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Dreser N, Zimmer B, Dietz C, Sügis E, Pallocca G, Nyffeler J, Meisig J, Blüthgen N, Berthold MR, Waldmann T, Leist M. Grouping of histone deacetylase inhibitors and other toxicants disturbing neural crest migration by transcriptional profiling. Neurotoxicology 2015; 50:56-70. [PMID: 26238599 DOI: 10.1016/j.neuro.2015.07.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/28/2015] [Accepted: 07/28/2015] [Indexed: 12/13/2022]
Abstract
Functional assays, such as the "migration inhibition of neural crest cells" (MINC) developmental toxicity test, can identify toxicants without requiring knowledge on their mode of action (MoA). Here, we were interested, whether (i) inhibition of migration by structurally diverse toxicants resulted in a unified signature of transcriptional changes; (ii) whether statistically-identified transcript patterns would inform on compound grouping even though individual genes were little regulated, and (iii) whether analysis of a small group of biologically-relevant transcripts would allow the grouping of compounds according to their MoA. We analyzed transcripts of 35 'migration genes' after treatment with 16 migration-inhibiting toxicants. Clustering, principal component analysis and correlation analyses of the data showed that mechanistically related compounds (e.g. histone deacetylase inhibitors (HDACi), PCBs) triggered similar transcriptional changes, but groups of structurally diverse toxicants largely differed in their transcriptional effects. Linear discriminant analysis (LDA) confirmed the specific clustering of HDACi across multiple separate experiments. Similarity of the signatures of the HDACi trichostatin A and suberoylanilide hydroxamic acid to the one of valproic acid (VPA), suggested that the latter compound acts as HDACi when impairing neural crest migration. In conclusion, the data suggest that (i) a given functional effect (e.g. inhibition of migration) can be associated with highly diverse signatures of transcript changes; (ii) statistically significant grouping of mechanistically-related compounds can be achieved on the basis of few genes with small regulations. Thus, incorporation of mechanistic markers in functional in vitro tests may support read-across procedures, also for structurally un-related compounds.
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Affiliation(s)
- Nadine Dreser
- Doerenkamp-Zbinden Chair of In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, Germany
| | - Bastian Zimmer
- Center for Stem Cell Biology, Sloan-Kettering Institute, New York City, NY, USA; Developmental Biology Program, Sloan-Kettering Institute, New York City, NY, USA.
| | - Christian Dietz
- Lehrstuhl für Bioinformatik und Information Mining, University of Konstanz, Konstanz, Germany
| | - Elena Sügis
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Giorgia Pallocca
- Doerenkamp-Zbinden Chair of In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, Germany
| | - Johanna Nyffeler
- Doerenkamp-Zbinden Chair of In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, Germany
| | - Johannes Meisig
- Institute of Pathology, Charité-Universitätsmedizin, 10117 Berlin, Germany; Integrative Research Institute for the Life Sciences and Institute for Theoretical Biology, Humboldt Universität, 10115 Berlin, Germany
| | - Nils Blüthgen
- Institute of Pathology, Charité-Universitätsmedizin, 10117 Berlin, Germany; Integrative Research Institute for the Life Sciences and Institute for Theoretical Biology, Humboldt Universität, 10115 Berlin, Germany
| | - Michael R Berthold
- Lehrstuhl für Bioinformatik und Information Mining, University of Konstanz, Konstanz, Germany
| | - Tanja Waldmann
- Doerenkamp-Zbinden Chair of In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, Germany
| | - Marcel Leist
- Doerenkamp-Zbinden Chair of In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, Germany
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