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Background  Human embryonic stem cells (hESCs) partially recapitulate early embryonic three germ layer development, allowing testing of potential teratogenic hazards. Because use of hESCs is ethically debated, we investigated the potential for human induced pluripotent stem cells (hiPSCs) to replace hESCs in such tests.    Methods  Three cell lines, comprising hiPSCs (foreskin and IMR90) and hESCs (H9) were differentiated for 14 days. Their transcriptome profiles were obtained on day 0 and day 14 and analyzed by comprehensive bioinformatics tools.    Results  The transcriptomes on day 14 showed that more than 70% of the “developmental genes” (regulated genes with > 2-fold change on day 14 compared to day 0) exhibited variability among cell lines. The developmental genes belonging to all three cell lines captured biological processes and KEGG pathways related to all three germ layer embryonic development. In addition, transcriptome profiles were obtained after 14 days of exposure to teratogenic valproic acid (VPA) during differentiation. Although the differentially regulated genes between treated and untreated samples showed more than 90% variability among cell lines, VPA clearly antagonized the expression of developmental genes in all cell lines: suppressing upregulated developmental genes, while inducing downregulated ones. To quantify VPA-disturbed development based on developmental genes, we estimated the “developmental potency” ( D    p  ) and “developmental index” ( D    i  ).    Conclusions  Despite differences in genes deregulated by VPA, uniform  D    i   values were obtained for all three cell lines. Given that the  D    i   values for VPA were similar for hESCs and hiPSCs,  D    i   can be used for robust hazard identification, irrespective of whether hESCs or hiPSCs are used in the test systems.    Electronic supplementary material  The online version of this article (doi:10.1186/s13287-016-0449-2) contains supplementary material, which is available to authorized users.

Comparison of a teratogenic transcriptome-based predictive test based on human embryonic versus inducible pluripotent stem cells