title: Fishing for contaminants: identification of three mechanism specific transcriptome signatures using Danio rerio embryos.
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.
authors.affiliation: Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany. jhausen@bio5.rwth-aachen.de.
authors.forename: Jonas
authors.identifier: http://orcid.org/0000-0003-1264-5802
authors.initials: J
authors.lastname: Hausen
authors.affiliation: Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
authors.forename: Jens C
authors.initials: JC
authors.lastname: Otte
authors.affiliation: Environment and Health, VU Amsterdam, De Boelelaan 1087, 1081 HV, Amsterdam, the Netherlands.
authors.forename: Jessica
authors.initials: J
authors.lastname: Legradi
authors.affiliation: Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
authors.forename: Lixin
authors.initials: L
authors.lastname: Yang
authors.affiliation: Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Strähle
authors.affiliation: Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group for Translational Medicine and Pharmacology, Forckenbeckstraße 6, 52074, Aachen, Germany.
authors.forename: Martina
authors.initials: M
authors.lastname: Fenske
authors.affiliation: School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada.
authors.forename: Markus
authors.initials: M
authors.lastname: Hecker
authors.affiliation: School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada.
authors.forename: Song
authors.initials: S
authors.lastname: Tang
authors.affiliation: Research Institute for Ecosystem Analysis and Assessment - gaiac, Kackertstraße 10, 52072, Aachen, Germany.
authors.forename: Monika
authors.initials: M
authors.lastname: Hammers-Wirtz
authors.affiliation: Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
authors.forename: Henner
authors.initials: H
authors.lastname: Hollert
authors.affiliation: Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.|Man-Technology-Environment Research Centre, Örebro University, SE-701 82, Örebro, Sweden.
authors.forename: Steffen H
authors.initials: SH
authors.lastname: Keiter
authors.affiliation: Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
authors.forename: Richard
authors.initials: R
authors.lastname: Ottermanns
mesh_terms: D000818:Animals; D020111:Chlorodiphenyl (54% Chlorine) / Q000009:adverse effects*; D004390:Chlorpyrifos / Q000009:adverse effects*; D004625:Embryo, Nonmammalian / Q000187:drug effects / Q000378:metabolism; D008767:Methylmercury Compounds / Q000009:adverse effects*; D059467:Transcriptome / Q000187:drug effects*; D014874:Water Pollutants, Chemical / Q000009:adverse effects*; D015027:Zebrafish / Q000378:metabolism*
chemical_list: D008767:Methylmercury Compounds; D014874:Water Pollutants, Chemical; D020111:Chlorodiphenyl (54% Chlorine); D004390:Chlorpyrifos
keywords: Aroclor 1254; Chlorpyrifos; Ecotoxicogenomics; Methylmercury; Pathway network analysis; Transcriptomics