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Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration

Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration

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PALLOCCA, Giorgia, Marianna GRINBERG, Margit HENRY, Tancred FRICKEY, Jan G. HENGSTLER, Tanja WALDMANN, Agapios SACHINIDIS, Jörg RAHNENFÜHRER, Marcel LEIST, 2016. Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration. In: Archives of Toxicology. 90(1), pp. 159-180. ISSN 0003-9446. eISSN 1432-0738. Available under: doi: 10.1007/s00204-015-1658-7

@article{Pallocca2016Ident-34006, title={Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration}, year={2016}, doi={10.1007/s00204-015-1658-7}, number={1}, volume={90}, issn={0003-9446}, journal={Archives of Toxicology}, pages={159--180}, author={Pallocca, Giorgia and Grinberg, Marianna and Henry, Margit and Frickey, Tancred and Hengstler, Jan G. and Waldmann, Tanja and Sachinidis, Agapios and Rahnenführer, Jörg and Leist, Marcel} }

<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/34006"> <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/28"/> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2016-05-20T06:15:49Z</dcterms:available> <dc:contributor>Frickey, Tancred</dc:contributor> <dc:language>eng</dc:language> <dc:creator>Pallocca, Giorgia</dc:creator> <dc:creator>Leist, Marcel</dc:creator> <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/34006/5/Pallocca_0-327012.pdf"/> <dcterms:issued>2016</dcterms:issued> <dc:creator>Frickey, Tancred</dc:creator> <dc:creator>Sachinidis, Agapios</dc:creator> <dcterms:abstract xml:lang="eng">The in vitro test battery of the European research consortium ESNATS ('novel stem cell-based test systems') has been used to screen for potential human developmental toxicants. As part of this effort, the migration of neural crest (MINC) assay has been used to evaluate chemical effects on neural crest function. It identified some drug-like compounds in addition to known environmental toxicants. The hits included the HSP90 inhibitor geldanamycin, the chemotherapeutic arsenic trioxide, the flame-retardant PBDE-99, the pesticide triadimefon and the histone deacetylase inhibitors valproic acid and trichostatin A. Transcriptome changes triggered by these substances in human neural crest cells were recorded and analysed here to answer three questions: (1) can toxicants be individually identified based on their transcript profile; (2) how can the toxicity pattern reflected by transcript changes be compacted/dimensionality-reduced for practical regulatory use; (3) how can a reduced set of biomarkers be selected for large-scale follow-up? Transcript profiling allowed clear separation of different toxicants and the identification of toxicant types in a blinded test study. We also developed a diagrammatic system to visualize and compare toxicity patterns of a group of chemicals by giving a quantitative overview of altered superordinate biological processes (e.g. activation of KEGG pathways or overrepresentation of gene ontology terms). The transcript data were mined for potential markers of toxicity, and 39 transcripts were selected to either indicate general developmental toxicity or distinguish compounds with different modes-of-action in read-across. In summary, we found inclusion of transcriptome data to largely increase the information from the MINC phenotypic test.</dcterms:abstract> <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/28"/> <dc:contributor>Leist, Marcel</dc:contributor> <dcterms:title>Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration</dcterms:title> <dc:creator>Waldmann, Tanja</dc:creator> <dc:contributor>Rahnenführer, Jörg</dc:contributor> <foaf:homepage rdf:resource="http://localhost:8080/jspui"/> <dc:contributor>Henry, Margit</dc:contributor> <dc:creator>Grinberg, Marianna</dc:creator> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2016-05-20T06:15:49Z</dc:date> <dc:contributor>Sachinidis, Agapios</dc:contributor> <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/> <dc:contributor>Hengstler, Jan G.</dc:contributor> <dc:contributor>Pallocca, Giorgia</dc:contributor> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/34006"/> <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by/4.0/"/> <dc:creator>Hengstler, Jan G.</dc:creator> <dc:creator>Henry, Margit</dc:creator> <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/34006/5/Pallocca_0-327012.pdf"/> <dc:contributor>Grinberg, Marianna</dc:contributor> <dc:creator>Rahnenführer, Jörg</dc:creator> <dc:rights>Attribution 4.0 International</dc:rights> <dc:contributor>Waldmann, Tanja</dc:contributor> </rdf:Description> </rdf:RDF>

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