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Transcriptomic profiles of zebrafish embryos exposed to silver (nanoparticles, bulk and ions) using HT-SuperSAGE in a Illumina GA2 platform

ABSTRACT: Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity, however, remain unclear. We examined the effects of exposure to silver in nano-, bulk- and ionic forms on zebrafish embryos (Danio rerio) using a Next Generation Sequencing approach in an Illumina platform (High-Throughput SuperSAGE). Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down-regulation of this pathway at 24h of exposure, but with a recovery at 48h. This finding was consistent with a dose-dependent decrease in oxygen consumption at 24h, but not at 48h, following exposure to silver ions. Overall, our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms.

ORGANISM(S): Danio rerio

PROVIDER: GSE38125 | GEO | 2013/06/17

SECONDARY ACCESSION(S): PRJNA167302

REPOSITORIES: GEO

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Transcriptomic profiles of zebrafish embryos exposed to silver (nanoparticles, bulk and ions) using HT-SuperSAGE in a Illumina GA2 platform

Project description:Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity, however, remain unclear. We examined the effects of exposure to silver in nano-, bulk- and ionic forms on zebrafish embryos (Danio rerio) using a Next Generation Sequencing approach in an Illumina platform (High-Throughput SuperSAGE). Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down-regulation of this pathway at 24h of exposure, but with a recovery at 48h. This finding was consistent with a dose-dependent decrease in oxygen consumption at 24h, but not at 48h, following exposure to silver ions. Overall, our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. mRNA profiles of whole zebrafish embryos at 24 and 48 hours post-fertilisation (hpf) exposed to silver in nano, bulk and ionic forms were generated by deep sequencing using HT-SuperSAGE (Illumina GA2).

2013-06-17 | E-GEOD-38125 | biostudies-arrayexpress

RNAseq of human epithelial lung carcinoma cell line A549 exposed to ceria, silver or zinc ions, micron-sized particles or nanoparticles

Project description:The toxicity of silver and zinc oxide nanoparticles is hypothesised to be mediated by dissolved metal ions and cerium dioxide nanoparticles (CeO2 NPs) are hypothesised to induce toxicity specifically by oxidative stress dependant on their surface redox state. To test these hypotheses, RNAseq was applied to characterise the molecular responses of cells to metal nanoparticle and metal ion exposures. The human epithelial lung carcinoma cell line A549 was exposed to different CeO2 NPs with different surface charges, micron-sized and nano-sized silver particles and silver ions, micron-sized and nano-sized zinc oxide particles and zinc ions, or control conditions, for 1 hour, 6 hours and 24 hours. Concentrations were the lower of either EC20 or 128 micrograms/mL. Transcriptional responses were characterised by RNAseq transcriptomics using an Illumina HiSeq2500 .

2018-02-01 | E-MTAB-5734 | biostudies-arrayexpress

Mechanisms of response to silver nanoparticles Enchytraeus albidus (Oligochaeta): survival, reproduction and gene expression profile

Project description:Due to its antimicrobial activity, silver nanoparticles (Ag-NPs) are among the most used NPs worldwide, yet little information is available regarding their effects, particularly in soil dwelling organisms. Enchytraeids (Oligochaeta) are important members of the soil fauna which actively contribute to the acceleration of organic matter decomposition and nutrient recycling processes. Hence, for hazard and risk assessment it is important to provide toxicity data for these organisms and to understand more in regard to the mode of action of Ag-NPs within organism. To study this we conducted toxicity experiments using the OECD standard guideline, testing Ag-NPs and AgNO3, having assessed survival, reproduction and differential gene expression. Population toxicity responses were assessed showing higher toxicity for the AgNO3. In an attempt to understand the mode of action we performed transcription profiling using the microarray. Gene expression profile of Enchytraeus albidus was analysed after 2 days of exposure to 100 and 200 mg/kg of two silver forms (nanoparticles and salt_silver nitrate) in OECD soil. Three biological replicates per test treatment and control (clean OECD soil) were used.

2013-05-22 | E-GEOD-42431 | biostudies-arrayexpress

Investigating the Mechanisms of Silver Nanoparticle Toxicity in Daphnia magna: A Multi-Omics Approach

Project description:Silver nanoparticles (AgNPs), one of the most common nanomaterials in use today, have been shown to enter the aquatic environment from use of commercially obtained products. Although acute toxicity has been shown in vitro and in vivo, there is still a great deal of uncertainty surrounding the molecular mechanism of AgNP-induced toxicity. Much of the current literature centres on the question of whether toxicity is induced by the AgNPs themselves or by ionic silver released from the nanoparticle surface. Here, I present research investigating AgNP toxicity to Daphnia magna, a keystone species of freshwater ecosystems the world over, using a multi-omics platform of transcriptomics and metabolomics techniques. Initially, the AgNPs were fully characterised and the exposure conditions optimised to accurately assess the impact of AgNP exposure to D. magna. This allowed for the design of sub-lethal AgNP exposures that had been fully controlled for the fraction of dissolved silver ions. Secondly, using this multi-omics platform, the role of Ag+ ions in AgNP toxicity to D. magna was determined. Finally a metabolic pathway perturbed by AgNP exposure was identified, as well as two constituent metabolites of key importance. Overall, this research advances the mechanistic understanding of AgNP toxicity to aquatic organisms, and further highlights the need for greater consideration of the nanoscale in regulative legislature.

2017-05-08 | MTBLS260 | MetaboLights

Waterborne exposure of adult zebrafish to silver nanoparticles and ionic silver results in silver accumulation and effects at cellular and molecular levels

Project description:Effects of silver nanoparticles (Ag NPs) on freshwater species have been reported in several studies, but there is not information on the potential long-term consequences of a previous exposure. In this work, we investigated the long-term effects of maltose-coated Ag NPs (20 nm) and of ionic silver (10 µg/L) after 21 days of exposure and at 6 months post-exposure (mpe) in adult zebrafish. Exposure resulted in significant silver accumulation in the whole body of fish exposed to ionic silver, but not in those exposed to Ag NPs. However, autometallography revealed metal accumulation in the liver and intestine of fish treated with the two silver forms and especially in the intestine of fish exposed to Ag NPs. X-ray microanalysis showed the presence of silver in gills, liver and intestine and of Ag NPs in gill and liver cells. Inflammation and hyperplasia were evident in the gills after both treatments and these histopathological conditions remained at 6 mpe. According to the hepatic transcriptome analysis, at 3 days ionic silver regulated a larger number of transcripts (410) than Ag NPs (129), while at 21 days Ag NPs provoked a stronger effect (799 vs 165 regulated sequences). Gene ontology terms such as “metabolic processes” and “response to stimulus” appeared enriched after all treatments, while “immune system” or “reproductive processes” were specifically enriched after the exposure to Ag NPs. This suggests that the toxicity of Ag NPs may not be solely related to the release of Ag ions, but also to the NP form. No evident effects were found on protein oxidation or on hepatocyte lysosomal membrane stability during exposure, but effects recorded on liver lysosomes and persistent damage on gill tissue at 6 mpe could indicate potential for long-term effects in exposed fish.

2018-06-12 | GSE89653 | GEO

Changes in Arabidopsis thaliana gene expression in response to silver nanoparticles and silver ions

Project description:The release of silver nanoparticles (SNPs) in the environment has raised concerns about their effects on living organisms, including plants. In this study, changes in gene expression in Arabidopsis thaliana exposed to SNPs and silver ions (Ag+) were analyzed using Affymetrix expression microarrays. Exposure to 5 mg SNPs L-1 (20 nm) for 10 days resulted in up-regulation of 286 genes and down-regulation of 81 genes by reference to non-exposed plants. Exposure to 5 mg Ag+ L-1 for 10 days resulted in up-regulation of 84 genes and down-regulation of 53 genes by reference to non-exposed plants. Many genes differentially expressed by SNPs and Ag+ were found to be involved in plant response to various stresses: up-regulated genes were primarily associated with response to metals and oxidative stress (e.g., vacuolar cation/proton exchanger, superoxide dismutase, cytochrome P-450-dependent oxidase, and peroxidase), while down-regulated genes were more associated with response to pathogens and hormonal stimuli (e.g., auxin-regulated gene involved in organ size (ARGOS), ethylene signaling pathway, and systemic acquired resistance (SAR) against fungi and bacteria). A significant overlap was observed between genes differentially expressed in response to SNPs and Ag+ (13% and 21% of total up- and down-regulated genes, respectively), suggesting that SNP-induced stress originates partly from silver toxicity and partly from nanoparticle-specific effects. Three highly up-regulated genes in the presence of SNPs, but not Ag+, belong to the thalianol biosynthetic pathway, which is thought to be involved in plant defense system. Results from this study provide insights into the molecular mechanisms of plant response to SNPs and Ag+.

2014-02-12 | E-MEXP-3950 | biostudies-arrayexpress

The effect of CuO nanoparticles on gene expression patterns in Daphnia magna

Project description:There is still a lot of contradiction on whether metal ions are solely responsible for the observed the toxicity of ZnO and CuO nanoparticles to aquatic species. While most tests have studied nanoparticle effects at organismal levels (e.g. mortality, reproduction), effects at suborganismal levels may clarify the role of metal ions, nanoparticles and nanoparticle aggregates. In this study, the effect of ZnO, CuO nanoparticles and zinc, copper salts was tested on the gene expression levels in Daphnia magna. D. magna was exposed during 96 hours to 10% immobilization concentrations of all chemicals, after which daphnids were sampled for a differential gene expression analysis using microarray. When comparing the nanoparticle exposed daphnids (ZnO or CuO) to the metal salt exposed daphnids (zinc or copper salt), the microarray results showed no significantly differentially expressed genes. These results indicate that the toxicity of the tested ZnO and CuO nanoparticles to D. magna caused is solely caused by toxic metal ions. 4 replicate exposures of ZnO nanoparticles, ZnCl2, Blank (for Zn); 4 replicate exposures of CuO nanoparticles, CuCl2.2H2O, Blank (for Cu); Individual reference design with swapped dyes for zinc (e.g. ZnO-REFZn; REFZn-bl) and copper exposure (e.g. CuO-REFCu; REFCu-bl); Zinc reference sample is a mixture of equal aliquots of ZnO nanoparticle, ZnCl2 and blank; Copper reference sample is a mixture of equal aliquots of CuO nanoparticle, CuCl2.2H2O and blank

2014-03-01 | E-GEOD-54738 | biostudies-arrayexpress

The effect of ZnO nanoparticles on gene expression patterns in Daphnia magna

2014-03-01 | E-GEOD-54736 | biostudies-arrayexpress

Assessing the exposure to nanosilver and silver nitrate on fathead minnow gill gene expression and mucus production

Project description:Silver exposure is toxic to fish due to disturbances of normal gill function. A proposed toxicity mechanism of silver nanoparticles (AgNP) is derived from the release of silver ions, similar to silver nitrate (AgNO3). However, some datasets support the fact that AgNP can have unique toxic effects that are mediated at the gill. To determine if differences between AgNO3 and AgNP toxicities exist, fathead minnows were exposed to 20 nm PVP- or citrate-coated silver nanoparticles (PVP-AgNP; citrate-AgNP) at the nominal concentration of 200 μg/L or AgNO3 at nominal 6 μg/L for 96 hr. This nominal concentration was applied to approximate the dissolved fraction of Ag in the AgNP suspensions. Mucus production in the water was measured. While mucus production was initially significantly increased in the first 4 h of exposure in all silver treatments compared to control, a decrease in mucus production was observed following 24-96 h of exposure. To determine which genes/pathways are driving this shift in mucus production, gills were dissected and microarray analysis was performed. Hierarchal clustering of differentially expressed genes revealed that all samples distinctly clustered by treatment. There were 109 differentially expressed genes shared among all Ag treatments compared to controls. However, there were 185, 423, and 615 differentially expressed genes unique to AgNO3, PVP-AgNP, and citrate-AgNP, relative to control. While functional analysis indicated several common enriched pathways, such as aryl hydrocarbon receptor signaling, this analysis also indicated some unique pathways between nanosilver and AgNO3. Our results show that AgNO3, PVP-AgNP, and citrate-AgNP exposure affected mucus production in fish gills and also lead to common and unique transcriptional changes.

2015-06-01 | GSE64259 | GEO

Toxicogenomic Responses of Nanotoxicity in Daphnia magna Exposed to Silver Nitrate and Coated Silver Nanoparticles

Project description:Applications for silver nanomaterials in consumer products are rapidly expanding, creating an urgent need for toxicological examination of the exposure potential and ecological effects of silver nanoparticles (AgNPs). The integration of genomic techniques into environmental toxicology has presented new avenues to develop exposure biomarkers and investigate the mode of toxicity of novel chemicals. In the present study we used a 15k oligonucleotide microarray for Daphnia magna, a freshwater crustacean and common indicator species for toxicity, to differentiate between particle specific and ionic silver toxicity and to develop exposure biomarkers for citrate-coated and PVP-coated AgNPs. Gene expression profiles revealed that AgNO3 and AgNPs have distinct expression profiles suggesting different modes of toxicity. However, the gene expression profiles of the different coated AgNPs were similar revealing similarities in the cellular effects of these two particles. Major biological processes disrupted by the AgNPs include protein metabolism and signal transduction. In contrast, AgNO3 caused a downregulation of developmental processes, particularly in sensory development. Metal responsive and DNA damage repair genes were induced by the PVP AgNPs, but not the other treatments. In addition, two specific biomarkers were developed for the environmental detection of PVP AgNPs; although further verification under different environmental conditions is needed. We exposed Daphnia magna to the 1/10 LC50 and LC25 of citrate coated and PVP-coated Ag nanoparticles and Ag+ as AgNO3 for 24-h. For each exposure condition, we performed 6 replicate exposures with 5 individuals in each. All exposures were compared to a unexposed laboratory control.

2012-08-04 | E-GEOD-35150 | biostudies-arrayexpress

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