A comparative transcriptomic study on the effects of valproic acid on two different hESCs lines in a neural teratogenicity test system

Bioinformatics Methods for Transcriptome Analysis on Teratogenesis Testing

Teratogenesis testing can be challenging due to the limitations of both in vitro and in vivo models. Test-systems, based especially on human embryonic cells, have been helping to overcome the difficulties when allied to omics strategies, such as transcriptomics. In these test-systems, cells exposed to different compounds are then analyzed in microarray or RNA-seq platforms regarding the impacts of the potential teratogens in the gene expression. Nevertheless, microarray and RNA-seq dataset processing requires computational resources and bioinformatics knowledge. Here, a pipeline for microarray and RNA-seq processing is presented, aiming to help researchers from any field to interpret the main transcriptome results, such as differential gene expression, enrichment analysis, and statistical interpretation. This chapter also discusses the main difficulties that can be encountered in a transcriptome analysis and the better alternatives to overcome these issues, describing both programming codes and user-friendly tools. Finally, specific issues in the teratogenesis field, such as time-course analysis, are also described, demonstrating how the pipeline can be applied in these studies.

Evaluation of postmortem microarray data in bipolar disorder using traditional data comparison and artificial intelligence reveals novel gene targets

Large-scale microarray studies on post-mortem brain tissues have been utilized to investigate the complex molecular pathology of bipolar disorder. However, a major challenge in characterizing the dysregulation of gene expression in patients with bipolar disorder includes the lack of convergence between different studies, limiting comprehensive understanding from individual results. In this study, we aimed to identify genes that are both validated in published literature and are important classification features of unsupervised machine learning analysis of Stanley Brain Bank microarray database, followed by augmented intelligence method to identify distinct patient molecular subgroups. Through combining traditional literature approaches and machine learning, we identified TBL1XR1, SMARCA2, and CHMP5 to be replicated in 3 of the 4 studies included our analysis. The expression of these genes segregated unique subgroups of patients with bipolar disorder. Our study suggests the involvement of PPARγ pathway regulation in patients with bipolar disorder.

A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood

Background

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects more than 1% of children in the USA. ASD risk is thought to arise from both genetic and environmental factors, with the perinatal period as a critical window. Understanding early transcriptional changes in ASD would assist in clarifying disease pathogenesis and identifying biomarkers. However, little is known about umbilical cord blood gene expression profiles in babies later diagnosed with ASD compared to non-typically developing and non-ASD (Non-TD) or typically developing (TD) children.

Methods

Genome-wide transcript levels were measured by Affymetrix Human Gene 2.0 array in RNA from cord blood samples from both the Markers of Autism Risk in Babies-Learning Early Signs (MARBLES) and the Early Autism Risk Longitudinal Investigation (EARLI) high-risk pregnancy cohorts that enroll younger siblings of a child previously diagnosed with ASD. Younger siblings were diagnosed based on assessments at 36 months, and 59 ASD, 92 Non-TD, and 120 TD subjects were included. Using both differential expression analysis and weighted gene correlation network analysis, gene expression between ASD and TD, and between Non-TD and TD, was compared within each study and via meta-analysis.

Results

While cord blood gene expression differences comparing either ASD or Non-TD to TD did not reach genome-wide significance, 172 genes were nominally differentially expressed between ASD and TD cord blood (log₂(fold change) > 0.1, p < 0.01). These genes were significantly enriched for functions in xenobiotic metabolism, chromatin regulation, and systemic lupus erythematosus (FDR q < 0.05). In contrast, 66 genes were nominally differentially expressed between Non-TD and TD, including 8 genes that were also differentially expressed in ASD. Gene coexpression modules were significantly correlated with demographic factors and cell type proportions.

Limitations

ASD-associated gene expression differences identified in this study are subtle, as cord blood is not the main affected tissue, it is composed of many cell types, and ASD is a heterogeneous disorder.

Conclusions

This is the first study to identify gene expression differences in cord blood specific to ASD through a meta-analysis across two prospective pregnancy cohorts. The enriched gene pathways support involvement of environmental, immune, and epigenetic mechanisms in ASD etiology.

Neural crest related gene transcript regulation by valproic acid analogues in the cardiac embryonic stem cell test

In vivo, neural crest (NC) cells contribute critically to heart formation. The embryonic stem cells in the cardiac Embryonic Stem cell Test (ESTc) differentiate into a heterogeneous cell population including non-cardiomyocyte cells. The use of molecular biomarkers from different mechanistic pathways can refine quantitative embryotoxicity assessment. Gene expression levels representing different signalling pathways that could relate to beating cardiomyocyte formation were analysed at different time-points. Immunocytochemistry showed NC cells were present in the ESTc and RT-qPCR showed upregulation of NC related gene expression levels in a time-dependent manner. NC related genes were sensitive to VPA and its analogues 2-ethylhexanoic acid (EHA) and 2-ethylhexanol (EHOL) and indicated VPA as the most potent one. STITCH ('search tool for interactions of chemicals') analysis showed relationships between the examined signalling pathways and suggested additional candidate marker genes. Biomarkers from dedicated mechanistic pathways, e.g. NC differentiation, provide promising tools for monitoring specific effects in ESTc.

Accuracy, discriminative properties and reliability of a human ESC-based in vitro toxicity assay to distinguish teratogens responsible for neural tube defects

The poor correlation of developmental toxicity studies in animals with human outcome data has emphasized the need for complementary assays based on human cells and tissues. As neural tube defects represent an important proportion of congenital malformations, we evaluated here the accuracy of a human embryonic stem cell (hESC)-based assay to predict chemically induced disruption of neural tube formation. As teratogenic compounds, we used cyclopamine (CPA), valproic acid (VPA), ochratoxin A (OTA) and mycophenolic acid (MMF), all suspected or known inducers of human neural tube defects, as well as theophylline and saccharin as negative control compounds. We analyzed their effects on the ability of hES cells to give rise to neural precursors (expressing specific marker Nestin), to form neural tube-like structures (rosettes), and to express specific markers (Sox1, Otx2, Lix1, EvI1, Rspo3) during rosette formation. The results showed that various effects of the selected compounds on early neural development could be specifically revealed in vitro through related alterations of neurogenic differentiation of hESC. Furthermore, it was possible to discriminate toxicants acting at different time points during embryonic development and, therefore, responsible for distinct adverse effects on neural tube formation. By comparing four different hESC lines, we observed a significant (up to fivefold) variability of the line-dependent response to toxicants. We highlight at least two sources of variability: one related to the heterogeneity of hESC lines in culture (stemness/commitment profiles); the second to possible genetically determined differences in individual sensitivity to teratogens.

A standardized human embryoid body platform for the detection and analysis of teratogens

Teratogens are compounds that can induce birth defects upon exposure of the developing fetus. To date, most teratogen studies utilize pregnant rodents to determine compound teratogenicity in vivo. However, this is a low throughput approach that cannot easily meet the need for comprehensive high-volume teratogen assessment, a goal of the US Environmental Protection Agency. In addition, rodent and human development differ substantially, and therefore the use of assays using relevant human cells has utility. For these reasons, interest has recently focused on the use of human embryonic stem cells for teratogen assessment. Here we present a highly standardized and quantitative system for the detection and analysis of teratogens that utilizes well-characterized and purified highly pluripotent stem cells. We have devised strategies to mass-produce thousands of uniformly sized spheroids of human ESCs (hESCs) that can be caused to undergo synchronous differentiation to yield embryoid bodies (EBs) in the presence and absence of suspected teratogens. The system uses all human cells and rigorously controlled and standardized EB culture conditions. Furthermore, the approach has been made quantitative by using high-content imaging approaches. Our system offers distinct advantages over earlier EB systems that rely heavily on the use on mouse ESCs and EB aggregates of stochastic sizes. Together, our results show that thousands of suspected teratogens could be assessed using human EB-based approaches.

Mood stabilizing drugs regulate transcription of immune, neuronal and metabolic pathway genes in Drosophila

RATIONALE

Lithium and valproate (VPA) are drugs used in the management of bipolar disorder. Even though they reportedly act on various pathways, the transcriptional targets relevant for disease mechanism and therapeutic effect remain unclear. Furthermore, multiple studies used lymphoblasts of bipolar patients as a cellular proxy, but it remains unclear whether peripheral cells provide a good readout for the effects of these drugs in the brain.

OBJECTIVES

We used Drosophila culture cells and adult flies to analyze the transcriptional effects of lithium and VPA and define mechanistic pathways.

METHODS

Transcriptional profiles were determined for Drosophila S2-cells and adult fly heads following lithium or VPA treatment. Gene ontology categories were identified using the DAVID functional annotation tool with a cut-off of p < 0.05. Significantly enriched GO terms were clustered using REVIGO and DAVID functional annotation clustering. Significance of overlap between transcript lists was determined with a Fisher's exact hypergeometric test.

RESULTS

Treatment of cultured cells and adult flies with lithium and VPA induces transcriptional responses in genes with similar ontology, with as most prominent immune response, neuronal development, neuronal function, and metabolism.

CONCLUSIONS

(i) Transcriptional effects of lithium and VPA in Drosophila S2 cells and heads show significant overlap. (ii) The overlap between transcriptional alterations in peripheral versus neuronal cells at the single gene level is negligible, but at the gene ontology and pathway level considerable overlap can be found. (iii) Lithium and VPA act on evolutionarily conserved pathways in Drosophila and mammalian models.