title: Stem Cell Transcriptome Responses and Corresponding Biomarkers That Indicate the Transition from Adaptive Responses to Cytotoxicity.
abstract: Analysis of transcriptome changes has become an established method to characterize the reaction of cells to toxicants. Such experiments are mostly performed at compound concentrations close to the cytotoxicity threshold. At present, little information is available on concentration-dependent features of transcriptome changes, in particular, at the transition from noncytotoxic concentrations to conditions that are associated with cell death. Thus, it is unclear in how far cell death confounds the results of transcriptome studies. To explore this gap of knowledge, we treated pluripotent stem cells differentiating to human neuroepithelial cells (UKN1 assay) for short periods (48 h) with increasing concentrations of valproic acid (VPA) and methyl mercury (MeHg), two compounds with vastly different modes of action. We developed various visualization tools to describe cellular responses, and the overall response was classified as "tolerance" (minor transcriptome changes), "functional adaptation" (moderate/strong transcriptome responses, but no cytotoxicity), and "degeneration". The latter two conditions were compared, using various statistical approaches. We identified (i) genes regulated at cytotoxic, but not at noncytotoxic, concentrations and (ii) KEGG pathways, gene ontology term groups, and superordinate biological processes that were only regulated at cytotoxic concentrations. The consensus markers and processes found after 48 h treatment were then overlaid with those found after prolonged (6 days) treatment. The study highlights the importance of careful concentration selection and of controlling viability for transcriptome studies. Moreover, it allowed identification of 39 candidate "biomarkers of cytotoxicity". These could serve to provide alerts that data sets of interest may have been affected by cell death in the model system studied.
authors.affiliation: In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Chair Foundation, University of Konstanz , 78457 Konstanz, Germany.
authors.forename: Tanja
authors.identifier: 0000-0001-9276-1592
authors.initials: T
authors.lastname: Waldmann
authors.affiliation: Department of Statistics, Technical University of Dortmund , D-44221 Dortmund, Germany.
authors.forename: Marianna
authors.initials: M
authors.lastname: Grinberg
authors.affiliation: Department of Statistics, Technical University of Dortmund , D-44221 Dortmund, Germany.
authors.forename: André
authors.initials: A
authors.lastname: König
authors.affiliation: Department of Statistics, Technical University of Dortmund , D-44221 Dortmund, Germany.
authors.forename: Eugen
authors.initials: E
authors.lastname: Rempel
authors.affiliation: In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Chair Foundation, University of Konstanz , 78457 Konstanz, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Schildknecht
authors.affiliation: Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne (UKK) , D-50931 Cologne, Germany.
authors.forename: Margit
authors.initials: M
authors.lastname: Henry
authors.affiliation: In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Chair Foundation, University of Konstanz , 78457 Konstanz, Germany.
authors.forename: Anna-Katharina
authors.initials: AK
authors.lastname: Holzer
authors.affiliation: In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Chair Foundation, University of Konstanz , 78457 Konstanz, Germany.
authors.forename: Nadine
authors.initials: N
authors.lastname: Dreser
authors.affiliation: Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne (UKK) , D-50931 Cologne, Germany.
authors.forename: Vaibhav
authors.initials: V
authors.lastname: Shinde
authors.affiliation: Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne (UKK) , D-50931 Cologne, Germany.
authors.forename: Agapios
authors.initials: A
authors.lastname: Sachinidis
authors.affiliation: Department of Statistics, Technical University of Dortmund , D-44221 Dortmund, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Rahnenführer
authors.affiliation: Leibniz Research Centre for Working Environment and Human Factors (IfADo), Technical University of Dortmund , D-44139 Dortmund, Germany.
authors.forename: Jan G
authors.initials: JG
authors.lastname: Hengstler
authors.affiliation: In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Chair Foundation, University of Konstanz , 78457 Konstanz, Germany.
authors.forename: Marcel
authors.initials: M
authors.lastname: Leist
mesh_terms: D015415:Biomarkers / Q000378:metabolism; D002454:Cell Differentiation / Q000187:drug effects; D002460:Cell Line; D015536:Down-Regulation / Q000187:drug effects; D000066449:Human Embryonic Stem Cells / Q000166:cytology / Q000187:drug effects / Q000378:metabolism; D006801:Humans; D008767:Methylmercury Compounds / Q000633:toxicity*; D009474:Neurons / Q000166:cytology / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D025341:Principal Component Analysis; D015398:Signal Transduction / Q000187:drug effects; D059467:Transcriptome / Q000187:drug effects*; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism; D015854:Up-Regulation / Q000187:drug effects; D014635:Valproic Acid / Q000633:toxicity*
chemical_list: D015415:Biomarkers; D008767:Methylmercury Compounds; D016159:Tumor Suppressor Protein p53; D014635:Valproic Acid; C004925:methylmercuric chloride