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Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE36242: Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells (RNA-Seq) GSE36243: Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells (Affymetrix) Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Stan Gaj

PROVIDER: E-GEOD-36244 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene.

van Delft Joost J Gaj Stan S Lienhard Matthias M Albrecht Marcus W MW Kirpiy Alexander A Brauers Karen K Claessen Sandra S Lizarraga Daneida D Lehrach Hans H Herwig Ralf R Kleinjans Jos J

Toxicological sciences : an official journal of the Society of Toxicology 20120813 2

Whole-genome transcriptome measurements are pivotal for characterizing molecular mechanisms of chemicals and predicting toxic classes, such as genotoxicity and carcinogenicity, from in vitro and in vivo assays. In recent years, deep sequencing technologies have been developed that hold the promise of measuring the transcriptome in a more complete and unbiased manner than DNA microarrays. Here, we applied this RNA-seq technology for the characterization of the transcriptomic responses in HepG2 ce ...[more]

PMID: 22889811

Similar Datasets

Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells (RNA-Seq)

Project description:Whole-genome transcriptome measurements are pivotal for characterizing carcinogenic mechanisms of chemicals and predicting toxic classes, such as genotoxicity, from in vitro and in vivo assays. DNA microarrays have evolved as the gold standard for this purpose. In recent years deep sequencing technologies have been developed that hold the promise of measuring the transcriptome with RNA-seq in a more accurate and unbiased manner than microarrays. So far, however, few applications have been published that assess the performance of RNA-seq within a toxicogenomics context. Here, we applied RNA-seq for the characterization of the in vitro transcriptomic responses in HepG2 cells upon exposure to benzo[a]pyrene (BaP), a well-known DNA damaging carcinogen. We demonstrate the performance of RNA-seq with respect to the identification of differentially expressed genes and associated pathways, in comparison with microarray technology. RNA-seq data generates more complete and thus accurate data on differentially expressed genes and affected pathways than microarrays. Additionally, we highlight the potential of RNA-seq for characterizing mechanisms related to alternative splicing and thereby gathering new information. Exposure to BaP alters the isoform distribution for many genes, including regulators of cell death and DNA repair such as TP53, BCL2 and XPA, which are relevant for genotoxic responses. Finally, we demonstrate that RNA-seq enables to investigate allele-specific gene expression, although no changes for that could be observed. Our results provide evidence that RNA-seq is a powerful tool for toxicology which, compared to microarrays, is capable of adding valuable information at the transcriptome level for characterizing toxic effects caused by chemicals. Examination of 2 biological replicates at 2 different timepoints

2012-11-16 | E-GEOD-36242 | biostudies-arrayexpress

Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells (Affymetrix)

2012-11-16 | E-GEOD-36243 | biostudies-arrayexpress

ribo-depleted RNA-Seq of human HepG2 cells exposed to Benzo[a]pyrene for 6, 12, 18, 24, 36 and 48 hours

Project description:HepG2 cells (human liver hepatocarcinoma) were exposed for 6 different time points (6,12,18,24,36 and 48h) to Benzo[a]pyrene (BaP) in duplicate. Total RNAs were ribo-depleted and sequenced on an Illumina Hiseq2000 in pair-end 100 bp reads. One of the duplicates for BaP-treated sample at the 24 hour time point was found to have a minor fastq file integrity issue and was removed from this data set as a precaution.

2015-08-02 | E-MTAB-3292 | biostudies-arrayexpress

Cytochrome P450 Monooxygenase Mediated Metabolic Utilization of Benzo(a)pyrene by Fungi

Project description:Soil dwelling Aspergillus fungi possess the versatile metabolic capability to utilize complex organic compounds which are toxic to humans, yet the mechanisms they employ remain largely unknown. Benzo(a)pyrene is a common carcinogenic contaminant, posing a significant concern for human health. Here, we report that Aspergillus fungi can degrade benzo(a)pyrene effectively. In Aspergillus nidulans, exposure to benzo(a)pyrene results in transcriptomic and metabolic changes associated with cellular growth and energy generation, implying that the fungus utilizes benzo(a)pyrene as a food. Importantly, we identify and characterize the conserved bapA gene encoding a cytochrome P450 monooxygenase that exerts the first step in the degradation of benzo(a)pyrene. We further demonstrate that the fungal NF-κB-type global regulators VeA and VelB are required for benzo(a)pyrene degradation in A. nidulans, which occurs through expression control of bapA in response to nutrient limitation. Our study illuminates fundamental knowledge of fungal benzo(a)pyrene metabolism and provides novel insights into enhancing bioremediation potential.

2018-07-10 | GSE116804 | GEO

Dynamic liver transcriptome response of Xenopus tropicalis to benzo[a]pyrene

Project description:Chronological RNA-seq of comparison of liver from xenopus tropicalis exposed or not to benzo[a]pyrene (10ﾵg/L)

2014-08-18 | E-MTAB-2444 | biostudies-arrayexpress

Sub-chronic forestomach transcriptional response in adult male MutaTMMouse following oral exposure to benzo(a)pyrene

Project description:Benzo(a)pyrene is a well-established human carcinogen in humans and rodents. In the present study, we sought to determine the dose- and time-dependent changes in gene expression upon oral exposure to benzo(a)pyrene. Adult male MutaTMMouse were exposed to three doses of benzo(a)pyrene or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

2013-09-27 | GSE43438 | GEO

Acute hepatic transcriptional response in male mice following oral exposure to benzo(a)pyrene

Project description:Benzo(a)pyrene is a well-established human carcinogen in humans and rodents. In the present study, we sought to determine the dose- and time-dependent changes in gene expression upon oral exposure to benzo(a)pyrene. Adult male B6C3F1 mice were exposed to four doses of benzo(a)pyrene or vehicle control for three days and sacrificed 4 or 24 hours after the final exposure.

2015-07-01 | GSE43633 | GEO

benzo(a)pyrene_MCF7_HepG2

Project description:MCF-7 and HepG2 cells were exposed to a range of concentrations of benzo(a)pyrene or benzo(e)pyrene (0-5 uM) for up to 48 h and gene expression analysis performed. Keywords: dose response

2006-10-24 | GSE5894 | GEO

Transcription profiling by array of human HepG2 cells treated with false positive genotoxins, true genotoxins and non-genotoxins

Project description:In this study we aimed to identify the molecular pathways modified by the false positive genotoxins Quercetin, 8-Hydroxyquinoline and 17beta-Estradiol that may explain their in vitro genotoxic and their in vivo non-genotoxic effects, by combining in vitro transcriptomics with phenotypic data. The effects of the false positive genotoxins were compared to the effects of the true genotoxins Benzo[a]pyrene and Aflatoxin B1 and the non-genotoxins 2,3,7,8-Tetrachlorodibenzodioxin, Cyclosporin A and Ampicillin C. <br><br>A custom CDF for use with the processed data file is available on the FTP site for this experiment.

2011-01-01 | E-MEXP-2574 | biostudies-arrayexpress

Modulating the Response to Benzo[a]pyrene when CYP1A1 and CYP1B1 are Knocked Down

Project description:Benzo[a]pyrene is a Group 1 carcinogen. It undergoes metabolism in the liver through CYP1A1 and CYP1B1 enzymes. This study was conducted to investigate the response to benzo[a]pyrene in the liver when these enzymes are knocked down.

2024-01-03 | GSE252339 | GEO

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