Comparison of gene expression regulation in mouse- and human embryonic stem cell assays during neural differentiation and in response to valproic acid exposure

StemPanTox: A fast and wide-target drug assessment system for tailor-made safety evaluations using personalized iPS cells

An alternative model that reliably predicts human-specific toxicity is necessary because the translatability of effects on animal models for human disease is limited to context. Previously, we developed a method that accurately predicts developmental toxicity based on the gene networks of undifferentiated human embryonic stem (ES) cells. Here, we advanced this method to predict adult toxicities of 24 chemicals in six categories (neurotoxins, cardiotoxins, hepatotoxins, two types of nephrotoxins, and non-genotoxic carcinogens) and achieved high predictability (AUC = 0.90-1.00) in all categories. Moreover, we screened for an induced pluripotent stem (iPS) cell line to predict the toxicities based on the gene networks of iPS cells using transfer learning of the gene networks of ES cells, and predicted toxicities in four categories (neurotoxins, hepatotoxins, glomerular nephrotoxins, and non-genotoxic carcinogens) with high performance (AUC = 0.82-0.99). This method holds promise for tailor-made safety evaluations using personalized iPS cells.

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.

Design and validation of an ontology-driven animal-free testing strategy for developmental neurotoxicity testing

Developmental neurotoxicity entails one of the most complex areas in toxicology. Animal studies provide only limited information as to human relevance. A multitude of alternative models have been developed over the years, providing insights into mechanisms of action. We give an overview of fundamental processes in neural tube formation, brain development and neural specification, aiming at illustrating complexity rather than comprehensiveness. We also give a flavor of the wealth of alternative methods in this area. Given the impressive progress in mechanistic knowledge of human biology and toxicology, the time is right for a conceptual approach for designing testing strategies that cover the integral mechanistic landscape of developmental neurotoxicity. The ontology approach provides a framework for defining this landscape, upon which an integral in silico model for predicting toxicity can be built. It subsequently directs the selection of in vitro assays for rate-limiting events in the biological network, to feed parameter tuning in the model, leading to prediction of the toxicological outcome. Validation of such models requires primary attention to coverage of the biological domain, rather than classical predictive value of individual tests. Proofs of concept for such an approach are already available. The challenge is in mining modern biology, toxicology and chemical information to feed intelligent designs, which will define testing strategies for neurodevelopmental toxicity testing.

Transcriptional and splicing dysregulation in the prefrontal cortex in valproic acid rat model of autism

Gene-environmental interaction could be the major cause of autism. The aim of the current study is to detect the effects of valproic acid on gene expression profiles and alternatively spliced genes in the prefrontal cortex in rat models of autism. Female rats received a single intraperitoneal injection of 600 mg/kg valproic acid at day 12.5 post-conception, and controls were injected with saline. Only male offspring were employed in the current study. RNA sequencing was used to investigate transcriptome in the prefrontal cortex of VPA-exposed rats. There were 3228 differently expressed genes and 637 alternative spliced genes, in VPA rats compared to controls. Pathways enrichment among the differently expressed genes and alternatively spliced genes were associated with neurological diseases and neural system development. The results implied VPA affected transcriptional and splicing events genome-wide and the transcriptional and splicing events may be associated with the autistic behaviors of VPA rats.

Adverse effect of valproic acid on an in vitro gastrulation model entails activation of retinoic acid signaling

Valproic acid (VPA), an antiepileptic drug, is a teratogen that causes neural tube and axial skeletal defects, although the mechanisms are not fully understood. We previously established a gastrulation model using mouse P19C5 stem cell embryoid bodies (EBs), which exhibits axial patterning and elongation morphogenesis in vitro. Here, we investigated the effects of VPA on the EB axial morphogenesis to gain insights into its teratogenic mechanisms. Axial elongation and patterning of EBs were inhibited by VPA at therapeutic concentrations. VPA elevated expression levels of various developmental regulators, including Cdx1 and Hoxa1, known transcriptional targets of retinoic acid (RA) signaling. Co-treatment of EBs with VPA and BMS493, an RA receptor antagonist, partially rescued axial elongation as well as gene expression profiles. These results suggest that VPA requires active RA signaling to interfere with EB morphogenesis.