Classifying polycyclic aromatic hydrocarbons by carcinogenic potency using in vitro biosignatures
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA656840 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12441064_1.fastq.gz | Fastqsanger.gz | |||
| SRR12441064_2.fastq.gz | Fastqsanger.gz | |||
| SRR12441065_1.fastq.gz | Fastqsanger.gz | |||
| SRR12441065_2.fastq.gz | Fastqsanger.gz | |||
| SRR12441066_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 58 |
Similar Datasets
Project description:In this study, we compare genomic signature safter treatment ofprimary human bronchial epithelial cells (HBEC) cultured in 3D with polycyclic aromatic hydrocarbons (PAHs) and identify genesets predictive of cancer risk.
2020-10-28 | GSE156147 | GEO
Project description:Polycyclic aromatic hydrocarbons degraders Raw sequence reads
| PRJNA590550 | ENA
Project description:One of the most difficult challenges for risk assessment is evaluation of chemicals that predominately co-occur in mixtures like polycyclic aromatic hydrocarbons (PAHs). We previously developed a classification model in which systems biology data collected from mice short-term after chemical exposure accurately predict tumor outcome. The present study demonstrates translation of this approach into a human in vitro model in which chemical-specific bioactivity profiles from 3D human bronchial epithelial cells (HBEC) classify PAHs by carcinogenic potency. Gene expression profiles were analyzed from HBEC exposed to carcinogenic and non-carcinogenic PAHs and classification accuracies were identified for individual pathway-based gene sets. Posterior probabilities of best performing gene sets were combined via Bayesian integration resulting in a classifier with four gene sets, including aryl hydrocarbon receptor signaling, regulation of epithelial mesenchymal transition, regulation of angiogenesis, and cell cycle G2-M. In addition, transcriptional benchmark dose modeling of benzo[a]pyrene (BAP) showed that the most sensitive gene sets to BAP regulation were largely dissimilar from those that best classified PAH carcinogenicity challenging current assumptions that BAP carcinogenicity (and subsequent mode of action) is reflective of overall PAH carcinogenicity. These results illustrate utility of using systems toxicology approaches to analyze global gene expression towards carcinogenic hazard assessment.
| S-EPMC7572825 | biostudies-literature
Project description:Polycyclic aromatic hydrocarbons-Polluted Soil Metagenome
| PRJNA656884 | ENA
Project description:Assessing the potential carcinogenicity of human toxins represents an ongoing challenge. Chronic rodent bioassays predict human cancer risk with limited reliability, and are expensive and time-consuming. To identify alternative prediction methods, we evaluated a transcriptomics-based human in vitro model to classify carcinogens by their modes of action. The aim of this study was to determine the transcriptomic response and identify specific molecular signatures of polycyclic aromatic hydrocarbons (PAHs), which can be used as predictors of carcinogenicity of environmental toxins in human in vitro systems. We found that characteristic molecular signatures facilitate identification and prediction of carcinogens.
2012-04-18 | GSE37326 | GEO
Project description:Polycyclic aromatic hydrocarbons (PAHs) that are bound to particulate matter can have adverse effects on human health. Particle size plays an important role in assessing health risks. The aim of this study was to compare concentrations of PAHs bound to particle fractions PM10, PM2.5, and PM₁, as well as to estimate their carcinogenic potency and relative contributions of the individual PAHs to the carcinogenic potency in relation to the size of the particle. Measurements of ten PAHs were carried out in 2014 at an urban location in the northern part of Zagreb, Croatia. 24-h samples of the PM10, PM2.5, and PM₁ particle fraction were collected over forty days per season. Carcinogenic potency of PAHs was estimated by calculating benzo(a)pyrene equivalent concentrations while using three different toxic equivalence factor (TEF) schemes. The total carcinogenic potency (TCP) and percentage contributions differed significantly depending on the TEF scheme used. The lowest PAH mass concentrations and TCPs were in summer and the highest in winter. The contributions of individual PAHs to the sum of PAH mass concentrations remained similar in all fractions and seasons, while in fractions PM10⁻2.5 and PM2.5⁻1 they varied significantly. Road traffic represented the important source of PAHs in all fractions and throughout all seasons. Other sources (wood and biomass burning, petroleum combustion) were also present, especially during winter as a consequence of household heating. The highest contribution to the TCP came from benzo(a)pyrene, dibenzo(ah)antrachene, indeno(1,2,3,cd)pyrene, and benzo(b)fluoranthene (together between 87% and 96%) in all fractions and seasons. In all cases, BaP showed the highest contribution to the TCP regardless relatively low contributions to the mass of total PAHs and it can be considered as a good representative for assessing the carcinogenicity of the PAH mixture. When comparing the TCP of PAHs in PM10 and PM2.5 fractions, it was found that about 21⁻26% of carcinogenic potency of the PAH mixture belonged to the PM2.5 fraction. Comparison of TCP in PM2.5 and PM₁ showed that about 86% of carcinogenic potency belonged to the PM₁ fraction, regardless of the TEF scheme used.
| S-EPMC6266409 | biostudies-literature
Project description:Polycyclic aromatic hydrocarbons (PAHs) are a class of hundreds of structurally similar chemicals ubiquitously present in our environment. They are created during the incomplete combustion of organic materials, such as oil, wood, tobacco, and charbroiled meat. As such, human exposure to mixtures of PAHs can occur through consumption of PAH-containing foods and water, inhalation of polluted air, or dermal contact. Several PAHs have been classified as carcinogenic to humans or probably carcinogenic to humans by the International Agency for Research on Cancer. The mice in this study were exposed to a mixture of 8 PAHs, benzo(a)pyrene, benz(a)anthracene, benzo(b)fluoranthene, benzo(ghi)perylene, benzo(k)fluoranthene, chrysene, dibenz(ah)anthracene, and indeno(123,cd)pyrene. In the present study, we sought to determine the dose-dependent changes in gene expression upon oral exposure to this PAH mixture in the lung tissue. Adult male MutaTMMouse were exposed to three doses of the mixture of 8 PAHs or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.
2017-01-01 | GSE87689 | GEO
Project description:Assessing the potential carcinogenicity of human toxins represents an ongoing challenge. Chronic rodent bioassays predict human cancer risk with limited reliability, and are expensive and time-consuming. To identify alternative prediction methods, we evaluated a transcriptomics-based human in vitro model to classify carcinogens by their modes of action. The aim of this study was to determine the transcriptomic response and identify specific molecular signatures of polycyclic aromatic hydrocarbons (PAHs), which can be used as predictors of carcinogenicity of environmental toxins in human in vitro systems. We found that characteristic molecular signatures facilitate identification and prediction of carcinogens. To evaluate the change in gene expression levels, human hepatocellular carcinoma (HepG2) cells were exposed to nine different PAHs (benzo[a]pyrene, dibenzo[a,h]anthracene, 3-methylcholanthrene, naphthalene, chrysene, phenanthrene, benzo[a]anthracene, benzo[k]fluoranthene, and indeno[1,2,3-c,d]pyrene) for 48 h. Gene expression analysis was conducted using a 44K whole human genome microarray (Agilent Technologies, USA).
2012-04-17 | E-GEOD-37326 | biostudies-arrayexpress
Project description:It has been reported that polycyclic aromatic hydrocarbons (PAHs) act on calcified tissue and suppress osteoblastic activity in the scales of teleost fish. In the present study, the differentially-expressed genes in the zebrafish scales treated with benzo[c]phenanthrene (BcP), a kind of PAH, or its metabolite 3-hydroxybenzo[c]phenanthrene (3-OHBcP) were investigated using GeneChip® oligonucleotide microarrays.
2020-11-12 | GSE161253 | GEO
Project description:To gain deeper insight into the mechanism of toxicity, it is important to identify and characterize miRNAs profiles involved in responses to specific classes of toxicants in conjunction with their impact on gene expression levels. However, few reports have described the effects of toxicants on miRNA expression profiles. Taking into account the prominent role of miRNAs in cancer development, progression, cell cycle control, and proliferation-related processes, it is likely that miRNAs are involved in the toxic response induced by carcinogens. Polycyclic aromatic hydrocarbons (PAHs) are a well-characterized class of human carcinogens. In the present study, we documented the different expression profiles of miRNAs in environmental carcinogen-exposed HepG2 cells by miRNA microarray analysis.
2013-07-22 | GSE49068 | GEO