Related Experiment Video
Updated: May 16, 2026
Human Pluripotent Stem Cell Based Developmental Toxicity Assays for Chemical Safety Screening and Systems Biology Data Generation
Published on: June 17, 2015
Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach
Anne K Krug1, Raivo Kolde, John A Gaspar
1Department of Biology, University of Konstanz, 78457 Constance, Germany.
Abstract:
Developmental neurotoxicity (DNT) and many forms of reproductive toxicity (RT) often manifest themselves in functional deficits that are not necessarily based on cell death, but rather on minor changes relating to cell differentiation or communication. The fields of DNT/RT would greatly benefit from in vitro tests that allow the identification of toxicant-induced changes of the cellular proteostasis, or of its underlying transcriptome network. Therefore, the 'human embryonic stem cell (hESC)-derived novel alternative test systems (ESNATS)' European commission research project established RT tests based on defined differentiation protocols of hESC and their progeny. Valproic acid (VPA) and methylmercury (MeHg) were used as positive control compounds to address the following fundamental questions: (1) Does transcriptome analysis allow discrimination of the two compounds? (2) How does analysis of enriched transcription factor binding sites (TFBS) and of individual probe sets (PS) distinguish between test systems? (3) Can batch effects be controlled? (4) How many DNA microarrays are needed? (5) Is the highest non-cytotoxic concentration optimal and relevant for the study of transcriptome changes? VPA triggered vast transcriptional changes, whereas MeHg altered fewer transcripts. To attenuate batch effects, analysis has been focused on the 500 PS with highest variability. The test systems differed significantly in their responses (<20 % overlap). Moreover, within one test system, little overlap between the PS changed by the two compounds has been observed. However, using TFBS enrichment, a relatively large 'common response' to VPA and MeHg could be distinguished from 'compound-specific' responses. In conclusion, the ESNATS assay battery allows classification of human DNT/RT toxicants on the basis of their transcriptome profiles.
Insights
The ESNATS assay battery effectively classifies human developmental and reproductive toxicants using transcriptome profiles. This novel approach identifies subtle cellular changes, offering a new in vitro method for toxicity testing.
Area of Science:
- Toxicology and pharmacology
- Stem cell biology
- Genomics and transcriptomics
Background:
- Developmental neurotoxicity (DNT) and reproductive toxicity (RT) often involve subtle cellular changes, not just cell death.
- Existing methods lack in vitro tests to detect toxicant-induced changes in cellular proteostasis or transcriptome networks.
- The ESNATS project aimed to develop novel alternative test systems using human embryonic stem cells (hESC).
Purpose of the Study:
- To establish and validate in vitro reproductive toxicity (RT) tests using hESC-derived differentiation protocols.
- To investigate the utility of transcriptome analysis for discriminating between toxicants like Valproic Acid (VPA) and Methylmercury (MeHg).
- To assess the influence of transcription factor binding sites (TFBS) and probe sets (PS) in differentiating toxicant responses.
Main Methods:
- Utilized human embryonic stem cell (hESC)-derived differentiation protocols for novel alternative test systems (ESNATS).
- Employed transcriptome analysis, including DNA microarrays, to study cellular responses to VPA and MeHg.
- Applied transcription factor binding site (TFBS) enrichment analysis to identify common and compound-specific responses.
Main Results:
- Valproic acid (VPA) induced extensive transcriptional changes, while methylmercury (MeHg) affected fewer transcripts.
- ESNATS test systems showed significant differences in toxicant response profiles with less than 20% overlap.
- TFBS enrichment successfully identified a common response pattern to both VPA and MeHg, distinguishing it from compound-specific effects.
Conclusions:
- The ESNATS assay battery, based on hESC differentiation and transcriptome profiling, can classify human DNT/RT toxicants.
- Transcriptome analysis combined with TFBS enrichment provides a sensitive method to detect and differentiate toxic effects at the molecular level.
- This approach offers a valuable in vitro alternative for assessing developmental and reproductive toxicity, moving beyond traditional cell death assays.
More Related Videos
09:02Protocol for the Differentiation of Human Induced Pluripotent Stem Cells into Mixed Cultures of Neurons and Glia for Neurotoxicity Testing
Published on: June 9, 2017
05:45Developmental Toxicity Assay Based on Real-Time Monitoring of Fibroblast Growth Factor Signal Disruption in Human Induced Pluripotent Stem Cells
Published on: October 10, 2025