, manufacture, medicine etc.The physicochemical characteristics of nanomaterials differ significantly from the corresponding indicators of aggregate materials and at least some of them are highly reactive and / or highly catalytic. This suggests their aggressiveness towards biological systems, including involvement in carcinogenesis. The review considers the areas of use of modern nanomaterials, with special attention paid to the description of medicine production using nanotechnologies, an analysis of the mechanisms of action of a number of nanomaterials already recognized as carcinogenic, and also presents the available experimental and mechanistic data obtained from the study of the carcinogenic / procarcinogenic effects of various groups of nanomaterials currently not classified as carcinogenic to humans.Preparing the review, information bases of biomedical literature were analysed: Scopus (307), PubMed (461), Web of Science (268), eLibrary.ru (190) were used. To obtain full-text documents, the electronic resources of PubMed Central (PMC), Science Direct, Research Gate, Sci-Hub and eLibrary.ru databases were used.
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Affiliation(s)
- G. A. Belitsky
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia
| | - K. I. Kirsanov
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia; Peoples’ Friendship University of Russia
| | - E. A. Lesovaya
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia; I.P. Pavlov Ryazan State Medical University
| | - M. G. Yakubovskaya
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia
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4
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Sun Q, Li T, Yu Y, Li Y, Sun Z, Duan J. The critical role of epigenetic mechanisms involved in nanotoxicology. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1789. [PMID: 35289073 DOI: 10.1002/wnan.1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Over the past decades, nanomaterials (NMs) have been widely applied in the cosmetic, food, engineering, and medical fields. Along with the prevalence of NMs, the toxicological characteristics exhibited by these materials on health and the environment have gradually attracted attentions. A growing number of evidences have indicated that epigenetics holds an essential role in the onset and development of various diseases. NMs could cause epigenetic alterations such as DNA methylation, noncoding RNA (ncRNA) expression, and histone modifications. NMs might alternate either global DNA methylation or the methylation of specific genes to affect the biological function. Abnormal upregulation or downregulation of ncRNAs might also be a potential mechanism for the toxic effects caused by NMs. In parallel, the phosphorylation, acetylation, and methylation of histones also take an important part in the process of NMs-induced toxicity. As the adverse effects of NMs continue to be explored, mechanisms such as chromosomal remodeling, genomic imprinting, and m6 A modification are also gradually coming into the limelight. Since the epigenetic alterations often occur in the early development of diseases, thus the relevant studies not only provide insight into the pathogenesis of diseases, but also screen for the prospective biomarkers for early diagnosis and prevention. This review summarizes the epigenetic alterations elicited by NMs, hoping to provide a clue for nanotoxicity studies and security evaluation of NMs. This article is categorized under: Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials.
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Affiliation(s)
- Qinglin Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China
| | - Tianyu Li
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China
| | - Yang Yu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China
| | - Yang Li
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China
| | - Junchao Duan
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing, China
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Epigenetic Mechanisms in Understanding Nanomaterial-Induced Toxicity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1357:195-223. [DOI: 10.1007/978-3-030-88071-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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MicroRNAs as a Suitable Biomarker to Detect the Effects of Long-Term Exposures to Nanomaterials. Studies on TiO 2NP and MWCNT. NANOMATERIALS 2021; 11:nano11123458. [PMID: 34947804 PMCID: PMC8707110 DOI: 10.3390/nano11123458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 01/01/2023]
Abstract
The presence of nanomaterials (NMs) in the environment may represent a serious risk to human health, especially in a scenario of chronic exposure. To evaluate the potential relationship between NM-induced epigenetic alterations and carcinogenesis, the present study analyzed a panel of 33 miRNAs related to the cell transformation process in BEAS-2B cells transformed by TiO2NP and long-term MWCNT exposure. Our battery revealed a large impact on miRNA expression profiling in cells exposed to both NMs. From this analysis, a small set of five miRNAs (miR-23a, miR-25, miR-96, miR-210, and miR-502) were identified as informative biomarkers of the transforming effects induced by NM exposures. The usefulness of this reduced miRNA battery was further validated in other previously generated transformed cell systems by long-term exposure to other NMs (CoNP, ZnONP, MSiNP, and CeO2NP). Interestingly, the five selected miRNAs were consistently overexpressed in all cell lines and NMs tested. These results confirm the suitability of the proposed set of mRNAs to identify the potential transforming ability of NMs. Particular attention should be paid to the epigenome and especially to miRNAs for hazard assessment of NMs, as wells as for the study of the underlying mechanisms of action.
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Moreira L, Costa C, Pires J, Teixeira JP, Fraga S. How can exposure to engineered nanomaterials influence our epigenetic code? A review of the mechanisms and molecular targets. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108385. [PMID: 34893164 DOI: 10.1016/j.mrrev.2021.108385] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 06/14/2023]
Abstract
Evidence suggests that engineered nanomaterials (ENM) can induce epigenetic modifications. In this review, we provide an overview of the epigenetic modulation of gene expression induced by ENM used in a variety of applications: titanium dioxide (TiO2), silver (Ag), gold (Au), silica (SiO2) nanoparticles and carbon-based nanomaterials (CNM). Exposure to these ENM can trigger alterations in cell patterns of DNA methylation, post-transcriptional histone modifications and expression of non-coding RNA. Such effects are dependent on ENM dose and physicochemical properties including size, shape and surface chemistry, as well as on the cell/organism sensitivity. The genes affected are mostly involved in the regulation of the epigenetic machinery itself, as well as in apoptosis, cell cycle, DNA repair and inflammation related pathways, whose long-term alterations might lead to the onset or progression of certain pathologies. In addition, some DNA methylation patterns may be retained as a form of epigenetic memory. Prenatal exposure to ENM may impair the normal development of the offspring by transplacental effects and/or putative transmission of epimutations in imprinting genes. Thus, understanding the impact of ENM on the epigenome is of paramount importance and epigenetic evaluation must be considered when assessing the risk of ENM to human health.
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Affiliation(s)
- Luciana Moreira
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Porto, Portugal; EPIUnit - Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal.
| | - Carla Costa
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Porto, Portugal; EPIUnit - Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal.
| | - Joana Pires
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Porto, Portugal; EPIUnit - Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (ICBAS-UP), Porto, Portugal.
| | - João Paulo Teixeira
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Porto, Portugal; EPIUnit - Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal.
| | - Sónia Fraga
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Porto, Portugal; EPIUnit - Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal.
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Scala G, Delaval MN, Mukherjee SP, Federico A, Khaliullin TO, Yanamala N, Fatkhutdinova LM, Kisin ER, Greco D, Fadeel B, Shvedova AA. Multi-walled carbon nanotubes elicit concordant changes in DNA methylation and gene expression following long-term pulmonary exposure in mice. CARBON 2021; 178:563-572. [PMID: 37206955 PMCID: PMC10193301 DOI: 10.1016/j.carbon.2021.03.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Pulmonary exposure to multi-walled carbon nanotubes (MWCNTs) causes inflammation and fibrosis. Our previous work has shown that industrially produced MWCNTs trigger specific changes in gene expression in the lungs of exposed animals. To elucidate whether epigenetic effects play a role for these gene expression changes, we performed whole genome bisulphite sequencing to assess DNA methylation patterns in the lungs 56 days after exposure to MWCNTs. Lung tissues were also evaluated with respect to histopathological changes and cytokine profiling of bronchoalveolar lavage (BAL) fluid was conducted using a multi-plex array. Integrated analysis of transcriptomics data and DNA methylation data revealed concordant changes in gene expression. Functional analysis showed that the muscle contraction, immune system/inflammation, and extracellular matrix pathways were the most affected pathways. Taken together, the present study revealed that MWCNTs exert epigenetic effects in the lungs of exposed animals, potentially driving the subsequent gene expression changes.
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Affiliation(s)
- Giovanni Scala
- Department of Biology, University of Naples, Naples, Italy
| | - Mathilde N. Delaval
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sourav P. Mukherjee
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Naveena Yanamala
- Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA
| | - Liliya M. Fatkhutdinova
- Department of Hygiene and Occupational Medicine, Kazan State Medical University, Kazan, Russia
| | - Elena R. Kisin
- Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Corresponding author. (D. Greco)
| | - Bengt Fadeel
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Corresponding author. (B. Fadeel)
| | - Anna A. Shvedova
- Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV, USA
- Corresponding author. Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA. (A.A. Shvedova)
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Barbarino M, Giordano A. Assessment of the Carcinogenicity of Carbon Nanotubes in the Respiratory System. Cancers (Basel) 2021; 13:cancers13061318. [PMID: 33804168 PMCID: PMC7998467 DOI: 10.3390/cancers13061318] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
In 2014, the International Agency for Research on Cancer (IARC) classified the first type of carbon nanotubes (CNTs) as possibly carcinogenic to humans, while in the case of other CNTs, it was not possible to ascertain their toxicity due to lack of evidence. Moreover, the physicochemical heterogeneity of this group of substances hamper any generalization on their toxicity. Here, we review the recent relevant toxicity studies produced after the IARC meeting in 2014 on an homogeneous group of CNTs, highlighting the molecular alterations that are relevant for the onset of mesothelioma. Methods: The literature was searched on PubMed and Web of Science for the period 2015-2020, using different combinations keywords. Only data on normal cells of the respiratory system after exposure to fully characterized CNTs for their physico-chemical characteristics were included. Recent studies indicate that CNTs induce a sustained inflammatory response, oxidative stress, fibrosis and histological alterations. The development of mesothelial hyperplasia, mesothelioma, and lungs tumors have been also described in vivo. The data support a strong inflammatory potential of CNTs, similar to that of asbestos, and provide evidence that CNTs exposure led to molecular alterations known to have a key role in mesothelioma onset. These evidences call for an urgent improvement of studies on exposed human populations and adequate systems for monitoring the health of workers exposed to this putative carcinogen.
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Affiliation(s)
- Marcella Barbarino
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
- Correspondence:
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
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Sar P, Dalai S. CRISPR/Cas9 in epigenetics studies of health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:309-343. [PMID: 34127198 DOI: 10.1016/bs.pmbts.2021.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epigenetics is the heritable phenotypic changes without altering the genotype. Epigenetic processes are such as histone methylation, acetylation, ubiquitination, sumoylation, phosphorylation, ADP ribosylation, DNA methylation and non-coding RNAs interactions associated with structural changes in chromatin. The change of structure is either open chromatin for "active" state or closed chromatin for "inactive" state, that regulates important biological phenomenon like chromatin condensation, gene expression, DNA repair, cellular development, differentiation and homeostasis, etc. However, dysregulation of epigenetic patterns causes diseases like cancer, diabetes, neurological disorder, infectious diseases, autoimmunity etc. Besides, the most important clinical uses of Epigenetics studies are i. identification of disease biomarkers and ii. development of their therapeutics. Epigenetic therapies include epi-drugs, combinatorial therapy, nanocarriers, plant-derived products that are being used for changing the epigenetic pattern to reverse gene expression. However, the developed epi- drugs cause off-target gene and transposable elements activation; promote mutagenesis and carcinogenesis in normal cells, are the major hurdles regarding their clinical use. Therefore, advanced epigenetic therapeutics are required to develop target-specific epigenetic modifications to reverse gene expression pattern. CRISPR-Cas9 (Clustered Regularly Interspaced Palindrome Repeats-associated protein 9) system-mediated gene activation mechanism paves new methods of target-specific epigenetic therapeutics to cure diseases. In this chapter, we discuss how CRISPR/Cas9 and dCas9 have recently been engineered for epigenome editing. Different strategies have been discussed used for epigenome editing based on their efficacy and complexity. Last but not least we have discussed the limitations, different uses of CRISPR/Cas9 and dCas9 in the area of genetic engineering.
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Affiliation(s)
- Pranati Sar
- Institute of Science, NIRMA University, Ahmedabad, India.
| | - Sarat Dalai
- Institute of Science, NIRMA University, Ahmedabad, India.
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Ahamed A, Liang L, Lee MY, Bobacka J, Lisak G. Too small to matter? Physicochemical transformation and toxicity of engineered nTiO 2, nSiO 2, nZnO, carbon nanotubes, and nAg. JOURNAL OF HAZARDOUS MATERIALS 2021; 404:124107. [PMID: 33035908 DOI: 10.1016/j.jhazmat.2020.124107] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/04/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Engineered nanomaterials (ENMs) refer to a relatively novel class of materials that are increasingly prevalent in various consumer products and industrial applications - most notably for their superlative physicochemical properties when compared with conventional materials. However, consumer products inevitably degrade over the course of their lifetime, releasing ENMs into the environment. These ENMs undergo physicochemical transformations and subsequently accumulate in the environment, possibly leading to various toxic effects. As a result, a significant number of studies have focused on identifying the possible transformations and environmental risks of ENMs, with the objective of ensuring a safe and responsible application of ENMs in consumer products. This review aims to consolidate the results from previous studies related to each stage of the pathway of ENMs from being embodied in a product to disintegration/transformation in the environment. The scope of this work was defined to include the five most prevalent ENMs based on recent projected production market data, namely: nTiO2, nSiO2, nZnO, carbon nanotubes, and nAg. The review focuses on: (i) models developed to estimate environmental concentrations of ENMs; (ii) the possible physicochemical transformations; (iii) cytotoxicity and genotoxicity effects specific to each ENM selected; and (iv) a discussion to identify potential gaps in the studies conducted and recommend areas where further investigation is warranted.
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Affiliation(s)
- Ashiq Ahamed
- Residues and Resource Reclamation Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, Singapore 637141 Singapore; Laboratory of Molecular Science and Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, FI-20500 Turku/Åbo, Finland
| | - Lili Liang
- Residues and Resource Reclamation Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, Singapore 637141 Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore; Interdisciplinary Graduate Program, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, Singapore 637141 Singapore
| | - Ming Yang Lee
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore
| | - Johan Bobacka
- Laboratory of Molecular Science and Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, FI-20500 Turku/Åbo, Finland
| | - Grzegorz Lisak
- Residues and Resource Reclamation Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, Singapore 637141 Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
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12
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Ballesteros S, Barguilla I, Marcos R, Hernández A. Nanoceria, alone or in combination with cigarette-smoke condensate, induce transforming and epigenetic cancer-like features in vitro. Nanomedicine (Lond) 2021; 16:293-305. [PMID: 33501851 DOI: 10.2217/nnm-2020-0367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: To detect cell transformation effects of nanoceria after long-term exposure (up to 6 weeks) and to determine their potential interactions with cigarette smoke condensate, as a model of environmental carcinogenic pollutant. Materials & methods: Human bronchial epithelial BEAS-2 cells were used to determine transformation effects (invasion and tumorspheres induction), as well as changes in the expression of a battery of miRNAs related to the carcinogenesis process. Results: Nanoceria- and co-exposed cells exhibit cell transforming potential, with significantly increased invasion and tumorsphere formation abilities. Likewise, these exposures produced a high impact on the battery of miRNAs used. Conclusion: Nanoceria exposure induces cell-transformation and shows a positive interaction with the cell-transforming effects of cigarette smoke condensate. Besides, cerium dioxide nanoparticles and the co-exposure produced potential toxicity at the transcriptome level, which is related to tumorigenesis.
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Affiliation(s)
- Sandra Ballesteros
- Department of Genetics & Microbiology, Group of Mutagenesis, Universitat Autònoma de Barcelona, Spain
| | - Irene Barguilla
- Department of Genetics & Microbiology, Group of Mutagenesis, Universitat Autònoma de Barcelona, Spain
| | - Ricard Marcos
- Department of Genetics & Microbiology, Group of Mutagenesis, Universitat Autònoma de Barcelona, Spain.,Consortium for Biomedical Research in Epidemiology & Public Health (CIBERESP), Carlos III Institute of Health, Madrid, Spain
| | - Alba Hernández
- Department of Genetics & Microbiology, Group of Mutagenesis, Universitat Autònoma de Barcelona, Spain.,Consortium for Biomedical Research in Epidemiology & Public Health (CIBERESP), Carlos III Institute of Health, Madrid, Spain
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13
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Xie D, Luo X. Identification of four methylation-driven genes as candidate biomarkers for monitoring single-walled carbon nanotube-induced malignant transformation of the lung. Toxicol Appl Pharmacol 2020; 412:115391. [PMID: 33387576 DOI: 10.1016/j.taap.2020.115391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 01/15/2023]
Abstract
Long-term exposure to carbon nanotubes (CNTs) has been reported to induce malignant transformation. This study aimed to screen candidate biomarkers for monitoring occupational workers to prevent the development of lung cancer. mRNA (GSE56104) and methylation (GSE153246) profiles of lung epithelial BEAS-2B cells exposed to malignant transformation dose of single-walled CNTs or control medium were downloaded from Gene Expression Omnibus database. A total of 1513 differentially expressed genes (DEGs) and 912 differentially methylated genes (DMGs) were identified using LIMMA method. The weighted correlation network analysis identified blue and turquoise modules were associated with malignant transformation of BEAS-2B cells, 124 DMGs of which were overlapped with DEGs. The mRNA and methylation levels of four methylation-driven DEGs were validated in both lung adenocarcinoma (LUAD) and squamous cell carcinomas (LUSC) of The Cancer Genome Atlas dataset and they were associated with overall survival of LUAD patients. Downregulation of PXMP4 and MCOLN2, while upregulation of MET was confirmed in both LUSC and LUAD via Human Protein Atlas analysis. PXMP4 and MET protein levels were also supported in the proteomic analysis of LUAD. Receiver operating characteristic (ROC) curve analysis showed the combination of four genes may be the optimal biomarker for predicting lung cancer, with the area under ROC curve >0.9. Function analysis revealed BARX2 may interact with CCND1 to regulate cell cycle; MET and PXMP4/MCOLN2 may positively correlate with CCR5/IL-6 or GATA3/HLA-DPB1/HLA-DPA1 to involve immune regulation. In conclusion, these four methylation-driven genes may be candidate prognostic and diagnostic biomarkers for single-walled CNT-related lung cancer.
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Affiliation(s)
- Dongli Xie
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiaogang Luo
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China.
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14
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Zhang W, Liu S, Han D, He Z. Engineered nanoparticle-induced epigenetic changes: An important consideration in nanomedicine. Acta Biomater 2020; 117:93-107. [PMID: 32980543 DOI: 10.1016/j.actbio.2020.09.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 12/27/2022]
Abstract
Engineered nanoparticles (ENPs) are now being applied across a range of disciplines, and as a result numerous studies have now assessed ENP-related bioeffects. Among them, ENP-induced epigenetic changes including DNA methylation, histone modifications, and miRNA-mediated regulation of gene expression have recently attracted attention. In this review, we describe the diversity of ENP-induced epigenetic changes, focusing on their interplay with related functional biological events, especially oxidative stress, MAPK pathway activation, and inflammation. In doing so, we highlight the underlying mechanisms and biological effects of ENP-induced epigenetic changes. We also summarize how high-throughput technologies have helped to uncover ENP-induced epigenetic changes. Finally, we discuss future perspectives and the challenges related to ENP-induced epigenetic changes that still need to be addressed.
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15
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Öner D, Ghosh M, Coorens R, Bové H, Moisse M, Lambrechts D, Ameloot M, Godderis L, Hoet PHM. Induction and recovery of CpG site specific methylation changes in human bronchial cells after long-term exposure to carbon nanotubes and asbestos. ENVIRONMENT INTERNATIONAL 2020; 137:105530. [PMID: 32062310 DOI: 10.1016/j.envint.2020.105530] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 01/21/2020] [Accepted: 01/25/2020] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Inhalation of asbestos induces lung cancer via different cellular mechanisms. Together with the increased production of carbon nanotubes (CNTs) grows the concern about adverse effects on the lungs given the similarities with asbestos. While it has been established that CNT and asbestos induce epigenetic alterations, it is currently not known whether alterations at epigenetic level remain stable after withdrawal of the exposure. Identification of DNA methylation changes after a low dose of CNT and asbestos exposure and recovery can be useful to determine the fibre/particle toxicity and adverse outcome. METHODS Human bronchial epithelial cells (16HBE) were treated with a low and non-cytotoxic dose (0.25 µg/ml) of multi-walled carbon nanotubes (MWCNTs-NM400) or single-walled carbon nanotubes (SWCNTs-SRM2483) and 0.05 µg/ml amosite (brown) asbestos for the course of four weeks (sub-chronic exposure). After this treatment, the cells were further incubated (without particle/fibre) for two weeks, allowing recovery from the exposure (recovery period). Nuclear depositions of the CNTs were assessed using femtosecond pulsed laser microscopy in a label-free manner. DNA methylation alterations were analysed using microarrays that assess more than 850 thousand CpG sites in the whole genome. RESULTS At non-cytotoxic doses, CNTs were noted to be incorporated with in the nucleus after a four weeks period. Exposure to MWCNTs induced a single hypomethylation at a CpG site and gene promoter region. No change in DNA methylation was observed after the recovery period for MWCNTs. Exposure to SWCNTs or amosite induced hypermethylation at CpG sites after sub-chronic exposure which may involve in 'transcription factor activity' and 'sequence-specific DNA binding' gene ontologies. After the recovery period, hypermethylation and hypomethylation were noted for both SWCNTs and amosite. Hippocalcinlike 1 (HPCAL1), protease serine 3 (PRSS3), kallikrein-related peptidase 3 (KLK3), kruppel like factor 3 (KLF3) genes were hypermethylated at different time points in either SWCNT-exposed or amosite-exposed cells. CONCLUSION These results suggest that the specific SWCNT (SRM2483) and amosite fibres studied induce hypo- or hypermethylation on CpG sites in DNA after very low-dose exposure and recovery period. This effect was not seen for the studied MWCNT (NM400).
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Affiliation(s)
- Deniz Öner
- KU Leuven, Department of Public Health and Primary Care, Unit of Environment and Health, Laboratory of Toxicology, 3000 Leuven, Belgium
| | - Manosij Ghosh
- KU Leuven, Department of Public Health and Primary Care, Unit of Environment and Health, Laboratory of Toxicology, 3000 Leuven, Belgium
| | - Robin Coorens
- KU Leuven, Department of Public Health and Primary Care, Unit of Environment and Health, Laboratory of Toxicology, 3000 Leuven, Belgium
| | - Hannelore Bové
- Hasselt University, Biomedical Research Institute, Agoralaan Building C, 3590 Diepenbeek, Belgium
| | - Matthieu Moisse
- KU Leuven, Department of Human Genetics, Laboratory for Translational Genetics, 3000 Leuven, Belgium
| | - Diether Lambrechts
- KU Leuven, Department of Human Genetics, Laboratory for Translational Genetics, 3000 Leuven, Belgium; VIB, VIB Center for Cancer Biology, Laboratory for Translational Genetics, 3000 Leuven, Belgium
| | - Marcel Ameloot
- Hasselt University, Biomedical Research Institute, Agoralaan Building C, 3590 Diepenbeek, Belgium
| | - Lode Godderis
- KU Leuven, Department of Public Health and Primary Care, Unit of Environment and Health, Laboratory of Toxicology, 3000 Leuven, Belgium; Idewe, External Service for Prevention and Protection at Work, B-3001 Leuven, Belgium
| | - Peter H M Hoet
- KU Leuven, Department of Public Health and Primary Care, Unit of Environment and Health, Laboratory of Toxicology, 3000 Leuven, Belgium.
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16
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Rossnerova A, Honkova K, Pelclova D, Zdimal V, Hubacek JA, Chvojkova I, Vrbova K, Rossner P, Topinka J, Vlckova S, Fenclova Z, Lischkova L, Klusackova P, Schwarz J, Ondracek J, Ondrackova L, Kostejn M, Klema J, Dvorackova S. DNA Methylation Profiles in a Group of Workers Occupationally Exposed to Nanoparticles. Int J Mol Sci 2020; 21:E2420. [PMID: 32244494 PMCID: PMC7177382 DOI: 10.3390/ijms21072420] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023] Open
Abstract
The risk of exposure to nanoparticles (NPs) has rapidly increased during the last decade due to the vast use of nanomaterials (NMs) in many areas of human life. Despite this fact, human biomonitoring studies focused on the effect of NP exposure on DNA alterations are still rare. Furthermore, there are virtually no epigenetic data available. In this study, we investigated global and gene-specific DNA methylation profiles in a group of 20 long-term (mean 14.5 years) exposed, nanocomposite, research workers and in 20 controls. Both groups were sampled twice/day (pre-shift and post-shift) in September 2018. We applied Infinium Methylation Assay, using the Infinium MethylationEPIC BeadChips with more than 850,000 CpG loci, for identification of the DNA methylation pattern in the studied groups. Aerosol exposure monitoring, including two nanosized fractions, was also performed as proof of acute NP exposure. The obtained array data showed significant differences in methylation between the exposed and control groups related to long-term exposure, specifically 341 CpG loci were hypomethylated and 364 hypermethylated. The most significant CpG differences were mainly detected in genes involved in lipid metabolism, the immune system, lung functions, signaling pathways, cancer development and xenobiotic detoxification. In contrast, short-term acute NP exposure was not accompanied by DNA methylation changes. In summary, long-term (years) exposure to NP is associated with DNA epigenetic alterations.
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Affiliation(s)
- Andrea Rossnerova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Katerina Honkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Daniela Pelclova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Vladimir Zdimal
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Jaroslav A. Hubacek
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, Videnska 1958/9, 140 21 Prague 4, Czech Republic;
| | - Irena Chvojkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Kristyna Vrbova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.V.); (P.R.)
| | - Pavel Rossner
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.V.); (P.R.)
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Stepanka Vlckova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Zdenka Fenclova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Lucie Lischkova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Pavlina Klusackova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Jaroslav Schwarz
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Jakub Ondracek
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Lucie Ondrackova
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Martin Kostejn
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Jiri Klema
- Department of Computer Science, Czech Technical University in Prague, Karlovo namesti 13, 121 35 Prague 2, Czech Republic;
| | - Stepanka Dvorackova
- Department of Machining and Assembly, Department of Engineering Technology, Department of Material Science, Faculty of Mechanical Engineering, Technical University in Liberec, Studentska 1402/2 Liberec, Czech Republic;
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17
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Yu J, Loh XJ, Luo Y, Ge S, Fan X, Ruan J. Insights into the epigenetic effects of nanomaterials on cells. Biomater Sci 2019; 8:763-775. [PMID: 31808476 DOI: 10.1039/c9bm01526d] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
With the development of nanotechnology, nanomaterials are increasingly being applied in health fields, such as biomedicine, pharmaceuticals, and cosmetics. Concerns have therefore been raised over their toxicity and numerous studies have been carried out to assess their safety. Most studies on the toxicity and therapeutic mechanisms of nanomaterials have revealed the effects of nanomaterials on cells at the transcriptome and proteome levels. However, epigenetic modifications, for example DNA methylation, histone modification, and noncoding RNA expression induced by nanomaterials, which play an important role in the regulation of gene expression, have not received sufficient attention. In this review, we therefore state the importance of studying epigenetic effects induced by nanomaterials; then we review the progress of nanomaterial epigenetic research in the assessment of toxicity, therapeutic, and other mechanisms. We also clarify the possible study directions for future nanomaterial epigenetic research. Finally, we discuss the future development and challenges of nanomaterial epigenetics that must still be addressed. We hope to understand the potential toxicity of nanomaterials and clearly understand the therapeutic mechanism through a thorough investigation of nanomaterial epigenetics.
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Affiliation(s)
- Jie Yu
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China. and Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Xian Jun Loh
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, #08-03, Singapore 138634, Singapore
| | - Yifei Luo
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, #08-03, Singapore 138634, Singapore
| | - Shengfang Ge
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China. and Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Xianqun Fan
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China. and Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Jing Ruan
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China. and Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
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18
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Pérez RF, Soto Fernández AY, Bousquets Muñoz P, Sierra MI, Tejedor JR, Morales-Sánchez P, Valdés AF, Santamaría R, Blanco C, Torrecillas R, Fraga MF, Fernández AF. No genome-wide DNA methylation changes found associated with medium-term reduced graphene oxide exposure in human lung epithelial cells. Epigenetics 2019; 15:283-293. [PMID: 31512544 DOI: 10.1080/15592294.2019.1666650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The presence of nanomaterials in our everyday life is ever increasing, and so too are concerns about the possible health consequences of exposure to them. While evidence of their biological activity is growing, there is still scant knowledge of the epigenetic mechanisms that could be at play in these processes. Moreover, the great variability in the chemical and physical structures of these compounds handicaps the study of their possible health risks. Here we have synthesized reduced graphene oxide (rGO) through the thermal exfoliation/reduction of graphite oxide, and characterized the resulting material. We have then made use of Illumina's MethylationEPIC arrays and bisulphite pyrosequencing to analyse the genome-wide and global DNA methylation dynamics associated with the medium-term exposure of human lung epithelial cells to rGO at concentrations of 1 and 10 µg/mL. The results show no genome-wide or global DNA methylation changes associated with either condition. Our observations thus suggest that medium-term rGO exposure does not have significant effects on the DNA methylation patterns of human lung epithelial cells.
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Affiliation(s)
- Raúl F Pérez
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC-ISPA), Universidad de Oviedo, El Entrego, Spain.,Cancer Epigenetics Laboratory, Instituto de Oncología de Asturias (IUOPA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Oviedo, Spain
| | - Anna Yunuen Soto Fernández
- Cancer Epigenetics Laboratory, Instituto de Oncología de Asturias (IUOPA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Oviedo, Spain
| | - Pablo Bousquets Muñoz
- Cancer Epigenetics Laboratory, Instituto de Oncología de Asturias (IUOPA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Oviedo, Spain
| | - Marta I Sierra
- Cancer Epigenetics Laboratory, Instituto de Oncología de Asturias (IUOPA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Oviedo, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics Laboratory, Instituto de Oncología de Asturias (IUOPA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Oviedo, Spain
| | - Paula Morales-Sánchez
- Cancer Epigenetics Laboratory, Instituto de Oncología de Asturias (IUOPA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Oviedo, Spain.,Endocrinology, Nutrition, Diabetes and Obesity Unit (ENDO). Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Oviedo, Spain
| | - Adolfo F Valdés
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC-ISPA), Universidad de Oviedo, El Entrego, Spain
| | | | - Clara Blanco
- Department of Chemistry of Materials, INCAR-CSIC-ISPA, Oviedo, Spain
| | - Ramón Torrecillas
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC-ISPA), Universidad de Oviedo, El Entrego, Spain
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC-ISPA), Universidad de Oviedo, El Entrego, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Instituto de Oncología de Asturias (IUOPA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Oviedo, Spain
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19
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Cole E, Ray JL, Bolten S, Hamilton RF, Shaw PK, Postma B, Buford M, Holian A, Cho YH. Multiwalled Carbon Nanotubes of Varying Size Lead to DNA Methylation Changes That Correspond to Lung Inflammation and Injury in a Mouse Model. Chem Res Toxicol 2019; 32:1545-1553. [PMID: 31265265 DOI: 10.1021/acs.chemrestox.9b00075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Diversity in physicochemical properties of engineered multiwalled carbon nanotubes (MWCNTs) increases the complexity involved in interpreting toxicity studies of these materials. Studies indicate that epigenetic changes could be at least partially involved in MWCNTs-induced pro-inflammatory and fibrotic lung pathology. Therefore, we examined distinct methylation changes in response to MWCNTs of varied sizes to identify potential epigenetic biomarkers of MWCNTs exposure and disease progression. C57BL/6 mice were exposed via oropharyngeal instillation to a single dose (50 μg) to one of three differently sized MWCNTs: "narrow short" (NS), "wide short" (WS), and "narrow long" (NL). Vehicle-treated control mice received dispersion media (DM) only. Whole lung lavage fluid (LLF) and lung tissue were collected 24 h and 7 days postexposure to evaluate pro-inflammatory cytokines, epigenetic, or histological responses at acute and subchronic intervals, respectively. Luminometric methylation assay and pyrosequencing were used to measure global DNA methylation as well as promoter methylation of inflammation and fibrosis-related genes, respectively. Pro-inflammatory cytokines, including IL-1ß, IL-6, and TNF-α, were measured using enzyme-linked immunosorbant assay, while airway thickening and interstitial collagen accumulation were measured in 7-day lung tissue using laser scanning cytometry. Distinct patterns of methylation (i.e., IL-1ß, IL-6, and TNF-α) among the different sized MWCNTs at 24 h postexposure corresponded to some pro-inflammatory cytokine measurements from whole LLF. Fibrosis-related gene, Thy-1, was significantly hypermethylated after exposures to WS and NL MWCNTs, while only NL MWCNTs induced significantly lower global DNA methylation. After 7 days, a hierarchy in airway thickness and interstitial collagen deposition was observed: NS < WS < NL. However, only airway thickness was significantly greater in the WS and NL MWCNTs-exposed groups than the DM-exposed group. These data suggest that methylation changes could be involved in the initial immune response of inflammation and tissue remodeling that precedes lung disease in response to different MWCNTs sizes.
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Affiliation(s)
- Elizabeth Cole
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences , University of Montana , Missoula , Montana 59812 , United States
| | - Jessica L Ray
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences , University of Montana , Missoula , Montana 59812 , United States
| | - Shannon Bolten
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences , University of Montana , Missoula , Montana 59812 , United States
| | - Raymond F Hamilton
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences , University of Montana , Missoula , Montana 59812 , United States
| | - Pamela K Shaw
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences , University of Montana , Missoula , Montana 59812 , United States
| | - Britten Postma
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences , University of Montana , Missoula , Montana 59812 , United States
| | - Mary Buford
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences , University of Montana , Missoula , Montana 59812 , United States
| | - Andrij Holian
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences , University of Montana , Missoula , Montana 59812 , United States
| | - Yoon Hee Cho
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences , University of Montana , Missoula , Montana 59812 , United States
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20
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Gurunathan S, Qasim M, Park CH, Arsalan Iqbal M, Yoo H, Hwang JH, Uhm SJ, Song H, Park C, Choi Y, Kim JH, Hong K. Cytotoxicity and Transcriptomic Analyses of Biogenic Palladium Nanoparticles in Human Ovarian Cancer Cells (SKOV3). NANOMATERIALS 2019; 9:nano9050787. [PMID: 31121951 PMCID: PMC6566439 DOI: 10.3390/nano9050787] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/15/2019] [Accepted: 05/15/2019] [Indexed: 11/16/2022]
Abstract
Ovarian cancer incidence continues to increase at an alarming rate. Although various therapeutic approaches exist for ovarian cancer, they have limitations, including undesired side effects. Therefore, nanoparticle (NP)-mediated therapy may be a viable, biocompatible, and suitable alternative. To the best of our knowledge, no comprehensive analysis has been undertaken on the cytotoxicity and cellular pathways involved in ovarian cancer cells, particularly SKOV3 cells. Here, we investigated the effect of palladium NPs (PdNPs) and the molecular mechanisms and cellular pathways involved in ovarian cancer. We assayed cell viability, proliferation, cytotoxicity, oxidative stress, DNA damage, and apoptosis and performed an RNA-Seq analysis. The results showed that PdNPs elicited concentration-dependent decreases in cell viability and proliferation and induced increasing cytotoxicity at increasing concentrations, as determined by leakage of lactate dehydrogenase, increased levels of reactive oxygen species and malondialdehyde, and decreased levels of antioxidants like glutathione and superoxide dismutase. Furthermore, our study revealed that PdNPs induce mitochondrial dysfunction by altering mitochondrial membrane potential, reducing adenosine triphosphate levels, inducing DNA damage, and activating caspase 3, all of which significantly induced apoptosis in SKOV3 cells following PdNPs treatment. Gene ontology (GO) term analysis of PdNPs-exposed SKOV3 cells showed various dysregulated pathways, particularly nucleosome assembly, telomere organization, and rDNA chromatin silencing. When genes downregulated by PdNPs were applied to GO term enrichment analysis, nucleosome assembly was the top-ranked biological pathway. We also provide evidence for an association between PdNPs exposure and multiple layers of epigenetic transcriptional control and establish a molecular basis for NP-mediated apoptosis. These findings provide a foundation, potential targets, and novel insights into the mechanism underlying toxicity and pathways in SKOV3 cells, and open new avenues to identify novel targets for ovarian cancer treatment.
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Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Muhammad Qasim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Chan Hyeok Park
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Muhammad Arsalan Iqbal
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Hyunjin Yoo
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Jeong Ho Hwang
- Animal Model Research Group, Jeonbuk Department of Inhalation Research, Korea Institute of Toxicology, 30 Baekhak1-gil, Jeongeup, Jeollabuk-do 56212, Korea.
| | - Sang Jun Uhm
- Department of Animal Science and Biotechnology, Sangji Youngseo College, Wonju 26339, Korea.
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
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21
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Roberti A, Valdes AF, Torrecillas R, Fraga MF, Fernandez AF. Epigenetics in cancer therapy and nanomedicine. Clin Epigenetics 2019; 11:81. [PMID: 31097014 PMCID: PMC6524244 DOI: 10.1186/s13148-019-0675-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/29/2019] [Indexed: 12/21/2022] Open
Abstract
The emergence of nanotechnology applied to medicine has revolutionized the treatment of human cancer. As in the case of classic drugs for the treatment of cancer, epigenetic drugs have evolved in terms of their specificity and efficiency, especially because of the possibility of using more effective transport and delivery systems. The use of nanoparticles (NPs) in oncology management offers promising advantages in terms of the efficacy of cancer treatments, but it is still unclear how these NPs may be affecting the epigenome such that safe routine use is ensured. In this work, we summarize the importance of the epigenetic alterations identified in human cancer, which have led to the appearance of biomarkers or epigenetic drugs in precision medicine, and we describe the transport and release systems of the epigenetic drugs that have been developed to date.
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Affiliation(s)
- Annalisa Roberti
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), ISPA-FINBA-Hospital Universitario Central de Asturias HUCA, Universidad de Oviedo, Avenida de Roma, 33011, Oviedo, Asturias, Spain
| | - Adolfo F Valdes
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC)-Universidad de Oviedo-Principado de Asturias, Avenida de Roma, 33011, Oviedo, Asturias, Spain
| | - Ramón Torrecillas
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC)-Universidad de Oviedo-Principado de Asturias, Avenida de Roma, 33011, Oviedo, Asturias, Spain
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC)-Universidad de Oviedo-Principado de Asturias, Avenida de Roma, 33011, Oviedo, Asturias, Spain.
| | - Agustin F Fernandez
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), ISPA-FINBA-Hospital Universitario Central de Asturias HUCA, Universidad de Oviedo, Avenida de Roma, 33011, Oviedo, Asturias, Spain.
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22
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Toxicity of carbon-based nanomaterials: Reviewing recent reports in medical and biological systems. Chem Biol Interact 2019; 307:206-222. [PMID: 31054282 DOI: 10.1016/j.cbi.2019.04.036] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 04/21/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023]
Abstract
Application of nanomaterials in our daily life is increasing, day in day out and concerns have raised about their toxicity for human and other organisms. In this manner, carbon-based nanomaterials have been applied to different products due to their unique physicochemical, electrical, mechanical properties, and biological compatibility. But, there are several reports about the negative effects of these materials on biological systems and cellular compartments. This review article describes the various types of carbon-based nanomaterials and methods that use for determining these toxic effects that are reported recently in the papers. Then, extensively discussed the toxic effects of these materials on the human and other living organisms and also their toxicity routs including Neurotoxicity, Hepatotoxicity, Nephrotoxicity, Immunotoxicity, Cardiotoxicity, Genotoxicity and epigenetic toxicity, Dermatotoxicity, and Carcinogenicity.
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23
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Emerce E, Ghosh M, Öner D, Duca RC, Vanoirbeek J, Bekaert B, Hoet PHM, Godderis L. Carbon Nanotube- and Asbestos-Induced DNA and RNA Methylation Changes in Bronchial Epithelial Cells. Chem Res Toxicol 2019; 32:850-860. [PMID: 30990028 DOI: 10.1021/acs.chemrestox.8b00406] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Carbon nanotubes (CNTs) are nanoscale tube-shaped carbon materials used in many industrial areas. Their fiber shape has caused concerns about their toxicity given their structural similarity with asbestos. The aim here was to elucidate the effect of CNTs and asbestos exposure on global DNA and RNA methylation and the methylation of genes associated with cell cycle, inflammation, and DNA damage processes in human lung cells. Human bronchial epithelial cells (16HBE14o-) were exposed for 24 h to 25 and 100 μg/mL CNTs (single-walled CNTs [SWCNTs] and multiwalled CNTs [MWCNTs]) and 2.5 μg/mL asbestos (chrysotile, amosite, and crocidolite). Global DNA and RNA (hydroxy)methylation to cytosines was measured by a validated liquid chromatography tandem-mass spectrometry method. Global RNA methylation to adenines was measured by a colorimetric ELISA-like assay. Gene-specific DNA methylation status at certain cytosine-phosphate-guanine (CpG) sites of cyclin-dependent kinase inhibitor 1A ( CDKN1A), serine/threonine kinase ( ATM), and TNF receptor-associated factor 2 ( TRAF2) were analyzed by using bisulfite pyrosequencing technology. Only MWCNT-exposed cells showed significant global DNA hypomethylation of cytosine and global RNA hypomethylation of adenosine. SWCNT, MWCNT, and amosite exposure decreased DNA methylation of CDKN1A. ATM methylation was affected by chrysotile, SWCNT, and MWCNT. However, SWCNT exposure led to DNA hypermethylation of TRAF2. These findings contribute to further understanding of the effect of CNTs on different carcinogenic pathways.
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Affiliation(s)
- Esra Emerce
- Department of Public Health and Primary Care, Unit of Environment and Health , KU Leuven , 3000 Leuven , Belgium.,Department of Toxicology, Faculty of Pharmacy , Gazi University , 06560 Ankara , Turkey
| | - Manosij Ghosh
- Department of Public Health and Primary Care, Unit of Environment and Health , KU Leuven , 3000 Leuven , Belgium
| | - Deniz Öner
- Department of Public Health and Primary Care, Unit of Environment and Health , KU Leuven , 3000 Leuven , Belgium
| | - Radu-Corneliu Duca
- Department of Public Health and Primary Care, Unit of Environment and Health , KU Leuven , 3000 Leuven , Belgium
| | - Jeroen Vanoirbeek
- Department of Public Health and Primary Care, Unit of Environment and Health , KU Leuven , 3000 Leuven , Belgium
| | - Bram Bekaert
- Forensic Biomedical Sciences, Department of Imaging and Pathology , KU Leuven - University of Leuven , 3000 Leuven , Belgium.,Department of Forensic Medicine, Laboratory of Forensic Genetics and Molecular Archaeology , University Hospitals Leuven , 3000 Leuven , Belgium
| | - Peter H M Hoet
- Department of Public Health and Primary Care, Unit of Environment and Health , KU Leuven , 3000 Leuven , Belgium
| | - Lode Godderis
- Department of Public Health and Primary Care, Unit of Environment and Health , KU Leuven , 3000 Leuven , Belgium.,External Service for Prevention and Protection at Work , IDEWE , B-3001 Leuven , Belgium
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24
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Gurunathan S, Qasim M, Park C, Yoo H, Choi DY, Song H, Park C, Kim JH, Hong K. Cytotoxicity and Transcriptomic Analysis of Silver Nanoparticles in Mouse Embryonic Fibroblast Cells. Int J Mol Sci 2018; 19:ijms19113618. [PMID: 30453526 PMCID: PMC6275036 DOI: 10.3390/ijms19113618] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/27/2018] [Accepted: 11/13/2018] [Indexed: 12/16/2022] Open
Abstract
The rapid development of nanotechnology has led to the use of silver nanoparticles (AgNPs) in biomedical applications, including antibacterial, antiviral, anti-inflammatory, and anticancer therapies. The molecular mechanism of AgNPs-induced cytotoxicity has not been studied thoroughly using a combination of cellular assays and RNA sequencing (RNA-Seq) analysis. In this study, we prepared AgNPs using myricetin, an anti-oxidant polyphenol, and studied their effects on NIH3T3 mouse embryonic fibroblasts as an in vitro model system to explore the potential biomedical applications of AgNPs. AgNPs induced loss of cell viability and cell proliferation in a dose-dependent manner, as evident by increased leakage of lactate dehydrogenase (LDH) from cells. Reactive oxygen species (ROS) were a potential source of cytotoxicity. AgNPs also incrementally increased oxidative stress and the level of malondialdehyde, depleted glutathione and superoxide dismutase, reduced mitochondrial membrane potential and adenosine triphosphate (ATP), and caused DNA damage by increasing the level of 8-hydroxy-2′-deoxyguanosine and the expressions of the p53 and p21 genes in NIH3T3 cells. Thus, activation of oxidative stress may be crucial for NIH3T3 cytotoxicity. Interestingly, gene ontology (GO) term analysis revealed alterations in epigenetics-related biological processes including nucleosome assembly and DNA methylation due to AgNPs exposure. This study is the first demonstration that AgNPs can alter bulk histone gene expression. Therefore, our genome-scale study suggests that the apoptosis observed in NIH3T3 cells treated with AgNPs is mediated by the repression of genes required for cell survival and the aberrant enhancement of nucleosome assembly components to induce apoptosis.
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Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Muhammad Qasim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Hyunjin Yoo
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Dong Yoon Choi
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
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25
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Yuan B, Zhang H, Wang X, Pan Y, Jiang J. Effect of Nano-SiO 2 on Expression and Aberrant Methylation of Imprinted Genes in Lung and Testis. NANOSCALE RESEARCH LETTERS 2018; 13:266. [PMID: 30182198 PMCID: PMC6123335 DOI: 10.1186/s11671-018-2673-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 08/20/2018] [Indexed: 05/11/2023]
Abstract
Nanotechnology has been developing rapidly and is now used in many cutting-edge medical therapeutics. However, there is increasing concern that exposure to nanoparticles (NPs) may induce different systemic diseases as epigenetic mechanisms are associated with more and more disease. The role of NP epigenomic modification is important to disease etiology. Our study aimed to determine the epigenetic mechanisms of damage in lung and testis cells by exposing cells to SiO2 NPs. We used male C57BL/6 mice to characterize the damaging effect of SiO2 NPs on lung and testis cells as well as the resulting methylation state at the imprinted Dlk1/Dio3 domain region. The A549 cells exposed to SiO2 NPs had cell apoptosis, and male mice exposed to SiO2 NPs had altered lung and testis tissues. The genes in the imprinted domains Dlk1/Dio3 region changed in both tissues; Dlk1, Rtl1, and Dio3 are upregulated in testis while Dlk1 and Dio3 are also upregulated in lung tissues. Bisulfite sequencing PCR of male adult lung and testis were mostly hypomethylated, with a few hypermethylated CpGs. These findings indicate that nanoparticles play an important role in DNA methylation of imprinted genes.
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Affiliation(s)
- Beilei Yuan
- College of Safety Science and Engineering, Nanjing Tech University, 200 Zhongshan North Rd, Nanjing, 210009, China.
| | - Huazhong Zhang
- Department of Emergency Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xuan Wang
- College of Safety Science and Engineering, Nanjing Tech University, 200 Zhongshan North Rd, Nanjing, 210009, China
| | - Yong Pan
- College of Safety Science and Engineering, Nanjing Tech University, 200 Zhongshan North Rd, Nanjing, 210009, China.
| | - Juncheng Jiang
- College of Safety Science and Engineering, Nanjing Tech University, 200 Zhongshan North Rd, Nanjing, 210009, China.
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26
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Scala G, Kinaret P, Marwah V, Sund J, Fortino V, Greco D. Multi-omics analysis of ten carbon nanomaterials effects highlights cell type specific patterns of molecular regulation and adaptation. NANOIMPACT 2018; 11:99-108. [PMID: 32140619 PMCID: PMC7043328 DOI: 10.1016/j.impact.2018.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/28/2018] [Accepted: 05/05/2018] [Indexed: 05/19/2023]
Abstract
New strategies to characterize the effects of engineered nanomaterials (ENMs) based on omics technologies are emerging. However, given the intricate interplay of multiple regulatory layers, the study of a single molecular species in exposed biological systems might not allow the needed granularity to successfully identify the pathways of toxicity (PoT) and, hence, portraying adverse outcome pathways (AOPs). Moreover, the intrinsic diversity of different cell types composing the exposed organs and tissues in living organisms poses a problem when transferring in vivo experimentation into cell-based in vitro systems. To overcome these limitations, we have profiled genome-wide DNA methylation, mRNA and microRNA expression in three human cell lines representative of relevant cell types of the respiratory system, A549, BEAS-2B and THP-1, exposed to a low dose of ten carbon nanomaterials (CNMs) for 48 h. We applied advanced data integration and modelling techniques in order to build comprehensive regulatory and functional maps of the CNM effects in each cell type. We observed that different cell types respond differently to the same CNM exposure even at concentrations exerting similar phenotypic effects. Furthermore, we linked patterns of genomic and epigenomic regulation to intrinsic properties of CNM. Interestingly, DNA methylation and microRNA expression only partially explain the mechanism of action (MOA) of CNMs. Taken together, our results strongly support the implementation of approaches based on multi-omics screenings on multiple tissues/cell types, along with systems biology-based multi-variate data modelling, in order to build more accurate AOPs.
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Affiliation(s)
- Giovanni Scala
- Faculty of Medicine and Life Sciences, University of Tampere, Finland
- Institute of Biosciences and Medical Technologies (BioMediTech), University of Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Finland
| | - Pia Kinaret
- Faculty of Medicine and Life Sciences, University of Tampere, Finland
- Institute of Biosciences and Medical Technologies (BioMediTech), University of Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Finland
| | - Veer Marwah
- Faculty of Medicine and Life Sciences, University of Tampere, Finland
- Institute of Biosciences and Medical Technologies (BioMediTech), University of Tampere, Finland
| | - Jukka Sund
- Faculty of Medicine and Life Sciences, University of Tampere, Finland
| | - Vittorio Fortino
- Faculty of Medicine and Life Sciences, University of Tampere, Finland
- Institute of Biosciences and Medical Technologies (BioMediTech), University of Tampere, Finland
- Institute of Biomedicine, University of Eastern Finland, Kuopio Campus, Finland
| | - Dario Greco
- Faculty of Medicine and Life Sciences, University of Tampere, Finland
- Institute of Biosciences and Medical Technologies (BioMediTech), University of Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Finland
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27
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RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells. Sci Rep 2018; 8:6668. [PMID: 29703973 PMCID: PMC5923294 DOI: 10.1038/s41598-018-25085-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/09/2018] [Indexed: 12/11/2022] Open
Abstract
Despite a considerable focus on the adverse effects of silver nanoparticles (AgNPs) in recent years, studies on the potential long-term effects of AgNPs are scarce. The aim of this study was to explore the effects of AgNPs following repeated low-dose, long-term exposure of human bronchial epithelial cells. To this end, the human BEAS-2B cell line was exposed to 1 µg/mL AgNPs (10 nm) for 6 weeks followed by RNA-sequencing (RNA-Seq) as well as genome-wide DNA methylation analysis. The transcriptomics analysis showed that a substantial number of genes (1717) were differentially expressed following AgNP exposure whereas only marginal effects on DNA methylation were observed. Downstream analysis of the transcriptomics data identified several affected pathways including the ‘fibrosis’ and ‘epithelial-mesenchymal transition’ (EMT) pathway. Subsequently, functional validation studies were performed using AgNPs of two different sizes (10 nm and 75 nm). Both NPs increased collagen deposition, indicative of fibrosis, and induced EMT, as evidenced by an increased invasion index, anchorage independent cell growth, as well as cadherin switching. In conclusion, using a combination of RNA-Seq and functional assays, our study revealed that repeated low-dose, long-term exposure of human BEAS-2B cells to AgNPs is pro-fibrotic, induces EMT and cell transformation.
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28
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Pinto SR, Helal-Neto E, Paumgartten F, Felzenswalb I, Araujo-Lima CF, Martínez-Máñez R, Santos-Oliveira R. Cytotoxicity, genotoxicity, transplacental transfer and tissue disposition in pregnant rats mediated by nanoparticles: the case of magnetic core mesoporous silica nanoparticles. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2018; 46:527-538. [PMID: 29688037 DOI: 10.1080/21691401.2018.1460603] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Whether in the cosmetic or as therapeutic, the use of nanoparticles has been increasing and taking on global proportion. However, there are few studies about the physical potential of long-term use or use in special conditions such as chronic, AIDS, pregnant women and other special health circumstances. In this context, the study of the mutagenicity and the transplacental passage represents an important and reliable model for the primary evaluation of potential health risks, especially maternal and child health. In this study we performed mutagenicity, cytotoxic and transplacental evaluation of magnetic core mesoporous silica nanoparticles, radiolabeled with 99mTc for determination of toxicogenic and embryonic/fetuses potential risk in animal model. Magnetic core mesoporous silica nanoparticles were produced and characterized by obtaining nanoparticles with a size of (58.9 ± 8.1 nm) in spherical shape and with intact magnetic core. The 99 m Tc radiolabeling process demonstrated high efficacy and stability in 98% yield over a period of 8 hours of stability. Mutagenicity assays were performed using Salmonella enteric serovar Typhimurium standard strains TA98, TA100 and TA102. Cytotoxicity assays were performed using WST-1. The transplacental evaluation assays were performed using the in vivo model with rats in two periods: embryonic and fetal stage. The results of both analyzes corroborate that the nanoparticles can i) generate DNA damage; ii) generate cytotoxic potential and iii) cross the transplantation barrier in both stages and bioaccumulates in both embryos and fetuses. The results suggest that complementary evaluations should be conducted in order to attest safety, efficacy and quality of nanoparticles before unrestricted approval of their use.
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Affiliation(s)
- Suyene Rocha Pinto
- a Nuclear Engineering Institute , Brazilian Nuclear Energy Commission , Rio de Janeiro , Brazil
| | - Edward Helal-Neto
- a Nuclear Engineering Institute , Brazilian Nuclear Energy Commission , Rio de Janeiro , Brazil
| | - Francisco Paumgartten
- b National School of Public Health , Oswaldo Cruz Foundation (FIOCRUZ) , Rio de Janeiro , Brazil
| | - Israel Felzenswalb
- c Departament of Biophysics and Biometrics, Environmental Mutagenesis Laboratory , Rio de Janeiro State University, Institute of Biology Roberto de Alcântara Gomes , Rio de Janeiro , Brazil
| | - Carlos Fernando Araujo-Lima
- c Departament of Biophysics and Biometrics, Environmental Mutagenesis Laboratory , Rio de Janeiro State University, Institute of Biology Roberto de Alcântara Gomes , Rio de Janeiro , Brazil
| | - Ramón Martínez-Máñez
- d Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) , Universitat Politècnica de València, Universitat de València , Valencia , Spain.,e Departamento de Química , Universidad Politécnica de Valencia , Valencia , Spain.,f CIBER de Bioingeniería , Biomateriales y Nanomedicina (CIBER-BBN) , Valencia , Spain
| | - Ralph Santos-Oliveira
- a Nuclear Engineering Institute , Brazilian Nuclear Energy Commission , Rio de Janeiro , Brazil.,g Laboratory of Nanoradiopharmaceuticals and Radiopharmacy , Zona Oeste State University , Rio de Janeiro , Brazil
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29
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Ghosh M, Öner D, Duca RC, Bekaert B, Vanoirbeek JAJ, Godderis L, Hoet PHM. Single-walled and multi-walled carbon nanotubes induce sequence-specific epigenetic alterations in 16 HBE cells. Oncotarget 2018; 9:20351-20365. [PMID: 29755656 PMCID: PMC5945544 DOI: 10.18632/oncotarget.24866] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/15/2018] [Indexed: 02/06/2023] Open
Abstract
Recent studies have identified carbon nanotube (CNT)-induced epigenetic changes as one of the key players in patho-physiological response. In the present study, we investigated whether CNT exposure is associated with epigenetic changes in human bronchial epithelial cells (16 HBE), in vitro. We focused on global DNA methylation, methylation of LINE-1 elements and promoter sequence of twelve functionally important genes (SKI, DNMT1, HDAC4, NPAT, ATM, BCL2L11, MAP3K10, PIK3R2, MYO1C, TCF3, FGFR 1 and AGRN). Additionally, we studied the influence of CNT exposure on miRNA expression. Using a LC-MS/MS method and pyrosequencing for LINE-1, we observed no significant changes in global DNA methylation (%) between the concentrations of multi-walled and single-walled CNT (MWCNT and SWCNT, respectively). Significant changes in sequence-specific methylation was observed in at least one CpG site for DNMT1 (SWCNT), HDAC4 (MWCNT), NPAT/ATM (MWCNT and SWCNT), MAP3K10 (MWCNT), PIK3R2 (MWCNT and SWCNT) and MYO1C (SWCNT). While changes in DNA methylation of the genes were relatively small, these changes were associated with changes in RNA expression, especially for MWCNT. However, the study did not reveal any significant alteration in the miRNA expression, associated with MWCNT and SWCNT exposure. Based on our results, mainly MWCNT influence DNA methylation and expression of the studied genes and could have significant impact on several critical cellular processes.
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Affiliation(s)
- Manosij Ghosh
- KU Leuven, Department of Public Health and Primary Care, Centre Environment and Health, B-3000 Leuven, Belgium
| | - Deniz Öner
- KU Leuven, Department of Public Health and Primary Care, Centre Environment and Health, B-3000 Leuven, Belgium
| | - Radu C Duca
- KU Leuven, Department of Public Health and Primary Care, Centre Environment and Health, B-3000 Leuven, Belgium
| | - Bram Bekaert
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, University of Leuven, Leuven, Belgium.,Department of Forensic Medicine, Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium
| | - Jeroen A J Vanoirbeek
- KU Leuven, Department of Public Health and Primary Care, Centre Environment and Health, B-3000 Leuven, Belgium
| | - Lode Godderis
- KU Leuven, Department of Public Health and Primary Care, Centre Environment and Health, B-3000 Leuven, Belgium.,Idewe, External Service for Prevention and Protection at Work, B-3001 Heverlee, Belgium
| | - Peter H M Hoet
- KU Leuven, Department of Public Health and Primary Care, Centre Environment and Health, B-3000 Leuven, Belgium
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30
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Öner D, Ghosh M, Bové H, Moisse M, Boeckx B, Duca RC, Poels K, Luyts K, Putzeys E, Van Landuydt K, Vanoirbeek JA, Ameloot M, Lambrechts D, Godderis L, Hoet PH. Differences in MWCNT- and SWCNT-induced DNA methylation alterations in association with the nuclear deposition. Part Fibre Toxicol 2018; 15:11. [PMID: 29426343 PMCID: PMC5807760 DOI: 10.1186/s12989-018-0244-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 01/18/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Subtle DNA methylation alterations mediated by carbon nanotubes (CNTs) exposure might contribute to pathogenesis and disease susceptibility. It is known that both multi-walled carbon nanotubes (MWCNTs) and single-walled carbon nanotubes (SWCNTs) interact with nucleus. Such, nuclear-CNT interaction may affect the DNA methylation effects. In order to understand the epigenetic toxicity, in particular DNA methylation alterations, of SWCNTs and short MWCNTs, we performed global/genome-wide, gene-specific DNA methylation and RNA-expression analyses after exposing human bronchial epithelial cells (16HBE14o- cell line). In addition, the presence of CNTs on/in the cell nucleus was evaluated in a label-free way using femtosecond pulsed laser microscopy. RESULTS Generally, a higher number of SWCNTs, compared to MWCNTs, was deposited at both the cellular and nuclear level after exposure. Nonetheless, both CNT types were in physical contact with the nuclei. While particle type dependency was noticed for the identified genome-wide and gene-specific alterations, no global DNA methylation alteration on 5-methylcytosine (5-mC) sites was observed for both CNTs. After exposure to MWCNTs, 2398 genes were hypomethylated (at gene promoters), and after exposure to SWCNTs, 589 CpG sites (located on 501 genes) were either hypo- (N = 493 CpG sites) or hypermethylated (N = 96 CpG sites). Cells exposed to MWCNTs exhibited a better correlation between gene promoter methylation and gene expression alterations. Differentially methylated and expressed genes induced changes (MWCNTs > SWCNTs) at different cellular pathways, such as p53 signalling, DNA damage repair and cell cycle. On the other hand, SWCNT exposure showed hypermethylation on functionally important genes, such as SKI proto-oncogene (SKI), glutathione S-transferase pi 1 (GTSP1) and shroom family member 2 (SHROOM2) and neurofibromatosis type I (NF1), which the latter is both hypermethylated and downregulated. CONCLUSION After exposure to both types of CNTs, epigenetic alterations may contribute to toxic or repair response. Moreover, our results suggest that the observed differences in the epigenetic response depend on particle type and differential CNT-nucleus interactions.
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Affiliation(s)
- Deniz Öner
- Laboratory of Toxicology, Unit of Environment and Health, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
| | - Manosij Ghosh
- Laboratory of Toxicology, Unit of Environment and Health, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
| | - Hannelore Bové
- Centre for Surface Chemistry and Catalysis, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
- Biomedical Research Institute, Agoralaan Building C, Hasselt University, 3590, Diepenbeek, Belgium
| | - Matthieu Moisse
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
- Laboratory for Translational Genetics, VIB Centre for Cancer Biology, VIB, 3000, Leuven, Belgium
| | - Bram Boeckx
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
- Laboratory for Translational Genetics, VIB Centre for Cancer Biology, VIB, 3000, Leuven, Belgium
| | - Radu C Duca
- Laboratory for Occupational and Environmental Hygiene, Unit of Environment and Health, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
| | - Katrien Poels
- Laboratory for Occupational and Environmental Hygiene, Unit of Environment and Health, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
| | - Katrien Luyts
- Laboratory of Toxicology, Unit of Environment and Health, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
| | - Eveline Putzeys
- Laboratory of Toxicology, Unit of Environment and Health, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
- Department of Oral Health Sciences, Unit of Biomaterials (BIOMAT), KU Leuven, 3000, Leuven, Belgium
| | - Kirsten Van Landuydt
- Department of Oral Health Sciences, Unit of Biomaterials (BIOMAT), KU Leuven, 3000, Leuven, Belgium
| | - Jeroen Aj Vanoirbeek
- Laboratory of Toxicology, Unit of Environment and Health, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
- Laboratory for Occupational and Environmental Hygiene, Unit of Environment and Health, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
| | - Marcel Ameloot
- Biomedical Research Institute, Agoralaan Building C, Hasselt University, 3590, Diepenbeek, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
- Laboratory for Translational Genetics, VIB Centre for Cancer Biology, VIB, 3000, Leuven, Belgium
| | - Lode Godderis
- Laboratory for Occupational and Environmental Hygiene, Unit of Environment and Health, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium
- External Service for Prevention and Protection at Work, IDEWE, B-3001, Leuven, Belgium
| | - Peter Hm Hoet
- Laboratory of Toxicology, Unit of Environment and Health, Department of Public Health and Primary Care, KU Leuven, 3000, Leuven, Belgium.
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