Using transcriptomics to evaluate thresholds in genotoxicity dose-response
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE74725 | GEO | 2016/12/31
SECONDARY ACCESSION(S): PRJNA301346
REPOSITORIES: GEO
Similar Datasets
Project description:In vitro gene expression signatures to predict toxicological responses can provide mechanistic context for human health risk assessment purposes. We previously developed the TGx-28.65 genomic biomarker from a database of gene expression profiles in human TK6 cells exposed to 28 well-known compounds, and it comprises 65 genes that can classify chemicals as DNA damaging or non-DNA damaging. In this study, we applied the TGx-28.65 genomic biomarker in parallel with the in vitro micronucleus (MN) assay to determine if two chemicals of regulatory interest at Health Canada, disperse orange (DO: the orange azo dye 3-[[4-[(4-Nitrophenyl)azo]phenyl]benzylamino]propanenitrile) and 1,2,4-benzenetriol (BT: a metabolite of benzene) are genotoxic or non-genotoxic. Both chemicals caused dose-dependent declines in relative survival (RS) and increases in apoptosis. A strong significant increase in micronucleus induction was observed for all concentrations of BT; the top two concentrations of DO also caused a statistically significant increase in MN, but these increases were less than 2-fold above controls. TGx-28.65 analysis classified BT as genotoxic at all three concentrations and DO as genotoxic at the mid and high concentrations. Thus, although DO only induces a small increase in MN, this response is sufficient to induce a cellular DNA damage response that is likely relevant for risk assessment. Benchmark dose modeling revealed that BT is much more potent than DO; the BT benchmark dose for MN induction was similar to that of benzo[a]pyrene, (BaP: a genotoxic carcinogen), which was used as a positive control. The results strongly suggest that follow-up work is required to assess whether DO and BT are also genotoxic in vivo. This is particularly important for DO, which may require metabolic activation by bacterial gut flora to fully induce its genotoxic potential. Our previously published data and this proof of concept study suggest that the TGx-28.65 genomic biomarker has the potential to add significant value to existing approaches used to assess genotoxicity.
2017-10-16 | GSE95188 | GEO
Project description:In vitro gene expression signatures to predict toxicological responses can provide mechanistic context for human health risk assessment purposes. We previously developed the TGx-28.65 genomic biomarker from a database of gene expression profiles in human TK6 cells exposed to 28 well-known compounds, and it comprises 65 genes that can classify chemicals as DNA damaging or non-DNA damaging. In this study, we applied the TGx-28.65 genomic biomarker in parallel with the in vitro micronucleus (MN) assay to determine if two chemicals of regulatory interest at Health Canada, disperse orange (DO: the orange azo dye 3-[[4-[(4-Nitrophenyl)azo]phenyl]benzylamino]propanenitrile) and 1,2,4-benzenetriol (BT: a metabolite of benzene) are genotoxic or non-genotoxic. Both chemicals caused dose-dependent declines in relative survival (RS) and increases in apoptosis. A strong significant increase in micronucleus induction was observed for all concentrations of BT; the top two concentrations of DO also caused a statistically significant increase in MN, but these increases were less than 2-fold above controls. TGx-28.65 analysis classified BT as genotoxic at all three concentrations and DO as genotoxic at the mid and high concentrations. Thus, although DO only induces a small increase in MN, this response is sufficient to induce a cellular DNA damage response that is likely relevant for risk assessment. Benchmark dose modeling revealed that BT is much more potent than DO; the BT benchmark dose for MN induction was similar to that of benzo[a]pyrene, (BaP: a genotoxic carcinogen), which was used as a positive control. The results strongly suggest that follow-up work is required to assess whether DO and BT are also genotoxic in vivo. This is particularly important for DO, which may require metabolic activation by bacterial gut flora to fully induce its genotoxic potential. Our previously published data and this proof of concept study suggest that the TGx-28.65 genomic biomarker has the potential to add significant value to existing approaches used to assess genotoxicity.
2017-10-16 | GSE95187 | GEO
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2011-11-01 | E-MTAB-810 | biostudies-arrayexpress
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
2007-06-23 | GSE8251 | 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: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:miRNAs are post-transcriptional repressors with wide variation in cellular abundance across cell types and disease states. Yet, the transcriptomic and biological impact of altering miRNA levels (rather than binary gain or loss) has not been systematically investigated. By genetic combination, we generated an allelic series of mice expressing varying levels of miR-218, a motor neuron-specific miRNA associated with amyotrophic lateral sclerosis (ALS). Modulation of miR-218 dose causes threshold-like neuromuscular synaptogenesis and mouse viability phenotypes and revealed heterogenous dose-response curves of target mRNA repression. A dose-response network analyses unmasked a specific regulon exhibiting an inflection point in repression concomitant with the emergence of motor phenotypes. Furthermore, we find that miR-218 indirectly activates a coherent peripheral neuronal genetic signature and that the magnitude of miR-218 mediated effects varies in distinct motor subpopulations. This work reveals miRNA dose as a potent, non-linear modulator of in vivo mRNA target selection, suggesting how cellular dysfunction might abruptly arise when miRNA levels fall below a critical threshold. For the data uploaded here, motor neurons carrying an Hb9:gfp reporter were FACS isolated based upon GFP expression and used for either bulk or single cell RNA sequencing (10x genomics). Motor neurons were either mouse embryonic stem cell derived motor neurons (ESMNs) or mouse motor neurons from developmental stage E12. ESMN samples carry unique mutations of the miR-218-2 promoter of distinct sizes, or are wild type. E12 motor neurons carry combinations of mutations to either miR-218-1 or miR-218-2 or the promoter for miR-218-2. For single cell RNA sequencing, we have WT and miR-218 double knockout (DKO) motor neurons in duplicate. We also sequenced 4 samples of dorsal root ganglia from E12 mice (DRG1-4).
2021-08-27 | E-MTAB-10571 | biostudies-arrayexpress
Project description:In vitro toxicogenomics signatures to predict mode of action can facilitate chemical screening. We recently demonstrated the use of the TGx-28.65 genomic biomarker (representing: toxicogenomics (TGx), developed using a 28 chemical training set, and comprising 65 genes) in classifying agents as genotoxic (DNA damaging) and non-genotoxic in human lymphoblastoid TK6 cells. Because TK6 cells do not possess cytochrome P450 activity, we confirmed accurate classification in cells co-exposed to 1% 5,6 benzoflavone/phenobarbital-induced rat liver S9 for metabolic activation. However, chemicals may require different types of S9 for activation. Here we conducted experiments in TK6 cells exposed to chemicals in the presence of 2% or 10% Aroclor-induced, or 5% ethanol-induced rat liver S9 to expand TGx-28.65 biomarker application. Gene expression profiles were produced 3-4 hr following a 4 hr co-exposure of TK cells to test chemicals (seven genotoxic and two non-genotoxic, three concentrations, and concurrent solvent controls) and S9. Relative survival and micronucleus frequency was assessed by flow cytometry in cells 20 hr after the exposure. We found that genotoxicity/non-genotoxicity could be accurately predicted for the test compounds using the different S9s. One technical replicate of cells co-treated with dexamethasone and 10% Aroclor-induced S9 was falsely predicted as genotoxic, suggesting caution in using high concentrations of S9. TGx-28.65 correctly classified low concentrations of genotoxic chemicals (those not causing cytotoxicity or micronuclei) as genotoxic, demonstrating that it is a sensitive biomarker of genotoxicity. Overall, the work confirms that different S9s can be used in TK6 cells without impairing predictivity using the TGx-28.65 biomarker.
2016-08-25 | GSE74216 | GEO
Project description:In this study we examined transcriptional responses to 29 ToxCast chemicals in dose-response format. The chemicals were selected because in vitro transcriptional effects could be extrapolated to in vivo effects including liver cancer and steatosis incidences using in vitro to in vivo extrapolation.
2020-03-24 | GSE147379 | GEO