Fishing for contaminants: identification of three mechanism specific transcriptome signatures using Danio rerio embryos
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In ecotoxicology, transcriptomics is an effective way to detect gene expression changes in response to environmental pollutants. Such changes can be used to identify contaminants or contaminant classes and can be applied as early warning signals for pollution. To do so, it is important to distinguish contaminant-specific transcriptomic changes from genetic alterations due to general stress. Here we present a first step in the identification of contaminant class-specific transcriptome signatures. Embryos of zebrafish (Danio rerio) were exposed to three substances (methylmercury, chlorpyrifos and Aroclor 1254, each from 24 to 48 hpf exposed) representing sediment typical contaminant classes. We analyzed the altered transcriptome to detect discriminative genes significantly regulated in reaction to the three applied contaminants. By comparison of the results of the three contaminants, we identified transcriptome signatures and biologically important pathways (using Cytoscape/ClueGO software) that react significantly to the contaminant classes. This approach increases the chance of finding genes that play an important role in contaminant class-specific pathways rather than more general processes.
KeywordsTranscriptomics Methylmercury Aroclor 1254 Chlorpyrifos Ecotoxicogenomics Pathway network analysis
The present study was part of the research funding project DanTox (DanTox—a novel joint research project using zebrafish (Danio rerio) to identify specific toxicity and molecular modes of action of sediment-bound pollutants). The authors acknowledge financial support by the German Federal Ministry of Education and Research (BMBF grant 02WU1053) and data provision from the GENDarT2 project (BMBF grant AZ:0315190 B). The authors thank Thomas-Benjamin Seiler for improving the language. The authors thank Leonie Nüßer and Daniel Koske for their help with the interpretation of the microarrays.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
- Churchill GA (2004) Using ANOVA to analyze microarray data. BioTechniques 37(173–5):177Google Scholar
- Garcia-Käufer M, Gartiser S, Hafner C et al (2015) Genotoxic and teratogenic effect of freshwater sediment samples from the Rhine and Elbe River (Germany) in zebrafish embryo using a multi-endpoint testing strategy. Environ Sci Pollut Res Int 22:16341–16357. doi: 10.1007/s11356-014-3894-4 CrossRefGoogle Scholar
- Giancarlo R, Lo Bosco G, Pinello L (2010) Distance functions, clustering algorithms and microarray data analysis. Lecture notes in computer science. Springer, Berlin Heidelberg, pp 125–138Google Scholar
- Jönsson ME, Jenny MJ, Woodin BR et al (2007) Role of AHR2 in the expression of novel cytochrome P450 1 family genes, cell cycle genes, and morphological defects in developing zebra fish exposed to 3,3′,4,4′,5-pentachlorobiphenyl or 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicol Sci 100:180–193. doi: 10.1093/toxsci/kfm207 CrossRefGoogle Scholar
- Keiter SH, Braunbeck T, Feiler U, et al. (2013) DanTox—Entwicklung und Anwendung eines Verfahrens zur Ermittlung spezifischer Toxizität und molekularer Wirkungsmechanismen sedimentgebundener Umweltschadstoffe mit dem Zebrabärbling (Danio rerio) : Schlussbericht.Google Scholar
- Legradi J (2011) Microarray based transcriptomics and the search for biomarker genes in zebrafish. Ruprecht-Karls Universität, HeidelbergGoogle Scholar
- Schlezinger JJ, Struntz WDJ, Goldstone JV, Stegeman JJ (2006) Uncoupling of cytochrome P450 1A and stimulation of reactive oxygen species production by co-planar polychlorinated biphenyl congeners. Aquatic toxicology (Amsterdam, Netherlands) 77:422–432. doi: 10.1016/j.aquatox.2006.01.012 CrossRefGoogle Scholar
- Villeneuve D, Volz DC, Embry MR et al (2014a) Investigating alternatives to the fish early-life stage test: a strategy for discovering and annotating adverse outcome pathways for early fish development. Environmental toxicology and chemistry / SETAC 33:158–169. doi: 10.1002/etc.2403 CrossRefGoogle Scholar