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Series GSE141253 Query DataSets for GSE141253
Status Public on Dec 03, 2019
Title Development of a neural rosette formation assay (RoFA) to identify neurodevelopmental toxicants and to characterize their transcriptome disturbances
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The first in vitro tests for developmental toxicity made use of rodent cells. Newer teratology tests, e.g. developed during the ESNATS project, use human cells and measure mechanistic endpoints (such as transcriptome changes). However, the toxicological implications of mechanistic parameters are hard to judge, without functional/morphological endpoints. To address this issue, we developed a new version of the human stem cell-based test STOP-tox(UKN). For this purpose, the capacity of the cells to self-organize to neural rosettes was assessed as functional endpoint: pluripotent stem cells were allowed to differentiate to neuroepithelial cells for six days in the presence or absence of toxicants. Then, both transcriptome changes were measured (standard STOP-tox(UKN)), and cells were allowed to form rosettes. After optimization of staining methods, an imaging algorithm for rosette quantification was implemented and used for an automated rosette formation assay (RoFA). Neural tube toxicants (like valproic acid), which are known to disturb human development at stages when rosette-forming cells are present, were used as positive controls. Established toxicants led to distinctly different tissue organization and differentiation stages. RoFA outcome and transcript changes largely correlated concerning (i) the concentration-dependence, (ii) the time-dependence, and (iii) the set of positive hits identified amongst 24 potential toxicants. Using such comparative data, a prediction model for the RoFA was developed. The comparative analysis was also used to identify gene dysregulations that are particularly predictive for disturbed rosette formation. This ‘RoFA predictor gene set’ may be used for a simplified and less costly setup of the STOP-tox(UKN) assay.
 
Overall design We applied a test system (referred as the STOP-tox(UKN) or UKN1 test system) of developmental toxicity, related to the generation of neuroectoderm from human embryonic stem cells (hESCs), and exposed cells for six days to 24 different compounds (dimethyl sulfoxide, BIO, CHIR99021, lithium chloride, retinoic acid, geldanamycin, galnon, gleevec, estradiol, bisphenol A, interferon beta, cycloporin A/FK506, valproic acid, trichostatin-A, vorinostat, belinostat, panobinostat and entinostat, methylmercury, thimerosal, mercury(II)chloride, mercury(II)bromide, 4-chloromercuribenzoic acid and phenylmercuric acid). After 6 days, total RNA was isolated and gene expression studies were performed applying the human Genome U133 plus 2.0 arrays. Expression changes are always shown relative to an untreated control. At least three independent experiments have been performed.
 
Contributor(s) Sachinidis A, Leist M
Citation(s) 31712839
Submission date Dec 02, 2019
Last update date Mar 04, 2020
Contact name Marcel Leist
E-mail(s) [email protected]
Organization name University of Konstanz
Lab In vitro toxicology and biomedicine
Street address Universitätsstraße 10
City Konstanz
ZIP/Postal code 78464
Country Germany
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (148)
GSM4199846 hESCs, CHIR (0.000002 M) for 6 days, D14_14MK_164
GSM4199847 hESCs, BIO (0.000002 M) for 6 days, D14_13MK_165
GSM4199848 hESCs, incubated with culturing medium for 6 days, D15_13MK_166
Relations
BioProject PRJNA592964

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Supplementary file Size Download File type/resource
GSE141253_RAW.tar 662.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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