Transcriptome meta-analysis of valproic acid exposure in human embryonic stem cells

Valproic acid (VPA) is a widely used antiepileptic drug not recommended in pregnancy because it is teratogenic. Many assays have assessed the impact of the VPA exposure on the transcriptome of human embryonic stem-cells (hESC), but the molecular perturbations that VPA exerts in neurodevelopment are not completely understood. This study aimed to perform a transcriptome meta-analysis of VPA-exposed hESC to elucidate the main biological mechanisms altered by VPA effects on the gene expression. Publicly available microarray and RNA-seq transcriptomes were selected in the Gene Expression Omnibus (GEO) repository. Samples were processed according to the standard pipelines for each technology in the Galaxy server and R. Meta-analysis was performed using the Fisher-P method. Overrepresented genes were obtained by evaluating ontologies, pathways, and phenotypes' databases. The meta-analysis performed in seven datasets resulted in 61 perturbed genes, 54 upregulated. Ontology and pathway enrichments suggested neurodevelopment and neuroinflammatory effects; phenotype overrepresentation included epilepsy-related genes, such as SCN1A and GABRB2. The NDNF gene upregulation was also identified; this gene is involved in neuron migration and survival during development. Sub-network analysis proposed TGFβ and BMP pathways activation. These results suggest VPA exerts effects in epilepsy-related genes even in embryonic cells. Neurodevelopmental genes, such as NDNF were upregulated and VPA might also disturb several development pathways. These mechanisms might help to explain the spectrum of VPA-induced congenital anomalies and the molecular effects on neurodevelopment.