Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site
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ABSTRACT:
ORGANISM(S): Fundulus heteroclitus
PROVIDER: GSE25245 | GEO | 2011/06/06
SECONDARY ACCESSION(S): PRJNA134661
REPOSITORIES: GEO
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Project description:This study presents statistical analyses of gene expression in 5, 10 and 15 day post-fertilization (dpf) embryos of the teleost Fundulus heteroclitus treated with control vehicle (DMSO) or a potent non-ortho-PCB (PCB-126; 3,3’,4,4’,5-pentachlorobiphenyl). The embryos were from two populations: a clean, reference population (SC, Scorton Creek, MA USA) and a polluted Superfund population (N, New Bedford Harbor, MA USA). For each site, eggs from 8 females (~1100 total) were fertilized using minced testes from 5 males. After non-fertile eggs were culled, embryos were exposed to vehicle (DMSO; 0.1%) or PCB-126 (50 nM) in filtered seawater (salinity 25 part per thousand, 65 embros per 20 ml in glass petri dish) for 4 hr at 20º C. After exposure, the embryos were washed in filtered seawater and incubated at 20º C under a 14-h light, 10-h dark cycle. At 5-, 10-, and 15-dpf, embryos were collected as three pools of 20 embryos from each treatment group and flash frozen in liquid nitrogen and stored at -80º C until used for RNA isolation. A loop design was used for the microarray hybridizations where each sample is hybridized to 2 arrays using both Cy3 and Cy5 labeled fluorophores. We used three loops in which each loop consisted of Cy3- and Cy5-labeled embryo aRNAs from 12 samples: one sample from each population-treatment-time combination. Within a population-treatment-time, embryos were randomly assigned to one of the three loops. In total, 36 embryos were hybridized to 36 microarrays. The loops formed were SC5C→ SC5P → NBH5C→ NBH5P →SC10C→ SC10P→ NBH10C→ NBH10P → SC15C→ SC15P → NBH15C → NBH15P → SC5C, where each arrow represents a separate hybridization (array) with the biological sample at the base of the arrow labeled with Cy3 and the biological sample at the head of the arrow labeled with Cy5. SC represents the Scorton Creek, Sandwich, MA population (reference), NBH represents the New Bedford Harbor, MA population, C represents control dose (DMSO), P represents the PCB-126 dose, 5 represents 5 dpf, 10 represents 10 dpf and 15 represents 15 dpf.
2011-06-06 | E-GEOD-25245 | biostudies-arrayexpress
Project description:RNA from PCB-126 exposed 10 days post-fertilization (dpf) embryos were sequenced to characterize the chemical exposure response of killifish from a PCB-resistant population (NBH, New Bedford Harbor, MA, Superfund site) as compared to a reference (SC, Scorton Creek, MA) population. Since the genome sequence was not available, we also performed shot-gun sequencing of RNA from 1-15 dpf embryos sampled every day from both populations to serve as a transcriptome assembly. The results suggest that the NBH fish possess a gene regulatory defect that is not limited to a few target genes. We detected multiple genes that were differentially expressed in these two populations. This study was the first application of pyrosequencing technology to combine transcriptome characterization and gene expression profiling in a marine animal.
2016-09-09 | GSE86593 | GEO
Project description:Embryos from 8 populations of killifish, four with evolved tolerances, were exposed to PCB-126. Approximately 5 replicate embryos per treatment/control were sequenced. Desensitization of aryl hydrocarbon receptor signaling to PCB-126 is found in all four populations with evolved pollution tolerance, and represents the strongest transcriptional difference between tolerant and sensitive populations.
2020-08-20 | GSE156460 | GEO
Project description:(Abstract) Toxicogenomics has great potential for enhancing our understanding of environmental chemical toxicity, hopefully leading to better-informed human health risk assessments. This study employed toxicogenomic technology to reveal species differences in response to two prototypical aryl hydrocarbon receptor (AHR) agonists, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and the polychlorinated biphenyl (PCB) congener PCB 126. Dose responses of primary cultures of rat and human hepatocytes were determined using species-specific microarrays sharing over 4,000 gene orthologs. Forty-seven human and 79 rat genes satisfied dose response criteria for both chemicals and were subjected to further analysis including the calculation of EC50 and the relative potency (REP) of PCB 126 for each gene. Only 5 responsive orthologous genes were shared between the two species, yet the geometric mean of the REPs for all rat and human modeled responsive genes were 0.06 (95% Confidence Interval (CI); 0.03-0.1) and 0.002 (95% CI; 0.001-0.005), respectively, suggesting broad species differences in the initial events that follow AHR activation but precede toxicity. This indicates that there are species differences in both the specific genes that responded and the agonist potency and relative potency for those genes. This observed insensitivity of human cells to PCB 126 is consistent with more traditional measurements of AHR activation (i.e., CYP1A1 enzyme activity) and suggests that the species difference in PCB 126 sensitivity is likely due to certain aspects of AHR function. That a species divergence also exists in this expanded AHR-regulated gene repertoire is a novel finding and should help when extrapolating animal data to humans. Experiment Overall Design: Primary hepatocyte cultures, separated into 2 pools of 3 female Sprague Dawley rats each, were treated with vehicle (0.5% DMSO), TCDD (-14 to -6.5 log10 M) , or PCB 126 (-12 to -5 log10 M) for 48h. Total RNA was extracted and screened with RG-U34A microarrays for dose response.
2009-09-17 | E-GEOD-14554 | biostudies-arrayexpress
Project description:(Abstract) Toxicogenomics has great potential for enhancing our understanding of environmental chemical toxicity, hopefully leading to better-informed human health risk assessments. This study employed toxicogenomic technology to reveal species differences in response to two prototypical aryl hydrocarbon receptor (AHR) agonists, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and the polychlorinated biphenyl (PCB) congener PCB 126. Dose responses of primary cultures of rat and human hepatocytes were determined using species-specific microarrays sharing over 4,000 gene orthologs. Forty-seven human and 79 rat genes satisfied dose response criteria for both chemicals and were subjected to further analysis including the calculation of EC50 and the relative potency (REP) of PCB 126 for each gene. Only 5 responsive orthologous genes were shared between the two species, yet the geometric mean of the REPs for all rat and human modeled responsive genes were 0.06 (95% Confidence Interval (CI); 0.03-0.1) and 0.002 (95% CI; 0.001-0.005), respectively, suggesting broad species differences in the initial events that follow AHR activation but precede toxicity. This indicates that there are species differences in both the specific genes that responded and the agonist potency and relative potency for those genes. This observed insensitivity of human cells to PCB 126 is consistent with more traditional measurements of AHR activation (i.e., CYP1A1 enzyme activity) and suggests that the species difference in PCB 126 sensitivity is likely due to certain aspects of AHR function. That a species divergence also exists in this expanded AHR-regulated gene repertoire is a novel finding and should help when extrapolating animal data to humans. Experiment Overall Design: Primary hepatocyte cultures derived from 3 human donors were treated with vehicle (0.5% DMSO), TCDD (-14 to -6.5 log10 M) , or PCB 126 (-12 to -5 log10 M) for 48h. Total RNA was extracted and screened with HG-U133A microarrays for dose response.
2009-09-05 | E-GEOD-14553 | biostudies-arrayexpress
Project description:Polychlorinated biphenyls (PCBs) are persistent and ubiquitously distributed environmental pollutants. Based on their chemical structure, PCBs are classified into non-ortho substituted and ortho-substituted congeners. Non-ortho-substituted PCBs are structurally similar to dioxin or TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) and their mode of action and toxic effects are well established. In contrast, much less is known about the effects of ortho-substituted PCBs. Studies conducted so far have focused on tissue-specific effects but there is limited knowledge about the effects on the whole organism, particularly the sensitive developmental stages in vertebrates. Hence, in this study we investigated the effects of exposure to an environmentally relevant ortho-substituted PCB (2,2’,4,4’,5,5’-hexachlorobiphenyl; PCB153) on zebrafish embryos. We exposed zebrafish embryos to either DMSO (0.1%; solvent control) or three different concentrations of PCB153 (0.1, 1 and 10 μM) from 4 hours post-fertilization (hpf) to 120 hpf. At the end of the exposure, larvae were sampled for determining transcriptional changes (RNA sequencing) and the remaining embryos were maintained in contaminant-free environment. At 7 and 14 days post-fertilization (dpf), zebrafish larvae were assessed for locomotory behavior. We did not observe any overt phenotypes during the exposure period, but observed a spinal phenotype in the 10μM PCB153 treated group starting at 7 dpf. This phenotype was observed in a dose-dependent manner and majority of the embryos with this phenotype died by 14 dpf. RNA sequencing of 5 dpf larvae exposed to PCB153 also revealed dose-dependent changes in gene expression patterns. A total of 633, 2227, and 3378 differentially expressed genes were observed in 0.1, 1 and 10 μM PCB153 treated embryos, respectively. Among these, 301 genes were common to all treatment groups, and KEGG pathway analysis revealed enrichment of genes related to circadian rhythm, FOXO signaling and insulin resistance pathways. We are currently investigating the functions of genes that are uniquely altered by different PCB153 concentrations. Overall, these results suggest that developmental exposure to PCB153, a PCB congener highly prevalent in the environment, targets multiple physiological processes including photoperiod regulation and metabolism. [Funded by NIH P01ES021923 and NSF OCE-1314642].
2017-12-31 | GSE93310 | GEO
Project description:Using standard morphometric methods and gene expression profiling with a DNA microarray, we explored the impacts of high CO2 conditions on development of the sea urchin, Lytechinus pictus, a pelagic larvae that forms a calcium carbonate endoskeleton. Larvae were raised from fertilization to pluteus stage in seawater with elevated CO2 conditions based upon IPCC emissions scenarios B1 (540ppm CO2) and A1FI (970ppm CO2). Larval L. pictus were cultured in seawater treated with three different concentrations of CO2. We aerated water in culture chambers with air that had been mixed to different CO2 concentrations chosen from IPCC predictions of future atmospheric CO2 levels (28). The B1 scenario, one of the most optimistic, predicts a stabilization of atmospheric CO2 levels at ~540 ppm by 2100, and the A1F1 scenario, which, reflecting a more âbusiness as usualâ scenario, predicts atmospheric CO2 levels of ~970 ppm by 2100. Compressed air (~380 ppm CO2) was used as a control condition. The culture chambers were 20 L buckets medified to allow aeration bubbles of the experimental gas to mix with and gently stir the culture water without contacting the larvae. Replacement seawater (0.35 μm filtered) was added at a constant rate of 0.5 L hr-1. Water pH of each chamber was monitored daily using a Radiometer Analytical PHM240 pH meter. Adult L. pictus were maintained in flowing seawater at ambient temperature (~15-18 ºC) and fed kelp until use. Spawning was induced by coelomic injection of 0.5 M KCl, and eggs were collected in 0.35 μm-filtered seawater. Eggs from 5 females were combined in approximately equal concentrations. Sperm from a single male was collected in the same way, diluted with filtered seawater and added to the egg mixture; thus, all the larvae are half-siblings. Immediately following fertilization, embryos were split into 12 culture chambers providing four replicates of the three CO2 treatments. At the 48 hour time point, a sample of 40,000 larvae was removed from each of the 8 cultures in the 380 and 970 ppm treatments and stored in1 mL Trizol at -80 ºC for later RNA analysis. The larval cDNA samples from each treatment were competitively hybridized on each microarray following a balanced incomplete block design (BIBD) with respect to the assignment of treatments to arrays. In this way, differential expression between all pairs of treatments is estimated with equal precision. Although dye swaps of technical replicates were not used, treatment and dye effects are orthogonal to one another, i.e. treatment effects can be estimated independently of dye effects.
2010-05-16 | E-GEOD-13655 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series:; GSE14553: Toxicogenomic Comparison of TCDD and PCB 126 Responsiveness in Primary Human Hepatocytes; GSE14554: Toxicogenomic Comparison of TCDD and PCB 126 Responsiveness in Primary Rat Hepatocytes Experiment Overall Design: Refer to individual Series
2009-09-05 | E-GEOD-14555 | biostudies-arrayexpress
Project description:Exposure to polychlorinated biphenyls (PCBs) and high fat diet (HFD) results in nonalcoholic steatohepatitis (NASH) in mice by altering intracellular signaling and inhibiting epidermal growth factor receptor (EGFR) signaling. Post-transcriptional chemical modification (PTM) of RNA regulates biological processes. This study tested the hypothesis that PCB exposure alters the global RNA epitranscriptome in HFD-fed male mouse liver. C57BL/6J male mice were fed a 42% milk fat diet (HFD) and exposed to Aroclor 1260 (20mg/kg), PCB 126 (20 µg/kg), both Aroclor 1260 and PCB 126, or vehicle control for 12 weeks. RNA modifications altered by PCB exposure were analyzed in comparison to the readers, writers, and erasers of these marks in the RNA transcriptome.
2021-09-29 | GSE173271 | GEO
Project description:There is growing evidence from epidemiological and experimental studies suggesting that early life exposure to environmental chemicals can have long-term consequences that are seen in adults and not apparent early in life. We recently demonstrated that developmental exposure of zebrafish embryos to low, non-embryotoxic levels of PCB126 did not affect larval behavior but caused changes in adult behavior (Glazer et al., 2016, NeuroToxicology 52:134-143). Zebrafish embryos were exposed to either vehicle (DMSO) or low concentrations of PCB126 (0.3, 0.6, 1.2 nM) for 20 h (4–24 h post fertilization), and then reared to adulthood in clean water. Locomotor activity of the larvae at 7 and 14 days post fertilization (dpf) was not affected by PCB126. In contrast, adult fish (4 months old) tested in novel tank and shoaling assays showed impaired habituation to a novel environment. In order to investigate the underlying molecular basis of these phenotypes, we determined the transcriptional profiles in whole embryos (48 hpf), larvae (5 dpf) and adult brain (4 mo) using strand-specific RNA-sequencing. Our results show that 0.3 nM PCB126 exposure induced cyp1a transcript levels 12.5-fold in 48-hpf embryos but there was no induction in 5-dpf larvae, suggesting transient activation of aryl hydrocarbon receptor during early development. No significant induction of cyp1a was observed in the brains of adults exposed as embryos to PCB126. However, we observed significant changes in gene expression profiles in the adult brain samples. A total of 2209 and 1628 genes were differentially expressed in 0.3 nM and 1.2 nM PCB126-exposed groups, respectively. KEGG pathway analysis of differentially expressed genes in the brain suggest enrichment of genes involved in oxidative phosphorylation, neurodegenerative diseases, circadian rhythm and calcium signaling pathways. We are currently investigating the role of these genes in altered behavior observed in the adults. Overall, our results suggest that PCB exposure during sensitive periods of early development alters normal development of the brain by reprogramming gene expression patterns. [Funded by NIH P01ES021923 and NSF OCE-1314642].
2017-08-10 | GSE98741 | GEO