DNA methylation changes from primary cultures through senescence-bypass in Syrian hamster fetal cells initially exposed to benzo[a]pyrene
Ontology highlight
ABSTRACT:
ORGANISM(S): Mesocricetus auratus Homo sapiens
PROVIDER: GSE220238 | GEO | 2023/02/10
REPOSITORIES: GEO
Similar Datasets
Project description:Di(2-ethylhexyl) phthalate (DEHP; CAS No. 117-81-7) belongs to the phthalate class of chemicals, and is commonly added to plastics for flexibility. DEHP has been identified as an index compound for group-TDI calculations owing to its extensive toxicological dataset. Humans are exposed to this ubiquitous environmental contaminant through multiple routes. DEHP has been designated as probably and possibly carcinogenic to humans based on its ability to induce rodent carcinogenicity, although the relevance of its mode of action (MoA) in humans remains unclear. The aim of this study was to investigate the carcinogenic potential of DEHP using an alternative method and explore the possible mode and mechanisms of action at the molecular level. Special attention has been paid to DEHP dissolution in cell media, leading to the use of a final concentration of 0.5% DMSO. Transcriptomics were conducted on cells treated with a cytotoxic concentration of DEHP (19.7 µg/mL) for 24 h. The aim of the microarray experiment was to analyze the molecular effects of the substance under the specific conditions of the Cell Transformation Assay protocol (BALB c/ 3T3 clone A31-1-1 CTA, according to the method validated by ECVAM, Sasaki et al., 2012), in order to provide mechanistic explanations of the test results derived from the CTA.
2024-06-17 | E-MTAB-13716 | biostudies-arrayexpress
Project description:This analysis utilised the \"Transformics Assay\" and evaluated the effect of cell exposure to 0.02 μg/ml of Benzo(a)pyrene, the lowest transforming concentration, using the BALB / c 3T3 A31-1-1 cell line. The Transformic assay is an integrated approach combining the Cell Transformation Assay (CTA), with the high throughput technology of transcriptomics. The CTA is a widely used in vitro assay that has been designed to evaluate the effects of chemicals on the growth of specific cell types and their potential progression through a transformation process from being normal cells to fully malignant cells. It has the potential to detect both genotoxic and some non-genotoxic carcinogens and shows a good correlation with rodent bioassay data. However lack of understanding of the mechanistic basis of the assays, and particularly of the mechanisms leading to cell malignancy, has limited its acceptance for regulatory purposes. The Transformics Assay introduces the RNA extraction and microarray experiment performed at specific time points along the process of in vitro transformation, helping to identify mechanisms of action leading to chemical-induced transformation. The experiment was conducted testing the carcinogen Benzo(a)pyrene (CAS No.50-32-8), which is a polycyclic aromatic hydrocarbon (PHA) and classified as carcinogenic to humans (Group 1) by IARC. Particularly Benzo(a)pyrene is a prototypical member of this class of chemicals and its toxic effects has been extensively studied, both in laboratory animals and human populations. Benzo(a)pyrene and others PAHs-induced carcinogenesis is a multi-step process, which since the last decade, was considered to be initiated and substantially sustained by the reaction and binding to DNA (oncogenic targets). Indeed, as other PHAs, Benzo(a)pyrene is metabolically activated to a series of reactive intermediates by CYP450 and related enzymes under control of the aryl-hydrocarbon receptor (AhR). These events support the genotoxic mode of carcinogenic action. Nevertheless it is now widely recognized that Benzo(a)pyrene can act via non-genotoxic modes of action too, including epigenetic mechanisms involving the AhR signaling pathway, oxidative stress, disruption of mitogenic and other cellular signaling. This study aimed to explore the molecular and cellular events necessary to sustain the transforming activity of Benzo(a)pyrene, at the lowest in vitro concentration capable of sustaining the process of oncotransformation. In order to find the lowest transforming concentration, a preliminary CTA has been conducted according to the EURL-ECVAM (EU Reference Laboratory European Centre for the Validation of Alternative Methods) validated protocol. The exposure time recommended by EURL-ECVAM, 72 hrs, represents both the exposure time of cells and the RNA extraction time point. According to previous studies 72 hrs exposure could be a critical timing to study the cell transformation process, during which differences in adverse and adaptive cell responses began to become visible at the transcriptional level.
2021-09-01 | E-MTAB-10405 | biostudies-arrayexpress
Project description:The current test strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Non-genotoxic carcinogens (NGTXC) are negative for genotoxicity and go undetected. Therefore, alternative tests to detect these chemicals are urgently needed. NGTXC act through different modes of action, which complicates the development of such assays. We have demonstrated recently in primary mouse hepatocytes that some, but certainly not all, NGTXC can be categorized according to their mode of action based on feature detection at a gene expression level (Schaap et al. 2012 (PMID 22710402)). Identification of a wider range of chemicals probably requires multiple in vitro systems. In the current study, we describe the added value of using mouse embryonic stem cells. In this study, the focus is on NGTXC, but we also included genotoxic carcinogens and non-carcinogens. This approach enables us to assess the robustness of this method and to evaluate the system for recognizing features of chemicals in general, which is important for application in future risk assessment. Primary mouse hepatocytes and mouse embryonic stem cells were exposed to 26 chemicals (non-genotoxic carcinogens and non-carcinogens) representing diverse modes of action. Upon profiling, an unsupervised comparison approach was applied to recognize similar features at the transcriptomic level. This Series consists of the gene expression data of the primary mouse hepatocytes. The expression data of the mouse embryonic stem cells is submitted separately under another accession number. In this study we tested 26 chemicals of which 16 non-genotoxic carcinogens, 4 genotoxic carcinogens, 2 genotoxic non-carcinogens and 4 non-carcinogens. Specification of the chemicals can be found in the readme file.
2014-10-23 | E-GEOD-44088 | biostudies-arrayexpress
Project description:The current test strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Non-genotoxic carcinogens (NGTXC) are negative for genotoxicity and go undetected. Therefore, alternative tests to detect these chemicals are urgently needed. NGTXC act through different modes of action, which complicates the development of such assays. We have demonstrated recently in primary mouse hepatocytes that some, but certainly not all, NGTXC can be categorized according to their mode of action based on feature detection at a gene expression level (Schaap et al. 2012 (PMID 22710402)). Identification of a wider range of chemicals probably requires multiple in vitro systems. In the current study, we describe the added value of using mouse embryonic stem cells. In this study, the focus is on NGTXC, but we also included genotoxic carcinogens and non-carcinogens. This approach enables us to assess the robustness of this method and to evaluate the system for recognizing features of chemicals in general, which is important for application in future risk assessment.
2014-10-23 | GSE44088 | GEO
Project description:The current test strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Non-genotoxic carcinogens (NGTXC) are negative for genotoxicity and go undetected. Therefore, alternative tests to detect these chemicals are urgently needed. NGTXC act through different modes of action, which complicates the development of such assays. We have demonstrated recently in primary mouse hepatocytes that some, but certainly not all, NGTXC can be categorized according to their mode of action based on feature detection at a gene expression level (Schaap et al. 2012, PMID22710402). Identification of a wider range of chemicals probably requires multiple in vitro systems. In the current study we describe the added value of using mouse embryonic stem cells. In this study the focus is on NGTXC, but we also included genotoxic carcinogens and non-carcinogens. This approach enables us to assess the robustness of this method and to evaluate the system for recognizing features of chemicals in general, which is important for application in future risk assessment. This serie consists of the gene expression data of the mouse embryonic stem cells. The expression data of the primary mouse hepatocytes cells is submitted separately under accession number GSE44088.
2014-10-27 | GSE47345 | GEO
Project description:Under REACH, the European Community Regulation on chemicals, the testing strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Given that non-genotoxic carcinogens are negative for genotoxicity, this class of carcinogens will not be detected. Therefore, alternative test are urgently needed. Non-genotoxic carcinogens, however, act through different modes of action, which complicates the development of such an assay. The aim of this study was to investigate whether gene expression profiling in primary mouse hepatocytes can be used to distinguish different modes of action of non-genotoxic carcinogens. Primary mouse hepatocytes were exposed to 16 non-genotoxic carcinogens with diverse modes of action. Upon profiling, pathway analysis was performed to obtain insight into the biological relevance of the observed changes in gene expression. To recognize similarities in mode of action at the transcriptomic level, both a supervised and an unsupervised comparison approach was applied.
2012-06-25 | E-GEOD-35058 | biostudies-arrayexpress
Project description:Under REACH, the European Community Regulation on chemicals, the testing strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Given that non-genotoxic carcinogens are negative for genotoxicity, this class of carcinogens will not be detected. Therefore, alternative test are urgently needed. Non-genotoxic carcinogens, however, act through different modes of action, which complicates the development of such an assay. The aim of this study was to investigate whether gene expression profiling in primary mouse hepatocytes can be used to distinguish different modes of action of non-genotoxic carcinogens.
2012-06-26 | GSE35058 | GEO
Project description:There is no accurate and well-validated short-term test for non-genotoxic carcinogens, necessitating an expensive two year rodent bioassay before a risk assessment can begin. We have developed a short-term in vivo rat assay that predicts whether non-genotoxic chemicals are likely to induce hepatic tumors based on transcript profiles in the liver. Using a large independent test set, assay accuracy was found to be superior to existing pathological and genomic markers. Comparison of the test chemical's signature profile to reference carcinogens of known mechanism can also identify a potential mode(s) of action, allowing an early assessment of human cancer risk. Guidelines for commercial use: http://www.iconixbiosciences.com/guidelineCommUse.pdf Keywords: dose response, time course, compound treatment Treatment of male Sprague-Dawley rats with 147 non-genotoxic compounds at various doses and durations, in biological triplicate, along with vehicle-matched control animals. Liver samples were assayed for gene expression. Hepatocarcinogenic and non-carcinogenic compounds were included. A classifier for carcinogenicity was built on a training set of 25 carcinogens and 75 noncarcinogens (randomly selected compounds, maximum tolerated dose, 5 day timepoints), and tested on the remaining 47 compounds at various timepoints. A total of 990 samples were hybridized to single-channel CodeLink RU1 arrays. Biological triplicates were combined with matched control samples to calculate log ratios.
2007-06-22 | E-GEOD-8251 | biostudies-arrayexpress
Project description:Background: Information on the carcinogenic potential of chemicals is only availably for High Production Volume products. There is however, a pressing need for alternative methods allowing for the chronic toxicity of substances, including carcinogenicity, to be detected earlier and more reliably. Here we applied advanced genomics to a cellular transformation assay to identify gene signatures useful for the prediction of risk for carcinogenicity. Methods: Genome wide gene expression analysis and qRT-PCR were applied to untransformed and transformed Balb/c 3T3 cells that exposed to 2, 4-diaminotoluene (DAT), benzo(a)pyrene (BaP), 2-Acetylaminoflourene (AAF) and 3-methycholanthrene (MCA) for 24h and 120h, at different concentrations, respectively. Furthermore, various bioinformatics tools were used to identify gene signatures predicting for the carcinogenic risk. Results: Bioinformatics analysis revealed distinct datasets for the individual chemicals tested while the number of significantly regulated genes increased with ascending treatment concentration of the cell cultures. Filtering of the data revealed a common gene signature that comprised of 13 genes whose regulation in cancer tissue has already been established. Strikingly, this gene signature was already identified prior to cell transformation therefore confirming the predictive power of this gene signature in identifying carcinogenic risks of chemicals. Comparison of fold changes determined by microarray analysis and qRT-PCR were in good agreement. Conclusion: Our data describes selective and commonly regulated carcinogenic pathways observed in an easy to use in vitro carcinogenicity assay. Here we defined a set of genes which can serve as a simply assay to predict the risk for carcinogenicity by use of an alternative in vitro testing strategy.
2010-10-02 | GSE22180 | GEO
Project description:The current test strategy for carcinogenicity consists initially of in vivo and in vitro genotoxicity tests. Non-genotoxic carcinogens do not directly induce DNA damage and, as such, go undetected under this test strategy. In a previous study we setup a comparison approach to categorize chemicals having similar modes of action, according to similarity in gene expression. In the current study we will investigate whether this comparison approach can be improved by omptimizing the concentration selection procedure and by testing a concentration range per chemical.
2016-12-23 | GSE53634 | GEO