Exposure to the heavy metal lead induces DNA copy number alterations in zebrafish cells
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PROVIDER: PRJNA628546 | ENA |
REPOSITORIES: ENA
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Project description:DNA copy number variants (CNVs) are associated with the development of complex neurological diseases and disorders including autism spectrum disorder, schizophrenia, Alzheimer’s disease, and Parkinson’s disease. Exposure to multiple environmental chemicals including various heavy metals is suggested as a risk factor in these neurological diseases and disorders, but few studies have addressed if heavy metal exposure can result in spontaneous DNA copy number changes as a genetic mechanism contributing to these disease outcomes. In this study to further investigate the relationship between heavy metal exposure and spontaneous copy number alterations (CNAs), zebrafish fibroblast cells were exposed to the neurotoxicant lead (Pb). A crystal violet assay was first used to determine exposure concentrations with greater than 80% cell confluency. Then a zebrafish-specific array comparative genomic hybridization (CGH) platform was used to detect CNAs following a 72 hour Pb exposure (0.24, 2.4, or 24 μM). The Pb exposure resulted in 72 CNA amplifications ranging in size from 5 to 329 kb. No deletions were detected. CNAs resulted in 15 copy number alteration regions (CNARs), leaving 7 singlet CNAs. Two of the singlets were within high repeat genomic locations. The number of CNAs tended to increase in a concentration dependent manner. Several CNARs encompassed genes previously reported to have altered expression with Pb exposure, suggesting a mechanistic link. In addition, almost all genes are associated within a molecular network with the amyloid precursor protein (APP). Overall, these findings show that Pb exposure results in spontaneous CNAs that could serve as a mechanism driving adverse health outcomes associated with Pb toxicity including neurological disease pathogenesis for further study.
2020-12-01 | GSE149382 | GEO
Project description:Heavy metals are essential integral parts of cells and environmental toxicants, whose deregulation is associated with severe cellular dysfunction and various diseases. The Hippo pathway plays a critical role in organ size control and cancer development. In this study, we use RNA-Seq to investigate the role of the Hippo pathway in regulating heavy metal response gene transcription. Specifically, the difference of transcriptional profiles between the wild-type and the Hippo pathway kinases LATS1/2-deficient HEK293A cells was examined under control- and heavy metals zinc and cadimuim treated-conditions.
2021-10-02 | GSE163156 | GEO
Project description:LATS regulates heavy metal response
| PRJNA685123 | ENA
Project description:Heavy metal contaminated soil Genome sequencing and assembly
| PRJNA663293 | ENA
Project description:Background: The high number of heavy metal resistance genes in the soil bacterium Cupriavidus metallidurans CH34 makes it an interesting model organism to study microbial responses to heavy metals. Results: In this study the transcriptional response of this bacterium was measured after challenging it to a wide range of sub-lethal concentrations of various essential or toxic metals. Considering the global transcriptional responses for each challenge as well as by identifying the overlap in upregulated genes between different metal responses, the sixteen metals could be clustered in three different groups. Additionally, next to the assessment of the transcriptional response of already known metal resistance genes, new metal response gene clusters were identified. The majority of the metal response loci showed similar expression profiles when cells were exposed to different metals, suggesting complex cross-talk at transcriptional level between the different metal responses. The highly redundant nature of these metal resistant regions – illustrated by the large number of paralogous genes – combined with the phylogenetic distribution of these metal response regions within evolutionary related and other metal resistant bacteria, provides important insights on the recent evolution of this naturally soil dwelling bacterium towards a highly metal-resistant strain found in harsh and anthropogenic environments. Conclusions: The metal-resistant soil bacterium Cupriavidus metallidurans CH34 displays myriads of gene expression patterns when exposed to a wide range of heavy metals at non-lethal concentrations. The interplay between the different gene expression clusters points towards a complex cross-regulated regulatory network governing heavy metal resistance in C. metallidurans CH34. Keywords: Cupriavidus metallidurans CH34, transcriptional regulation, heavy metal resistance
2011-06-28 | GSE23876 | GEO
Project description:Heavy metal contaminated soil viral metagenome Raw sequence reads
| PRJNA793839 | ENA
Project description:Background: The high number of heavy metal resistance genes in the soil bacterium Cupriavidus metallidurans CH34 makes it an interesting model organism to study microbial responses to heavy metals. Results: In this study the transcriptional response of this bacterium was measured after challenging it to a wide range of sub-lethal concentrations of various essential or toxic metals. Considering the global transcriptional responses for each challenge as well as by identifying the overlap in upregulated genes between different metal responses, the sixteen metals could be clustered in three different groups. Additionally, next to the assessment of the transcriptional response of already known metal resistance genes, new metal response gene clusters were identified. The majority of the metal response loci showed similar expression profiles when cells were exposed to different metals, suggesting complex cross-talk at transcriptional level between the different metal responses. The highly redundant nature of these metal resistant regions – illustrated by the large number of paralogous genes – combined with the phylogenetic distribution of these metal response regions within evolutionary related and other metal resistant bacteria, provides important insights on the recent evolution of this naturally soil dwelling bacterium towards a highly metal-resistant strain found in harsh and anthropogenic environments. Conclusions: The metal-resistant soil bacterium Cupriavidus metallidurans CH34 displays myriads of gene expression patterns when exposed to a wide range of heavy metals at non-lethal concentrations. The interplay between the different gene expression clusters points towards a complex cross-regulated regulatory network governing heavy metal resistance in C. metallidurans CH34. Keywords: Cupriavidus metallidurans CH34, transcriptional regulation, heavy metal resistance Two-condition experiments. Comparing samples after induction with heavy metals versus non-induced samples. Biological duplicate or triplicate. Each array contains 3 or 4 technical replicates.
2011-06-28 | E-GEOD-23876 | biostudies-arrayexpress
Project description:microplastic and heavy-metal contaminated soils Raw sequence reads
| PRJNA1012747 | ENA
Project description:Classical ecotoxicological test and high-throughput molecular tools (microarray) were conducted on C. elegans to assess the effectiveness and ecosafety of a nanoremediation strategy applied to a highly polluted soil environment with heavy metals (HMs). We stablished a profiled gene expression in C. elegans exposed to the polluted soil, treated and untreated with nZVI. The results obtained showed that the percentage of differentially expressed genes decreased with the exposure time to nZVI. The expression profile of genes associated with stress response, metal toxicity, proteolysis, immune response, and cuticle development resulted affected. At short term, when a more effective HMs immobilization has occurred genes related to specific heavy metal detoxification mechanisms or to response to metal stress, were down regulated. After longer exposure time, we found decreased effectiveness of nZVI and increased HMs toxicity, whereas the transcriptional oxidative and metal-induced responses were attenuated.
2022-01-24 | GSE145995 | GEO
Project description:Transcriptional profile of stress in fission yeast (S. pombe) cells. Five different types of stress were employed on wild type and mutant cells (sty1 and atf1 knock-out cells). The 5 stresses were heat, and four types of compound: heavy metal, oxidation, alkylation and osmosis.
2004-10-31 | E-MEXP-29 | biostudies-arrayexpress