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A reduced transcriptome approach to assess environmental toxicants using zebrafish embryo tests
Wang, P., P. Xia, J. Yang, Z. Wang, Y. Peng, W. Shi, Dan Villeneuve, H. Yu, AND X. Zhang. A reduced transcriptome approach to assess environmental toxicants using zebrafish embryo tests. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, 52(2):821-830, (2018).
Modern transcriptomics technologies hold great promise as tools to conduct broad spectrum surveillance of the potential bioactivities associated with chemicals or chemical mixtures found in environmental samples. However, routine applications of transcriptomics in chemical safety assessment and environmental monitoring has been limited by the high cost of whole transcriptome measurements. The current research explores the use of novel technology that combines polymerase-chain-reaction mediated amplification of gene targets with high throughput sequencing to monitor the expression of over 1600 genes in zebrafish. Taking advantage of the fact that many genes are co-regulated, and thus have expression that is correlated, this smaller subset of gene responses may still be used to infer broad impacts on biological pathways. The current work represents the first pilot testing of this technology for single chemical assessment (bisphenol A in this case), and evaluating water samples. Results show that both effect concentrations and impacted pathways can be inferred using these methods. This lays the groundwork for future development and application of cost effective and implementable methods that may be of use to states, Regions, and program offices charged with chemical safety assessment. This work is a result of the EPA-China Most collaboration and directly addresses objectives of the CSS Adverse Outcome Pathway Discovery and Development project (CSS 17.01).
This paper reports on the pilot testing of a new bioassay platform that monitors expression of 1600 genes in zebrafish embryos exposed to either single chemicals or complex water samples. The method provides a more cost effective, high throughput means to broadly evaluate the potential impacts of a chemical or complex mixture on fish biology. With additional development, it may prove a tractable technology for both environmental monitoring and chemical safety assessment applications and help meet needs of the states, EPA program offices, and regions to monitor for potential adverse effects of chemicals in the environment. Omics approaches can monitor responses of biological pathways at genome-scale, which are useful to predict potential adverse effects by environmental toxicants. However, high throughput application of transcriptomics in chemical assessment is limited due to the high cost and lack of matured dose response models. Here, a reduced zebrafish transcriptome (RZT) approach was developed to represent the whole transcriptome and to profile bioactivity of chemical and environmental mixtures in zebrafish embryo. Quantitative analysis of RZT gene expression by RNA-ampliseq technology was used to identify differentially expressed genes (DEGs) at 32 hpf following exposure to reference chemical, BPA, and four water samples ranging from wastewater to drinking water. Concentration-response modeling was used to calculate the effect concentrations (ECs) of DEGs and corresponding molecular pathways. RZT gene set of 1637 zebrafish Entrez genes was designed to cover a wide range of biological processes, and faithfully captured gene-level and pathway-level changes by toxicants compared with the whole transcriptome. The RZT-ampliseq-embryo approach was able to differentiate low dose response from a wide spectrum of biological activities for BPA. Finally, water quality was benchmarked based on the sensitivity distribution curve of biological pathways detected using RZT-ampliseq-embryo, and the most sensitive biological pathways were identified. RZT-ampliseq-embryo approach provides an efficient and cost-effective tool to derive pathway-based information of environmental toxicants.