Stem Cell transcriptome responses and corresponding biomarkers that indicate the transition from adaptive responses to cytotoxicity

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2017
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Grinberg, Marianna
König, André
Rempel, Eugen
Henry, Margit
Shinde, Vaibhav
Sachinidis, Agapios
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Chemical research in toxicology. 2017, 30(4), pp. 905-922. ISSN 0893-228X. eISSN 1520-5010. Available under: doi: 10.1021/acs.chemrestox.6b00259
Zusammenfassung

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.

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ISO 690WALDMANN, Tanja, Marianna GRINBERG, André KÖNIG, Eugen REMPEL, Stefan SCHILDKNECHT, Margit HENRY, Anna-Katharina HOLZER, Nadine DRESER, Vaibhav SHINDE, Agapios SACHINIDIS, Jörg RAHNENFÜHRER, Jan G HENGSTLER, Marcel LEIST, 2017. Stem Cell transcriptome responses and corresponding biomarkers that indicate the transition from adaptive responses to cytotoxicity. In: Chemical research in toxicology. 2017, 30(4), pp. 905-922. ISSN 0893-228X. eISSN 1520-5010. Available under: doi: 10.1021/acs.chemrestox.6b00259
BibTex
@article{Waldmann2017-04-17trans-36721,
  year={2017},
  doi={10.1021/acs.chemrestox.6b00259},
  title={Stem Cell transcriptome responses and corresponding biomarkers that indicate the transition from adaptive responses to cytotoxicity},
  number={4},
  volume={30},
  issn={0893-228X},
  journal={Chemical research in toxicology},
  pages={905--922},
  author={Waldmann, Tanja and Grinberg, Marianna and König, André and Rempel, Eugen and Schildknecht, Stefan and Henry, Margit and Holzer, Anna-Katharina and Dreser, Nadine and Shinde, Vaibhav and Sachinidis, Agapios and Rahnenführer, Jörg and Hengstler, Jan G and Leist, Marcel}
}
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