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Fishing for contaminants: identification of three mechanism specific transcriptome signatures using Danio rerio embryos

  • Effect-related evaluation of anthropogenic trace substances, -concepts for genotoxicity, neurotoxicity and, endocrine effects
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Abstract

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.

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Acknowledgements

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.

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Authors and Affiliations

  1. Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany

    Jonas Hausen, Henner Hollert, Steffen H. Keiter & Richard Ottermanns

  2. Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany

    Jens C. Otte, Lixin Yang & Uwe Strähle

  3. Environment and Health, VU Amsterdam, De Boelelaan 1087, 1081 HV, Amsterdam, the Netherlands

    Jessica Legradi

  4. Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group for Translational Medicine and Pharmacology, Forckenbeckstraße 6, 52074, Aachen, Germany

    Martina Fenske

  5. School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada

    Markus Hecker & Song Tang

  6. Research Institute for Ecosystem Analysis and Assessment - gaiac, Kackertstraße 10, 52072, Aachen, Germany

    Monika Hammers-Wirtz

  7. Man-Technology-Environment Research Centre, Örebro University, SE-701 82, Örebro, Sweden

    Steffen H. Keiter

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  1. Jonas Hausen
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Correspondence to Jonas Hausen.

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Responsible editor: Philippe Garrigues

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ESM 1

List of all GO-groups and contained functional terms. A table of all significantly enriched GO-terms as well as their respective GO-groups for all three treatments. Table includes p-values and Benjamini-Hochberg corrected p-values of each term. (CSV 9 kb)

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Hausen, J., Otte, J.C., Legradi, J. et al. Fishing for contaminants: identification of three mechanism specific transcriptome signatures using Danio rerio embryos. Environ Sci Pollut Res 25, 4023–4036 (2018). https://doi.org/10.1007/s11356-017-8977-6

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