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.

A New Strategy for the Old Challenge of Thalidomide: Systems Biology Prioritization of Potential Immunomodulatory Drug (IMiD)-Targeted Transcription Factors.

Several molecular mechanisms of thalidomide embryopathy (TE) have been investigated, from anti-angiogenesis to oxidative stress to cereblon binding. Recently, it was discovered that thalidomide and its analogs, named immunomodulatory drugs (IMiDs), induced the degradation of C2H2 transcription factors (TFs). This mechanism might impact the strict transcriptional regulation of the developing embryo. Hence, this study aims to evaluate the TFs altered by IMiDs, prioritizing the ones associated with embryogenesis through transcriptome and systems biology-allied analyses. This study comprises only the experimental data accessed through bioinformatics databases. First, proteins and genes reported in the literature as altered/affected by the IMiDs were annotated. A protein systems biology network was evaluated. TFs beta-catenin (CTNNB1) and SP1 play more central roles: beta-catenin is an essential protein in the network, while SP1 is a putative C2H2 candidate for IMiD-induced degradation. Separately, the differential expressions of the annotated genes were analyzed through 23 publicly available transcriptomes, presenting 8624 differentially expressed genes (2947 in two or more datasets). Seventeen C2H2 TFs were identified as related to embryonic development but not studied for IMiD exposure; these TFs are potential IMiDs degradation neosubstrates. This is the first study to suggest an integration of IMiD molecular mechanisms through C2H2 TF degradation.

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 TGFß 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.

Neurodevelopment in Children Exposed to Zika in utero: Clinical and Molecular Aspects.

Five years after the identification of Zika virus as a human teratogen, we reviewed the early clinical manifestations, collectively called congenital Zika syndrome (CZS). Children with CZS have a very poor prognosis with extremely low performance in motor, cognitive, and language development domains, and practically all feature severe forms of cerebral palsy. However, these manifestations are the tip of the iceberg, with some children presenting milder forms of deficits. Additionally, neurodevelopment can be in the normal range in the majority of the non-microcephalic children born without brain or eye abnormalities. Vertical transmission and the resulting disruption in development of the brain are much less frequent when maternal infection occurs in the second half of the pregnancy. Experimental studies have alerted to the possibility of other behavioral outcomes both in prenatally infected children and in postnatal and adult infections. Cofactors play a vital role in the development of CZS and involve genetic, environmental, nutritional, and social determinants leading to the asymmetric distribution of cases. Some of these social variables also limit access to multidisciplinary professional treatment.

National congenital anomaly registers in the world: historical and operational aspects. / Registros nacionais de anomalias congênitas no mundo: aspectos históricos e operacionais.

OBJECTIVE: To identify registers of congenital anomalies with national coverage currently available around the world, highlighting their main historical and operational characteristics. METHODS: This was a documentary study by means of a Medline database search (via PubMed) and searches involving reports, official documents and websites. Studies reporting at least one national registry were included. RESULTS: 40 registers of national congenital anomalies were identified in 39 different countries. All registers included in the study were concentrated in upper-middle or high-income countries located in Europe. Most of the registers were population-based, compulsory notification and with a time limit for notification of up to 1 year of age. The Brazilian register showed the highest annual coverage. CONCLUSION: The registers analyzed showed different characteristics, related to the reality of each country. The results presented provide support for the theme of congenital anomalies surveillance, especially in places where such activity is intended to be implemented.

National registries of congenital anomalies in the world: historical and operational aspects / Registros nacionales de anomalías congénitas en el mundo: aspectos históricos y operativos / Registros nacionais de anomalias congênitas no mundo: aspectos históricos e operacionais

Objective: To identify registries of congenital anomalies with national coverage existing around the world, highlighting its main historical and operational characteristics. Methods: Document review of literature on the Medline/Pubmed database and data from reports, official documents and websites. Works relating at least one national register were included. Results: 40 national registries of congenital anomalies were identified in 39 different countries. All registries included in the study were located in high- or uppermiddle-income countries, with a concentration in Europe. Most of the registries were population-based, with mandatory notification and time limit of notification of up to one year of age. The Brazilian registry presented the highest annual coverage. Conclusion: The registries discussed here presented different characteristics, which were related to the reality of each country. The presented results provide subsidies for surveillance of congenital anomalies, especially in places that wish to implement such an activity.

Objetivo: Identificar registros de anomalias congênitas com cobertura nacional existentes no mundo, destacando suas principais características históricas e operacionais. Métodos: Revisão documental, mediante busca na base Medline/Pubmed e consulta a dados provenientes de relatórios, documentos oficiais e sítios eletrônicos. Foram incluídos trabalhos com relato de pelo menos um registro nacional. Resultados: Identificou-se 40 registros nacionais de anomalias congênitas em 39 países diferentes. Todos os registros incluídos no estudo localizavam-se em países de renda alta ou média superior, com concentração na Europa. A maior parte dos registros foi de base populacional, de notificação compulsória e com tempo limite para notificação de até um ano de idade. O registro brasileiro apresentou a maior cobertura anual. Conclusão: Os registros discutidos apresentaram características diversas, relacionadas à realidade de cada país. Os resultados apresentados fornecem subsídios para a temática da vigilância das anomalias congênitas, sobretudo em locais onde se deseja implementar tal atividade.

Comparative Genomics Identifies Putative Interspecies Mechanisms Underlying Crbn-Sall4-Linked Thalidomide Embryopathy.

The identification of thalidomide-Cereblon-induced SALL4 degradation has brought new understanding for thalidomide embryopathy (TE) differences across species. Some questions, however, regarding species variability, still remain. The aim of this study was to detect sequence divergences between species, affected or not by TE, and to evaluate the regulated gene co-expression in a murine model. Here, we performed a comparative analysis of proteins experimentally established as affected by thalidomide exposure, evaluating 14 species. The comparative analysis, regarding synteny, neighborhood, and protein conservation, was performed in 42 selected genes. Differential co-expression analysis was performed, using a publicly available assay, GSE61306, which evaluated mouse embryonic stem cells (mESC) exposed to thalidomide. The comparative analyses evidenced 20 genes in the upstream neighborhood of NOS3, which are different between the species who develop, or not, the classic TE phenotype. Considering protein sequence alignments, RECQL4, SALL4, CDH5, KDR, and NOS2 proteins had the biggest number of variants reported in unaffected species. In co-expression analysis, Crbn was a gene identified as a driver of the co-expression of other genes implicated in genetic, non-teratogenic, limb reduction defects (LRD), such as Tbx5, Esco2, Recql4, and Sall4; Crbn and Sall4 were shown to have a moderate co-expression correlation, which is affected after thalidomide exposure. Hence, even though the classic TE phenotype is not identified in mice, a deregulatory Crbn-induced mechanism is suggested in this animal. Functional studies are necessary, especially evaluating the genes responsible for LRD syndromes and their interaction with thalidomide-Cereblon.

Genetic Susceptibility to Drug Teratogenicity: A Systematic Literature Review.

Since the 1960s, drugs have been known to cause teratogenic effects in humans. Such teratogenicity has been postulated to be influenced by genetics. The aim of this review was to provide an overview of the current knowledge on genetic susceptibility to drug teratogenicity in humans and reflect on future directions within the field of genetic teratology. We focused on 12 drugs and drug classes with evidence of teratogenic action, as well as 29 drugs and drug classes with conflicting evidence of fetal safety in humans. An extensive literature search was performed in the PubMed and EMBASE databases using terms related to the drugs of interest, congenital anomalies and fetal development abnormalities, and genetic variation and susceptibility. A total of 29 studies were included in the final data extraction. The eligible studies were published between 1999 and 2020 in 10 different countries, and comprised 28 candidate gene and 1 whole-exome sequencing studies. The sample sizes ranged from 20 to 9,774 individuals. Several drugs were investigated, including antidepressants (nine studies), thalidomide (seven studies), antiepileptic drugs (five studies), glucocorticoids (four studies), acetaminophen (two studies), and sex hormones (estrogens, one study; 17-alpha hydroxyprogesterone caproate, one study). The main neonatal phenotypic outcomes included perinatal complications, cardiovascular congenital anomalies, and neurodevelopmental outcomes. The review demonstrated that studies on genetic teratology are generally small, heterogeneous, and exhibit inconsistent results. The most convincing findings were genetic variants in SLC6A4, MTHFR, and NR3C1, which were associated with drug teratogenicity by antidepressants, antiepileptics, and glucocorticoids, respectively. Notably, this review demonstrated the large knowledge gap regarding genetic susceptibility to drug teratogenicity, emphasizing the need for further efforts in the field. Future studies may be improved by increasing the sample size and applying genome-wide approaches to promote the interpretation of results. Such studies could support the clinical implementation of genetic screening to provide safer drug use in pregnant women in need of drugs.

Registros nacionais de anomalias congênitas no mundo: aspectos históricos e operacionais / Registros nacionales de anomalías congénitas en el mundo: aspectos históricos y operativos / National congenital anomaly registers in the world: historical and operational aspects

Objetivo: Identificar registros de anomalias congênitas com cobertura nacional existentes no mundo, destacando suas principais características históricas e operacionais. Métodos: Revisão documental, mediante busca na base Medline/Pubmed e consulta a dados provenientes de relatórios, documentos oficiais e sítios eletrônicos. Foram incluídos trabalhos com relato de pelo menos um registro nacional. Resultados: Foram identificados 40 registros nacionais de anomalias congênitas em 39 países diferentes. Todos os registros incluídos no estudo localizavam-se em países de renda alta ou média superior, com concentração na Europa. A maior parte dos registros foi de base populacional, de notificação compulsória e com tempo limite para notificação de até 1 ano de idade. O registro brasileiro apresentou a maior cobertura anual. Conclusão: Os registros discutidos apresentaram características diversas, relacionadas à realidade de cada país. Os resultados apresentados fornecem subsídios para a temática da vigilância das anomalias congênitas, sobretudo em locais onde se deseja implementar tal atividade.

Objetivo: Identificar registros de anomalías congénitas con cobertura nacional existentes en el mundo, destacando sus principales características históricas y operativas. Métodos: Revisión documental de literatura en la base de datos Medline/Pubmed y datos de informes, documentos oficiales y sitios web. Se incluyeron trabajos con informes de al menos un registro nacional. Resultados: Se identificaron 40 registros nacionales de anomalías congénitas en 39 países diferentes. Todos los registros incluidos se ubicaron en países de ingresos altos y medianos altos, con una concentración en Europa. La mayoría de los registros eran de base poblacional, con notificación obligatoria y un límite de tiempo de notificación de hasta 1 año. El registro brasileño presentá la cobertura anual más alta. Conclusión: Los registros discutidos presentaban características diferentes y relacionadas con la realidad de cada país. Los resultados presentados proporcionan subsidios para la vigilancia de anomalías congénitas, especialmente en lugares que deseen implementar dicha actividad.

Objective: To identify registers of congenital anomalies with national coverage currently available around the world, highlighting their main historical and operational characteristics. Methods: This was a documentary study by means of a Medline database search (via PubMed) and searches involving reports, official documents and websites. Studies reporting at least one national registry were included. Results: 40 registers of national congenital anomalies were identified in 39 different countries. All registers included in the study were concentrated in upper-middle or high-income countries located in Europe. Most of the registers were population-based, compulsory notification and with a time limit for notification of up to 1 year of age. The Brazilian register showed the highest annual coverage. Conclusion: The registers analyzed showed different characteristics, related to the reality of each country. The results presented provide support for the theme of congenital anomalies surveillance, especially in places where such activity is intended to be implemented.

Anticonvulsants and Chromatin-Genes Expression: A Systems Biology Investigation.

Embryofetal development is a critical process that needs a strict epigenetic control, however, perturbations in this balance might lead to the occurrence of congenital anomalies. It is known that anticonvulsants potentially affect epigenetics-related genes, however, it is not comprehended whether this unbalance could explain the anticonvulsants-induced fetal syndromes. In the present study, we aimed to evaluate the expression of epigenetics-related genes in valproic acid, carbamazepine, or phenytoin exposure. We selected these three anticonvulsants exposure assays, which used murine or human embryonic stem-cells and were publicly available in genomic databases. We performed a differential gene expression (DGE) and weighted gene co-expression network analysis (WGCNA), focusing on epigenetics-related genes. Few epigenetics genes were differentially expressed in the anticonvulsants' exposure, however, the WGCNA strategy demonstrated a high enrichment of chromatin remodeling genes for the three drugs. We also identified an association of 46 genes related to Fetal Valproate Syndrome, containing SMARCA2 and SMARCA4, and nine genes to Fetal Hydantoin Syndrome, including PAX6, NEUROD1, and TSHZ1. The evaluation of stem-cells under drug exposure can bring many insights to understand the drug-induced damage to the embryofetal development. The candidate genes here presented are potential biomarkers that could help in future strategies for the prevention of congenital anomalies.

CRL4-Cereblon complex in Thalidomide Embryopathy: a translational investigation.

The Cereblon-CRL4 complex has been studied predominantly with regards to thalidomide treatment of multiple myeloma. Nevertheless, the role of Cereblon-CRL4 in Thalidomide Embryopathy (TE) is still not understood. Not all embryos exposed to thalidomide develop TE, hence here we evaluate the role of the CRL4-Cereblon complex in TE variability and susceptibility. We sequenced CRBN, DDB1, CUL4A, IKZF1, and IKZF3 in individuals with TE. To better interpret the variants, we suggested a score and a heatmap comprising their regulatory effect. Differential gene expression after thalidomide exposure and conservation of the CRL4-Cereblon protein complex were accessed from public repositories. Results suggest a summation effect of Cereblon variants on pre-axial longitudinal limb anomalies, and heatmap scores identify the CUL4A variant rs138961957 as potentially having an effect on TE susceptibility. CRL4-Cereblon gene expression after thalidomide exposure and CLR4-Cereblon protein conservation does not explain the difference in Thalidomide sensitivity between species. In conclusion, we suggest that CRL4-Cereblon variants act through several regulatory mechanisms, which may influence CRL4-Cereblon complex assembly and its ability to bind thalidomide. Human genetic variability must be addressed not only to further understand the susceptibility to TE, but as a crucial element in therapeutics, including in the development of pharmacogenomics strategies.

The role of ESCO2, SALL4 and TBX5 genes in the susceptibility to thalidomide teratogenesis.

Thalidomide is widely used for several diseases; however, it causes malformations in embryos exposed during pregnancy. The complete understanding of the mechanisms by which thalidomide affects the embryo development has not yet been obtained. The phenotypic similarity makes TE a phenocopy of syndromes caused by mutations in ESCO2, SALL4 and TBX5 genes. Recently, SALL4 and TBX5 were demonstrated to be thalidomide targets. To understand if these genes act in the TE development, we sequenced them in 27 individuals with TE; we verified how thalidomide affect them in human pluripotent stem cells (hPSCs) through a differential gene expression (DGE) analysis from GSE63935; and we evaluated how these genes are functionally related through an interaction network analysis. We identified 8 variants in ESCO2, 15 in SALL4 and 15 in TBX5. We compared allelic frequencies with data from ExAC, 1000 Genomes and ABraOM databases; eight variants were significantly different (p < 0.05). Eleven variants in SALL4 and TBX5 were previously associated with cardiac diseases or malformations; however, in TE sample there was no association. Variant effect prediction tools showed 97% of the variants with potential to influence in these genes regulation. DGE analysis showed a significant reduction of ESCO2 in hPSCs after thalidomide exposure.

Assembling systems biology, embryo development and teratogenesis: What do we know so far and where to go next?

The recognition of molecular mechanisms of a teratogen can provide insights to understand its embryopathy, and later to plan strategies for the prevention of new exposures. In this context, experimental research is the most invested approach. Despite its relevance, these assays require financial and time investment. Hence, the evaluation of such mechanisms through systems biology rise as an alternative for this conventional methodology. Systems biology is an integrative field that connects experimental and computational analyses, assembling interaction networks between genes, proteins, and even teratogens. It is a valid strategy to generate new hypotheses, that can later be confirmed in experimental assays. Here, we present a literature review of the application of systems biology in embryo development and teratogenesis studies. We provide a glance at the data available in public databases, and evaluate common mechanisms between different teratogens. Finally, we discuss the advantages of using this strategy in future teratogenesis researches.

Zika Virus as a Possible Risk Factor for Autism Spectrum Disorder: Neuroimmunological Aspects.

The recent outbreak of the Zika virus (ZIKV) and the discovery that perinatal Zika exposure can lead to the Congenital Zika Syndrome has promoted a call for prevention measures. Due to the increased number of babies born with microcephaly, structural brain abnormalities, and neurological alterations in regions affected by ZIKV, investigations were carried out in order to better understand this process. The maternal immune system directly influences the fetal central nervous system, and complications during pregnancy have been associated with neurodevelopmental disorders. Autism spectrum disorder (ASD), a neurodevelopmental disorder commonly manifested in the first years of life, is a disease with multifactorial etiology and is manifested typically by social and communication impairments, as well as stereotyped behaviors. Brain abnormalities, including both anatomically and functionally, can be observed in this disorder, suggesting delays in neuronal maturation and altered brain connectivity. It is known that some viral congenital infections, such as rubella, and cytomegalovirus can interfere with brain development, being associated with brain calcification, microcephaly, and ASD. Here, we reviewed a range of studies evaluating the aspects concerning brain development, immunological status during pregnancy, and neuroimmunomodulation in congenital viral infections, and we discuss if the fetal brain infection caused by ZIKV could predispose to ASD. Finally, we suggest a mechanism encompassing neurological and immunological pathways that could play a role in the development of ASD in infants after ZIKV infection in pregnancy.

Genetic susceptibility to thalidomide embryopathy in humans: Study of candidate development genes.

Thalidomide is a drug used worldwide for several indications, but the molecular mechanisms of its teratogenic property are not fully understood. Studies in animal models suggest the oxidative stress, the inhibition of angiogenesis, and the binding to E3-ubiquitin ligase complex as mechanisms by which thalidomide can change the expression of genes important to embryonic development. In this study, seven polymorphisms in genes related to development (FGF8, FGF10, BMP4, SHH, TP53, TP63, and TP73) were analyzed in people with thalidomide embryopathy (TE) and compared to people without malformations. The sample consisted of 36 people with TE and 135 unrelated and nonsyndromic people who had their DNA genotyped by PCR real-time. Although no allelic or genotypic differences were observed between the groups, we hypothesized that other regions in these genes and related genes may play an important role in thalidomide teratogenesis, which is known to have a genetic contribution. Identifying such molecular mechanisms is essential for the development of a molecule that will be analogue to thalidomide but safe enough to avoid the emergence of new cases of TE.