title: Definition of transcriptome-based indices for quantitative characterization of chemically disturbed stem cell development: introduction of the STOP-Toxuknand STOP-Toxukktests.
abstract: Stem cell-based in vitro test systems can recapitulate specific phases of human development. In the UKK test system, human pluripotent stem cells (hPSCs) randomly differentiate into cells of the three germ layers and their derivatives. In the UKN1 test system, hPSCs differentiate into early neural precursor cells. During the normal differentiation period (14 days) of the UKK system, 570 genes [849 probe sets (PSs)] were regulated >fivefold; in the UKN1 system (6 days), 879 genes (1238 PSs) were regulated. We refer to these genes as 'developmental genes'. In the present study, we used genome-wide expression data of 12 test substances in the UKK and UKN1 test systems to understand the basic principles of how chemicals interfere with the spontaneous transcriptional development in both test systems. The set of test compounds included six histone deacetylase inhibitors (HDACis), six mercury-containing compounds ('mercurials') and thalidomide. All compounds were tested at the maximum non-cytotoxic concentration, while valproic acid and thalidomide were additionally tested over a wide range of concentrations. In total, 242 genes (252 PSs) in the UKK test system and 793 genes (1092 PSs) in the UKN1 test system were deregulated by the 12 test compounds. We identified sets of 'diagnostic genes' appropriate for the identification of the influence of HDACis or mercurials. Test compounds that interfered with the expression of developmental genes usually antagonized their spontaneous development, meaning that up-regulated developmental genes were suppressed and developmental genes whose expression normally decreases were induced. The fraction of compromised developmental genes varied widely between the test compounds, and it reached up to 60 %. To quantitatively describe disturbed development on a genome-wide basis, we recommend a concept of two indices, 'developmental potency' (Dp) and 'developmental index' (Di), whereby Dpis the fraction of all developmental genes that are up- or down-regulated by a test compound, and Diis the ratio of overrepresentation of developmental genes among all genes deregulated by a test compound. The use of Dimakes hazard identification more sensitive because some compounds compromise the expression of only a relatively small number of genes but have a high propensity to deregulate developmental genes specifically, resulting in a low Dpbut a high Di. In conclusion, the concept based on the indices Dpand Dioffers the possibility to quantitatively express the propensity of test compounds to interfere with normal development.
authors.affiliation: Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), University of Cologne (UKK), Robert-Koch-Str. 39, 50931, Cologne, Germany.
authors.forename: Vaibhav
authors.initials: V
authors.lastname: Shinde
authors.affiliation: Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box: M657, 78457, Constance, Germany.|Konstanz Graduate School Chemical Biology KORS-CB, University of Konstanz, 78457, Constance, Germany.
authors.forename: Lisa
authors.initials: L
authors.lastname: Hoelting
authors.affiliation: Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), University of Cologne (UKK), Robert-Koch-Str. 39, 50931, Cologne, Germany.
authors.forename: Sureshkumar Perumal
authors.initials: SP
authors.lastname: Srinivasan
authors.affiliation: Institute of Pathology, Charité Universitätsmedizin, 10117, Berlin, Germany.|Integrative Research Institute for the Life Sciences, Institute for Theoretical Biology, Humboldt Universität, 10115, Berlin, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Meisig
authors.affiliation: Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), University of Cologne (UKK), Robert-Koch-Str. 39, 50931, Cologne, Germany.
authors.forename: Kesavan
authors.initials: K
authors.lastname: Meganathan
authors.affiliation: Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), University of Cologne (UKK), Robert-Koch-Str. 39, 50931, Cologne, Germany.
authors.forename: Smita
authors.initials: S
authors.lastname: Jagtap
authors.affiliation: Department of Statistics, TU Dortmund University, Dortmund, Germany.
authors.forename: Marianna
authors.initials: M
authors.lastname: Grinberg
authors.affiliation: Leibniz Research Centre for Working Environment and Human Factors at the Technical, University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Liebing
authors.affiliation: Institute of Pathology, Charité Universitätsmedizin, 10117, Berlin, Germany.|Integrative Research Institute for the Life Sciences, Institute for Theoretical Biology, Humboldt Universität, 10115, Berlin, Germany.
authors.forename: Nils
authors.initials: N
authors.lastname: Bluethgen
authors.affiliation: Department of Statistics, TU Dortmund University, Dortmund, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Rahnenführer
authors.affiliation: Department of Statistics, TU Dortmund University, Dortmund, Germany.|Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany.
authors.forename: Eugen
authors.initials: E
authors.lastname: Rempel
authors.affiliation: Leibniz Research Centre for Working Environment and Human Factors at the Technical, University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany.
authors.forename: Regina
authors.initials: R
authors.lastname: Stoeber
authors.affiliation: Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box: M657, 78457, Constance, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Schildknecht
authors.affiliation: Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box: M657, 78457, Constance, Germany.
authors.forename: Sunniva
authors.initials: S
authors.lastname: Förster
authors.affiliation: Leibniz Research Centre for Working Environment and Human Factors at the Technical, University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany.
authors.forename: Patricio
authors.initials: P
authors.lastname: Godoy
authors.affiliation: Leibniz Research Centre for Working Environment and Human Factors at the Technical, University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: van Thriel
authors.affiliation: Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), University of Cologne (UKK), Robert-Koch-Str. 39, 50931, Cologne, Germany.
authors.forename: John Antonydas
authors.initials: JA
authors.lastname: Gaspar
authors.affiliation: Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), University of Cologne (UKK), Robert-Koch-Str. 39, 50931, Cologne, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Hescheler
authors.affiliation: Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box: M657, 78457, Constance, Germany.
authors.forename: Tanja
authors.initials: T
authors.lastname: Waldmann
authors.affiliation: Leibniz Research Centre for Working Environment and Human Factors at the Technical, University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany. hengstler@ifado.de.
authors.forename: Jan G
authors.initials: JG
authors.lastname: Hengstler
authors.affiliation: Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box: M657, 78457, Constance, Germany. marcel.leist@uni-konstanz.de.
authors.forename: Marcel
authors.initials: M
authors.lastname: Leist
authors.affiliation: Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), University of Cologne (UKK), Robert-Koch-Str. 39, 50931, Cologne, Germany. a.sachinidis@uni-koeln.de.
authors.forename: Agapios
authors.initials: A
authors.lastname: Sachinidis
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000187:drug effects / Q000235:genetics; D002460:Cell Line; D053595:Embryonic Stem Cells / Q000187:drug effects; D018507:Gene Expression Regulation, Developmental / Q000187:drug effects*; D006801:Humans; D051379:Mice; D039904:Pluripotent Stem Cells / Q000187:drug effects; D013234:Stem Cells / Q000187:drug effects* / Q000502:physiology; D013723:Teratogens / Q000633:toxicity; D018675:Toxicity Tests / Q000379:methods*; D059467:Transcriptome / Q000187:drug effects* / Q000235:genetics
chemical_list: D013723:Teratogens
keywords: Developmental toxicity; Genomics biomarkers; Human stem cells; In vitro test systems; Transcriptome