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Transcriptomic responses to Deepwater Horizon oil in mahi-mahi (Coryphaena hippurus) embryos reveals time and oil-dependent linkages between molecular initiating events and developmental toxicity

ABSTRACT: Purpose:To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, transcriptomic profiles in mahi-mahi (Coryphaena hippurus) embryos exposed to different DWH oils (source and artificially weathered oil) were evaluated at different critical windows of development using High Throughput Sequencing (HTS). Methods:Total mRNA profiles of 24, 48, 96 hpf mahi-mahi larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. qRT–PCR validation was performed using SYBR Green assays. Results: Exposure to slick oil induced more pronounced changes in gene expression over time than did exposure to source oil. Predominant transcriptomic responses included alteration of E1F2 signaling, steroid biosynthesis, ribosome biogenesis, perturbation in eye development and peripheral nervous, and activation of P450 pathway. Comparisons of changes of cardiac / Ca2+-associated genes with phenotypic responses revealed reduced heart rate and increased pericardial edema in larvae exposed to slick oil but not source oil.

ORGANISM(S): Coryphaena hippurus

PROVIDER: GSE79675 | GEO | 2016/07/07

SECONDARY ACCESSION(S): PRJNA316679

REPOSITORIES: GEO

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Transcriptomic responses to Deepwater Horizon oil in mahi-mahi (Coryphaena hippurus) embryos reveals time and oil-dependent linkages between molecular initiating events and developmental toxicity

Project description:Purpose:To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, transcriptomic profiles in mahi-mahi (Coryphaena hippurus) embryos exposed to different DWH oils (source and artificially weathered oil) were evaluated at different critical windows of development using High Throughput Sequencing (HTS). Methods:Total mRNA profiles of 24, 48, 96 hpf mahi-mahi larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. qRTâPCR validation was performed using SYBR Green assays. Results: Exposure to slick oil induced more pronounced changes in gene expression over time than did exposure to source oil. Predominant transcriptomic responses included alteration of E1F2 signaling, steroid biosynthesis, ribosome biogenesis, perturbation in eye development and peripheral nervous, and activation of P450 pathway. Comparisons of changes of cardiac / Ca2+-associated genes with phenotypic responses revealed reduced heart rate and increased pericardial edema in larvae exposed to slick oil but not source oil. Total mRNA profiles of 24, 48, 96 hpf mahi-mahi larvae after slick and source (mass) oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

2016-07-07 | E-GEOD-79675 | biostudies-arrayexpress

MicroRNA profiles in red drum (Sciaenops ocellatus) larvae exposed to Deepwater Horizon oil

Project description:Purpose:To help identify molecular regulatory mechanisms of developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, microRNA profiles in red drum larvae exposed to different DWH oils (source/mass and artificially weathered oil) were evaluated using High Throughput Sequencing (HTS). Methods:Total microRNA profiles of 48 hpf red drum larvae after source oil (0.135%, 0.27%, and 0.54%) and slick oil (1.25%, 2.5% and 5%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSeq 500. Results: Source and slick oil significantly dysregulated the expression of miR-18a, miR-27b, and miR-203a across all exposure concentrations. The target genes of these miRNAs were predominantly involved in the neuro-cardio system development processes and associated key signaling pathways such as axonal guidance signaling, CREB signaling in neurons, synaptic long-term potentiation pathway, calcium signaling and role of NFAT in cardiac hypertrophy.

2019-01-09 | GSE120670 | GEO

Dose-responsive microRNA profiles in mahi-mahi (Coryphaena hippurus) larvae exposed to Deepwater Horizon oil

Project description:Purpose: To help identify molecular regulatory mechanisms of developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, microRNA profiles in mahi-mahi (Coryphaena hippurus) larvae exposed to different DWH oils (source/mass and artificially weathered oil) were evaluated using High Throughput Sequencing (HTS). Methods: Total microRNA profiles of 48 hpf mahi-mah larvae after slick (0.5%, 1%, and 2%) and source/mass oil (0.125%, 0.25% and 5%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ v2. Results: Among over 100 significant DE miRNAs, DE miRNAs that were inversely correlated with target mRNAs after slick and source oil exposure were identfied. miR-34b, miR-181b, miR-23b, and miR-203a responsive to both slick and source oil exposure were further filtered to predict downstream biological functions. The target genes of these four miRNAs were involved AhR signaling, Cardiac β-adrenergic signaling, nNOS signaling in neurons, xenobiotic metabolism signaling, p53 signaling, cell cycle regulation, etc., as well as potential diseases including cardiovascular disease, neurological disease, developmental disorder, ophthalmic disease, metabolism disease, etc.

2019-02-20 | GSE116711 | GEO

Dose-responsive transcriptomic profiles in red drum (Sciaenops ocellatus) larvae exposed to Deepwater Horizon oil

Project description:Purpose:To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for estuary fish exposed to different concentrations of Deepwater Horizon (DWH) oil, transcriptomic profiles in red drum (Sciaenops ocellatus) embryos exposed to different DWH oils (source/mass and artificially weathered oil) were evaluated using High Throughput Sequencing (HTS). Methods:Total mRNA profiles of 48 hpf red drum larvae after slick (1.25%, 2.5%, and 5%) and source/mass oil (0.135%, 0.27% and 0.54%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ v2. Results:To determine the potential biological impact of oil exposure at system level, a gene ontology (GO) term analysis on biological processes (BPs) was conducted by analyzing the DEGs using DAVID. After exposure to source oil, the top enriched biological processes were terms associated with oxidation-reduction process, metabolic process (e.g. steroid), and organism development. Similar biological processes were also among the most significant biological processes by slick oil exposure. Among the top biological process list a significant number of nervous system related terms were highly enriched by both source and slick oil exposure, including midbrain development, motor neuron axon guidance, nervous system development, eye development, neuron development, neuron differentiation etc.

2019-01-09 | GSE119934 | GEO

Dose-responsive transcriptomic profiles in mahi-mahi (Coryphaena hippurus) larvae exposed to Deepwater Horizon oil (mRNA profiles)

Project description:Purpose:To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to different concentrations of Deepwater Horizon (DWH) oil, transcriptomic profiles in mahi-mahi (Coryphaena hippurus) embryos exposed to different DWH oils (source and artificially weathered oil) were evaluated using High Throughput Sequencing (HTS). Methods:Total mRNA profiles of 48 hpf mahi-mah larvae after slick (0.5%, 1%, and 2%) and source/mass oil (0.125%, 0.25% and 5%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ v2. Results:To determine the potential biological impact of oil exposure at system level, a gene ontology (GO) term analysis on biological processes (BPs) was conducted by analyzing the DEGs using ToppGene. The profile of BPs was dose- and oil type- dependent. After exposure to 0.125% slick oil, the top enriched biological processes were RNA processing and RNA metabolism terms. Metabolic and catabolic process and terms associated with embryo development were some of the most enriched BPs at 0.25% slick oil. The top enriched BPs at 0.5% slick oil were organic acid metabolic process and cardiovascular system development. For source oil, cell cycle process, metabolic process, and RNA processing were the most enriched by 0.125% source oil exposure, which were also highly enriched by 0.25% source oil exposure, while more ‘response’ BPs were enriched by 0.25% source oil exposure, such as regulation of response to stress, response to endogenous stimulus, response to hormone, cellular response to light stimulus, etc. The most significantly enrich BP by 0.5% source oil was cardiovascular system development followed by organic acid metabolic process and cell junction assembly.

2019-02-20 | GSE116639 | GEO

Regulation of microRNAs in response to Deepwater Horizon oil in mahi-mahi (Coryphaena hippurus) embryos at 3 different stages.

Project description:Purpose:To help identify the role miRNAs in molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, miRNA-mRNA networks in mahi-mahi (Coryphaena hippurus) embryos exposed to different DWH oils (source and artificially weathered oil) were evaluated at different critical windows of development using High Throughput Sequencing (HTS). Methods:miRNA profiles of 24, 48, 96 hpf mahi-mah larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina NextSeq v2. qRT–PCR validation was performed using SYBR Green assays. Results: Exposure of embryos to slick oil resulted in more DE miRNAs than source oil at all developmental stages 24hpf, 48hpf, and 96hpf. There was also an increase in the number of DE miRNA as development progressed, with 96hpf having the highest number of DE miRNAs. The expression of miRNAs and their target mRNA was further compared using advanced bioinformatics with subsequent target organ predictions based on their interactions. Gene ontology (GO) analysis on the target mRNAs was consistent with pathway analysis of miRNAs, predicting disruption of cardiovascular system development after oil exposure and showed that specific miRNA–mRNA interactions may contribute to these effects.

2017-12-04 | GSE102966 | GEO

Genome-wide transcriptional responses to Deepwater Horizon oil in red drum (Sciaenops ocellatus) embryos and larvae

Project description:Purpose:To investigate the transcriptomic profiles in red drum embryos reflective of the DWH oil toxicity at different critical windows of development and to predict the most impacted biological processes and pathways based on differentially expressed gene transcripts at different developmental stages using High Throughput Sequencing (HTS). Methods:Total mRNA profiles of 24, 48, 72 hpf red drum larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. Results:Oil type-dependent transcriptional effects were observed, with more significant by source oil exposure at 24 and 48 h, and similar responses by source and slick at 72 hpf. Informatic analyses indicated source oil exposure started significant perturbation in metabolism, AhR, visual, and cardiac-associated genes as early as 24 hpf. Both source and slick oil significantly affected EIF2 pathway, nervous and cardiovascular systems from 48 hpf to 72 hpf.

2017-11-14 | GSE90113 | GEO

BP oil spill - lab - gill

Project description:In this study we characterize the gill transcriptome changes in Gulf killifish (Fundulus grandis) that coincide with controlled laboratory-based exposure to various concentrations of experimentally-weathered south Louisiana crude oil. Gill transcription was contrasted between doses and across timepoints following dosing.

2014-08-11 | E-MTAB-2834 | biostudies-arrayexpress

BP oil spill - lab - liver

Project description:In this study we characterize the liver transcriptome changes in Gulf killifish (Fundulus grandis) that coincide with controlled laboratory-based exposure to various concentrations of experimentally-weathered south Louisiana crude oil. Liver transcription was contrasted between doses and across timepoints following dosing.

2014-08-13 | E-MTAB-2841 | biostudies-arrayexpress

Cod larvae oil exposure

Project description:This experiment was conducted in order to evaluate the potential contribution of oil droplets to the toxicity of dispersed oil to fish larvae. Atlantic cod larvae were exposed to five concentrations of either dispersed oil (D1-D5) (containing oil droplets [medium size 10-14 µm based on volume] and water soluble fraction [WSF]) or the filtered dispersion containing only WSF of oil (W1-W5) for four days and harvested for transcriptional analysis at 13 days post hatching. The most significant differently expressed genes were observed in cod larvae exposed to the highest concentration of the dispersed oil (containing 10.41 ± 0.46 µg ∑PAH/L), with CYP1A showing the strongest response. Functional analysis further showed that the top scored network as analyzed with Ingenuity Pathway Analysis was “Drug Metabolism, Endocrine System Development and Function, Lipid Metabolism”. Oil exposure also increased the expression of genes involved in bone resorption and decreased the expression of genes related to bone formation. In conclusion, oil exposure affects drug metabolism, endocrine regulation, cell differentiation and proliferation, apoptosis, fatty acid biosynthesis and tissue development in Atlantic cod larvae. The altered gene transcription was dominated by the WSF and the oil droplet fraction only had a moderate impact on the observed changes.

2011-09-01 | E-TABM-1136 | biostudies-arrayexpress

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