Transcriptomic response patterns of hornyhead turbot (Pleuronichthys verticalis) dosed with polychlorinated biphenyls and polybrominated diphenyl ethers.

To evaluate the impact of environmental contaminants on aquatic health, extensive surveys of fish populations have been conducted using bioaccumulation as an indicator of impairment. While these studies have reported mixtures of chemicals in fish tissues, the relationship between specific contaminants and observed adverse impacts remains poorly understood. The present study aimed to characterize the toxicological responses induced by persistent organic pollutants in wild-caught hornyhead turbot (P. verticalis). To do so, hornyhead turbot were interperitoneally injected with a single dose of PCB or PBDE congeners prepared using environmentally realistic mixture proportions. After 96-hour exposure, the livers were excised and analyzed using transcriptomic approaches and analytical chemistry. Concentrations of PCBs and PBDEs measured in the livers indicated clear differences across treatments, and congener profiles closely mirrored our expectations. Distinct gene profiles were characterized for PCB and PBDE exposed fish, with significant differences observed in the expression of genes associated with immune responses, endocrine-related functions, and lipid metabolism. Our findings highlight the key role that transcriptomics can play in monitoring programs to assess chemical-induced toxicity in heterogeneous group of fish (mixed gender and life stage) as is typically found during field surveys. Altogether, the present study provides further evidence of the potential of transcriptomic tools to improve aquatic health assessment and identify causative agents.

How consistent are we? Interlaboratory comparison study in fathead minnows using the model estrogen 17α-ethinylestradiol to develop recommendations for environmental transcriptomics.

Fundamental questions remain about the application of omics in environmental risk assessments, such as the consistency of data across laboratories. The objective of the present study was to determine the congruence of transcript data across 6 independent laboratories. Male fathead minnows were exposed to a measured concentration of 15.8 ng/L 17α-ethinylestradiol (EE2) for 96 h. Livers were divided equally and sent to the participating laboratories for transcriptomic analysis using the same fathead minnow microarray. Each laboratory was free to apply bioinformatics pipelines of its choice. There were 12 491 transcripts that were identified by one or more of the laboratories as responsive to EE2. Of these, 587 transcripts (4.7%) were detected by all laboratories. Mean overlap for differentially expressed genes among laboratories was approximately 50%, which improved to approximately 59.0% using a standardized analysis pipeline. The dynamic range of fold change estimates was variable between laboratories, but ranking transcripts by their relative fold difference resulted in a positive relationship for comparisons between any 2 laboratories (mean R2 > 0.9, p < 0.001). Ten estrogen-responsive genes encompassing a fold change range from dramatic (>20-fold; e.g., vitellogenin) to subtle (∼2-fold; i.e., block of proliferation 1) were identified as differentially expressed, suggesting that laboratories can consistently identify transcripts that are known a priori to be perturbed by a chemical stressor. Thus, attention should turn toward identifying core transcriptional networks using focused arrays for specific chemicals. In addition, agreed-on bioinformatics pipelines and the ranking of genes based on fold change (as opposed to p value) should be considered in environmental risk assessment. These recommendations are expected to improve comparisons across laboratories and advance the use of omics in regulations. Environ Toxicol Chem 2017;36:2593-2601. © 2017 SETAC.

Ecotoxicogenomics: Microarray interlaboratory comparability.

Transcriptomic analysis can complement traditional ecotoxicology data by providing mechanistic insight, and by identifying sub-lethal organismal responses and contaminant classes underlying observed toxicity. Before transcriptomic information can be used in monitoring and risk assessment, it is necessary to determine its reproducibility and detect key steps impacting the reliable identification of differentially expressed genes. A custom 15K-probe microarray was used to conduct transcriptomics analyses across six laboratories with estuarine amphipods exposed to cyfluthrin-spiked or control sediments (10 days). Two sample types were generated, one consisted of total RNA extracts (Ex) from exposed and control samples (extracted by one laboratory) and the other consisted of exposed and control whole body amphipods (WB) from which each laboratory extracted RNA. Our findings indicate that gene expression microarray results are repeatable. Differentially expressed data had a higher degree of repeatability across all laboratories in samples with similar RNA quality (Ex) when compared to WB samples with more variable RNA quality. Despite such variability a subset of genes were consistently identified as differentially expressed across all laboratories and sample types. We found that the differences among the individual laboratory results can be attributed to several factors including RNA quality and technical expertise, but the overall results can be improved by following consistent protocols and with appropriate training.