Genetics of human neural tube defects

Moderate levels of folic acid benefit outcomes for cilia based neural tube defects

Folic acid (FA) supplementation is a potent tool to reduce devastating birth defects known as neural tube defects (NTDs). Though effective, questions remain how FA achieves its protective effect and which gene mutations are sensitive to folic acid levels. We explore the relationship between FA dosage and NTD rates using NTD mouse models. We demonstrate that NTD rates in mouse models harboring mutations in cilia genes depend on FA dosage. Cilia mutant mouse models demonstrate reductions in NTD rates when exposed to moderate levels of FA that are not observed at higher fortified levels of FA. This trend continues with a moderate level of FA being beneficial for primary and motile cilia formation. We present a mechanism through which fortified FA levels reduce basal levels of reactive oxygen species (ROS) which in turn reduces ROS-sensitive GTPase activity required for ciliogenesis. Our data indicates that genes involved in cilia formation and function represent a FA sensitive category of mutations and a possible avenue for further reducing NTD and ciliopathy incidences.

Preconceptional and Periconceptional Folic Acid Supplementation in the Visegrad Group Countries for the Prevention of Neural Tube Defects

Neural tube defects (NTDs) are malformations of the central nervous system that represent the second most common cause of congenital morbidity and mortality, following cardiovascular abnormalities. Maternal nutrition, particularly folic acid, a B vitamin, is crucial in the etiology of NTDs. FA plays a key role in DNA methylation, synthesis, and repair, acting as a cofactor in one-carbon transfer reactions essential for neural tube development. Randomized trials have shown that FA supplementation during preconceptional and periconceptional periods reduces the incidence of NTDs by nearly 80%. Consequently, it is recommended that all women of reproductive age take 400 µg of FA daily. Many countries have introduced FA fortification of staple foods to prevent NTDs, addressing the high rate of unplanned pregnancies. These policies have increased FA intake and decreased NTD incidence. Although the precise mechanisms by which FA protects against NTDs remain unclear, compelling evidence supports its efficacy in preventing most NTDs, leading to national recommendations for FA supplementation in women. This review focuses on preconceptional and periconceptional FA supplementation in the female population of the Visegrad Group countries (Slovakia, Czech Republic, Poland, and Hungary). Our findings emphasize the need for a comprehensive approach to NTDs, including FA supplementation programs, tailored counseling, and effective national-level policies.

Bayesian polygenic risk estimation approach to nuclear families with discordant sib-pairs for myelomeningocele

Myelomeningocele (MMC) is the most severe and disabling form of spina bifida with chronic health multisystem complications and social and economic family and health systems burden. In the present study, we aimed to investigate the genetic risk estimate for MMC in a cohort of 203 Mexican nuclear families with discordant siblings for the defect. Utilizing a custom Illumina array, we analyzed 656 single nucleotide polymorphisms (SNPs) of 395 candidate genes to identify a polygenic risk profile for MMC. Through a family-based analysis employing the transmission disequilibrium test (TDT) and Bayesian analysis, we assessed risk alleles transmission and calculated conditional probabilities estimating a polygenic risk for MMC. Our findings reveal significant associations of six genes related to neural tube closure (PSMB4, ATIC, DKK2, PSEN2, C2CD3, and PLCB2), showing differences in risk allele transmission between affected and unaffected siblings. Bayesian analysis identified changes in the risk profile after initiating folic acid fortification in Mexico, showing an evident decline in the conditional risk from 1/156 to 1/304 respectively. Despite the decline, this represents a 5.84-fold increase in risk before fortification and a 2.99-fold increase post-fortification compared to the baseline risk level (1/910). Our study highlights the advantage of incorporating a Bayesian analytical methodology in families with discordant sib-pairs, offering insights into the polygenic risk estimate for MMC and, most probably, for other congenital malformations.

Associations between exposure to extreme ambient heat and neural tube defects in Georgia, USA: A population-based case-control study

INTRODUCTION

The association between extreme ambient heat exposures during pregnancy and neural tube defects (NTDs) in offspring remains unclear. This study sought to estimate the association between exposure to extreme ambient heat during periconception and NTDs.

METHODS

This population-based case-control study in Georgia, USA (1994-2017) included 825 isolated NTD cases (473 anencephaly, 352 spina bifida) and 3,300 controls matched 1:4 on county of residence and time period of delivery. Daily ambient temperature data were linked to fetal death and birth records by county of residence. Extreme ambient heat exposure was defined as the number of consecutive days the daily apparent temperature exceeded the county-specific 95th percentile (derived over 1980-2010) during an eight-week periconception period. We calculated adjusted odds ratios (aORs) and 95% confidence intervals (CI) using conditional logistic regression models adjusted for maternal age, education, and ethnicity and month and year of last menstrual period.

RESULTS

The aORs for NTDs were 1.09 (95% CI 1.01, 1.17), 1.18 (95% CI 1.03, 1.36), and 1.29 (95% CI 1.04, 1.58) for exposure to 1-2, 3-5, and 6 or more consecutive days with apparent ambient temperatures exceeding the county-specific 95th percentile during periconception, respectively, compared to no days of extreme ambient heat exposure. Weekly analysis of extreme heat exposure indicated consistently elevated odds of offspring NTDs during periconception. These results were largely driven by spina bifida cases.

CONCLUSIONS

Our results highlight potential health threats posed by increasing global average temperatures for pregnant people with implications for increased risk of neural tube defects in their offspring.

Maternal arsenic exposure modifies associations between arsenic, folate and arsenic metabolism gene variants, and spina bifida risk: A case‒control study in Bangladesh

BACKGROUND

Spina bifida is a type of neural tube defect (NTD); NTDs are developmental malformations of the spinal cord that result from failure of neural tube closure during embryogenesis and are likely caused by interactions between genetic and environmental factors. Arsenic induces NTDs in animal models, and studies demonstrate that mice with genetic defects related to folate metabolism are more susceptible to arsenic's effects. We sought to determine whether 25 single-nucleotide polymorphisms (SNPs) in genes involved in folate and arsenic metabolism modified the associations between maternal arsenic exposure and risk of spina bifida (a common NTD) among a hospital-based case-control study population in Bangladesh.

METHODS

We used data from 262 mothers and 220 infants who participated in a case‒control study at the National Institutes of Neurosciences & Hospital and Dhaka Shishu Hospital in Dhaka, Bangladesh. Neurosurgeons assessed infants using physical examinations, review of imaging, and we collected histories using questionnaires. We assessed arsenic from mothers' toenails using inductively coupled plasma mass spectrometry (ICP-MS), and we genotyped participants using the Illumina Global Screening Array v1.0. We chose candidate genes and SNPs through a review of the literature. We assessed SNP-environment interactions using interaction terms and stratified models, and we assessed gene-environment interactions using interaction sequence/SNP-set kernel association tests (iSKAT).

RESULTS

The median toenail arsenic concentration was 0.42 μg/g (interquartile range [IQR]: 0.27-0.86) among mothers of cases and 0.47 μg/g (IQR: 0.30-0.97) among mothers of controls. We found an two SNPs in the infants' AS3MT gene (rs11191454 and rs7085104) and one SNP in mothers' DNMT1 gene (rs2228611) were associated with increased odds of spina bifida in the setting of high arsenic exposure (rs11191454, OR 3.01, 95% CI: 1.28-7.09; rs7085104, OR 2.33, 95% CI: 1.20-4.and rs2228611, OR 2.11, 95% CI: 1.11-4.01), along with significant SNP-arsenic interactions. iSKAT analyses revealed significant interactions between mothers' toenail concentrations and infants' AS3MT and MTR genes (p = 0.02), and mothers' CBS gene (p = 0.05).

CONCLUSIONS

Our results support the hypothesis that arsenic increases spina bifida risk via interactions with folate and arsenic metabolic pathways and suggests that individuals in the population who have certain genetic polymorphisms in genes involved with arsenic and folate metabolism may be more susceptible than others to the arsenic teratogenicity.

Congenital syndromic Chiari-like malformation (CSCM) in Holstein cattle: towards unravelling of possible genetic causes

BACKGROUND

Chiari malformation type II (CMII) was originally reported in humans as a rare disorder characterized by the downward herniation of the hindbrain and towering cerebellum. The congenital brain malformation is usually accompanied by spina bifida, a congenital spinal anomaly resulting from incomplete closure of the dorsal aspect of the spinal neural tube, and occasionally by other lesions. A similar disorder has been reported in several animal species, including cattle, particularly as a congenital syndrome. A cause of congenital syndromic Chiari-like malformation (CSCM) in cattle has not been reported to date. We collected a series of 14 CSCM-affected Holstein calves (13 purebred, one Red Danish Dairy F1 cross) and performed whole-genome sequencing (WGS). WGS was performed on 33 cattle, including eight cases with parents (trio-based; group 1), three cases with one parent (group 2), and three single cases (solo-based; group 3).

RESULTS

Sequencing-based genome-wide association study of the 13 Holstein calves with CSCM and 166 controls revealed no significantly associated genome region. Assuming a single Holstein breed-specific recessive allele, no region of shared homozygosity was detected suggesting heterogeneity. Subsequent filtering for protein-changing variants that were only homozygous in the genomes of the individual cases allowed the identification of two missense variants affecting different genes, SHC4 in case 4 in group 1 and WDR45B in case 13 in group 3. Furthermore, these two variants were only observed in Holstein cattle when querying WGS data of > 5,100 animals. Alternatively, potential de novo mutational events were assessed in each case. Filtering for heterozygous private protein-changing variants identified one DYNC1H1 frameshift variant as a candidate causal dominant acting allele in case 12 in group 3. Finally, the presence of larger structural DNA variants and chromosomal abnormalities was investigated in all cases. Depth of coverage analysis revealed two different partial monosomies of chromosome 2 segments in cases 1 and 7 in group 1 and a trisomy of chromosome 12 in the WDR45B homozygous case 13 in group 3.

CONCLUSIONS

This study presents for the first time a detailed genomic evaluation of CSCM in Holstein cattle and suggests an unexpected genetic and allelic heterogeneity considering the mode of inheritance, as well as the type of variant. For the first time, we propose candidate causal variants that may explain bovine CSCM in a certain proportion of affected calves. We present cattle as a large animal model for human CMII and propose new genes and genomic variants as possible causes for related diseases in both animals and humans.

Seasonal trend in the occurrence of myelomeningocele in nigeria: a hypothesis of climate-induced oxidative stress

PURPOSE

Myelomeningocele is the most severe birth defect compatible with long-term survival. It accounts for 5.7% of neurological surgeries in Nigeria. However, the exact cause of this neural tube defect remains unidentified. This study aims to determine if seasonal variation is a potential environmental contributor.

METHOD

This study prospectively recruited 242 children diagnosed with myelomeningocele at the University of Nigeria Teaching Hospital (UNTH), Enugu, Nigeria, between January 2010 and December 2022. Our primary outcome was the seasonal occurrence of myelomeningocele, while covariates included gender, birth order, maternal folic acid supplementation (FAS), and parental age. The estimated month of conception was derived from the mother's last menstrual period (LMP), and the occurrence of myelomeningocele across the various seasons in which these babies were conceived was assessed using the Lorenz curve and the Gini coefficient.

RESULTS

242 patients were studied with a male-to-female ratio of 1.26. The majority of cases were lumbosacral (93.4%), and none of the mothers commenced FAS before conception. The highest proportion of cases (39.7%) occurred during the hottest period of the dry season (January-March), while the lowest proportion (15.7%) occurred during the early wet season (April-June). The Gini index of 0.29, and the Gini coefficient derived from 100,000 Monte Carlo simulations of 0.24, indicate a significant variation in the distribution of myelomeningocele cases across different seasons of conception.

CONCLUSION

The seasonal occurrence of myelomeningocele with a peak in January-March suggests a potential association with environmental factors including oxidative stress induced by solar radiation.

Genome-wide analysis of spina bifida risk variants in a case-control study from Bangladesh

BACKGROUND

Human studies of genetic risk factors for neural tube defects, severe birth defects associated with long-term health consequences in surviving children, have predominantly been restricted to a subset of candidate genes in specific biological pathways including folate metabolism.

METHODS

In this study, we investigated the association of genetic variants spanning the genome with risk of spina bifida (i.e., myelomeningocele and meningocele) in a subset of families enrolled from December 2016 through December 2022 in a case-control study in Bangladesh, a population often underrepresented in genetic studies. Saliva DNA samples were analyzed using the Illumina Global Screening Array. We performed genetic association analyses to compare allele frequencies between 112 case and 121 control children, 272 mothers, and 128 trios.

RESULTS

In the transmission disequilibrium test analyses with trios only, we identified three novel exonic spina bifida risk loci, including rs140199800 (SULT1C2, p = 1.9 × 10-7), rs45580033 (ASB2, p = 4.2 × 10-10), and rs75426652 (LHPP, p = 7.2 × 10-14), after adjusting for multiple hypothesis testing. Association analyses comparing cases and controls, as well as models that included their mothers, did not identify genome-wide significant variants.

CONCLUSIONS

This study identified three novel single nucleotide polymorphisms involved in biological pathways not previously associated with neural tube defects. The study warrants replication in larger groups to validate findings and to inform targeted prevention strategies.

ARMC5 controls the degradation of most Pol II subunits, and ARMC5 mutation increases neural tube defect risks in mice and humans

BACKGROUND

Neural tube defects (NTDs) are caused by genetic and environmental factors. ARMC5 is part of a novel ubiquitin ligase specific for POLR2A, the largest subunit of RNA polymerase II (Pol II).

RESULTS

We find that ARMC5 knockout mice have increased incidence of NTDs, such as spina bifida and exencephaly. Surprisingly, the absence of ARMC5 causes the accumulation of not only POLR2A but also most of the other 11 Pol II subunits, indicating that the degradation of the whole Pol II complex is compromised. The enlarged Pol II pool does not lead to generalized Pol II stalling or a generalized decrease in mRNA transcription. In neural progenitor cells, ARMC5 knockout only dysregulates 106 genes, some of which are known to be involved in neural tube development. FOLH1, critical in folate uptake and hence neural tube development, is downregulated in the knockout intestine. We also identify nine deleterious mutations in the ARMC5 gene in 511 patients with myelomeningocele, a severe form of spina bifida. These mutations impair the interaction between ARMC5 and Pol II and reduce Pol II ubiquitination.

CONCLUSIONS

Mutations in ARMC5 increase the risk of NTDs in mice and humans. ARMC5 is part of an E3 controlling the degradation of all 12 subunits of Pol II under physiological conditions. The Pol II pool size might have effects on NTD pathogenesis, and some of the effects might be via the downregulation of FOLH1. Additional mechanistic work is needed to establish the causal effect of the findings on NTD pathogenesis.

Fetal gene therapy

Fetal gene therapy was first proposed toward the end of the 1990s when the field of gene therapy was, to quote the Gartner hype cycle, at its "peak of inflated expectations." Gene therapy was still an immature field but over the ensuing decade, it matured and is now a clinical and market reality. The trajectory of treatment for several genetic diseases is toward earlier intervention. The ability, capacity, and the will to diagnose genetic disease early-in utero-improves day by day. A confluence of clinical trials now signposts a trajectory toward fetal gene therapy. In this review, we recount the history of fetal gene therapy in the context of the broader field, discuss advances in fetal surgery and diagnosis, and explore the full ambit of preclinical gene therapy for inherited metabolic disease.

Folate deficiency reduced aberrant level of DOT1L-mediated histone H3K79 methylation causes disruptive SHH gene expression involved in neural tube defects

BACKGROUND

Neural tube defects (NTDs) are one of the most severe congenital abnormalities characterized by failures of the neural tube to close during early embryogenesis. Maternal folate deficiency could impact the occurrence of NTDs, however, the mechanisms involved in the cause of NTDs are poorly defined.

RESULTS

Here, we report that histone H3 methyltransferase disruptor of telomeric silencing 1-like (DOT1L) expression was significantly downregulated, and low levels of H3K79me2 were found in the corresponding NTDs samples with their maternal serum folate under low levels. Using ChIP-seq assays, we found that a decrease of H3K79me2 downregulates the expression of Shh and Sufu in mouse embryonic stem cells (mESC) under folate deficiency. Interestingly, folate antagonist methotrexate treatment led to attenuation of H3K79me2 due to Dot1l, affecting Shh and Sufu genes regulation. Upon further analysis, we find that the genes Shh and Sufu are both downregulated in the brain tissues of mice and humans with NTDs. There was a positive correlation between the transcription levels of Shh, Sufu and the protein levels of DOT1L by Pearson correlation analysis.

CONCLUSION

Our results indicate that abnormal Shh and Sufu genes expression reduced by aberrant Dot1l-mediated H3K79me2 levels could be the cause of NTDs occurrence.

Transcriptional Signature of Valproic Acid-Induced Neural Tube Defects in Human Spinal Cord Organoids

In vertebrates, the entire central nervous system is derived from the neural tube, which is formed through a conserved early developmental morphogenetic process called neurulation. Although the perturbations in neurulation caused by genetic or environmental factors lead to neural tube defects (NTDs), the most common congenital malformation and the precise molecular pathological cascades mediating NTDs are not well understood. Recently, we have developed human spinal cord organoids (hSCOs) that recapitulate some aspects of human neurulation and observed that valproic acid (VPA) could cause neurulation defects in an organoid model. In this study, we identified and verified the significant changes in cell-cell junctional genes/proteins in VPA-treated organoids using transcriptomic and immunostaining analysis. Furthermore, VPA-treated mouse embryos exhibited impaired gene expression and NTD phenotypes, similar to those observed in the hSCO model. Collectively, our data demonstrate that hSCOs provide a valuable biological resource for dissecting the molecular pathways underlying the currently unknown human neurulation process using destructive biological analysis tools.

A quest for genetic causes underlying signaling pathways associated with neural tube defects

Neural tube defects (NTDs) are serious congenital deformities of the nervous system that occur owing to the failure of normal neural tube closures. Genetic and non-genetic factors contribute to the etiology of neural tube defects in humans, indicating the role of gene-gene and gene-environment interaction in the occurrence and recurrence risk of neural tube defects. Several lines of genetic studies on humans and animals demonstrated the role of aberrant genes in the developmental risk of neural tube defects and also provided an understanding of the cellular and morphological programs that occur during embryonic development. Other studies observed the effects of folate and supplementation of folic acid on neural tube defects. Hence, here we review what is known to date regarding altered genes associated with specific signaling pathways resulting in NTDs, as well as highlight the role of various genetic, and non-genetic factors and their interactions that contribute to NTDs. Additionally, we also shine a light on the role of folate and cell adhesion molecules (CAMs) in neural tube defects.

Pluripotent Stem Cells as a Model for Human Embryogenesis

Pluripotent stem cells (PSCs; embryonic stem cells and induced pluripotent stem cells) can recapitulate critical aspects of the early stages of embryonic development; therefore, they became a powerful tool for the in vitro study of molecular mechanisms that underlie blastocyst formation, implantation, the spectrum of pluripotency and the beginning of gastrulation, among other processes. Traditionally, PSCs were studied in 2D cultures or monolayers, without considering the spatial organization of a developing embryo. However, recent research demonstrated that PSCs can form 3D structures that simulate the blastocyst and gastrula stages and other events, such as amniotic cavity formation or somitogenesis. This breakthrough provides an unparalleled opportunity to study human embryogenesis by examining the interactions, cytoarchitecture and spatial organization among multiple cell lineages, which have long remained a mystery due to the limitations of studying in utero human embryos. In this review, we will provide an overview of how experimental embryology currently utilizes models such as blastoids, gastruloids and other 3D aggregates derived from PSCs to advance our understanding of the intricate processes involved in human embryo development.

Dual mechanism underlying failure of neural tube closure in the Zic2 mutant mouse

Understanding the molecular mechanisms that lead to birth defects is an important step towards improved primary prevention. Mouse embryos homozygous for the Kumba (Ku) mutant allele of Zic2 develop severe spina bifida with complete lack of dorsolateral hinge points (DLHPs) in the neuroepithelium. Bone morphogenetic protein (BMP) signalling is overactivated in Zic2Ku/Ku embryos, and the BMP inhibitor dorsomorphin partially rescues neural tube closure in cultured embryos. RhoA signalling is also overactivated, with accumulation of actomyosin in the Zic2Ku/Ku neuroepithelium, and the myosin inhibitor Blebbistatin partially normalises neural tube closure. However, dorsomorphin and Blebbistatin differ in their effects at tissue and cellular levels: DLHP formation is rescued by dorsomorphin but not Blebbistatin, whereas abnormal accumulation of actomyosin is rescued by Blebbistatin but not dorsomorphin. These findings suggest a dual mechanism of spina bifida origin in Zic2Ku/Ku embryos: faulty BMP-dependent formation of DLHPs and RhoA-dependent F-actin accumulation in the neuroepithelium. Hence, we identify a multi-pathway origin of spina bifida in a mammalian system that may provide a developmental basis for understanding the corresponding multifactorial human defects.

Loss-of-Function of p21-Activated Kinase 2 Links BMP Signaling to Neural Tube Patterning Defects

Closure of the neural tube represents a highly complex and coordinated process, the failure of which constitutes common birth defects. The serine/threonine kinase p21-activated kinase 2 (PAK2) is a critical regulator of cytoskeleton dynamics; however, its role in the neurulation and pathogenesis of neural tube defects (NTDs) remains unclear. Here, the results show that Pak2^-/- mouse embryos fail to develop dorsolateral hinge points (DLHPs) and exhibit craniorachischisis, a severe phenotype of NTDs. Pak2 knockout activates BMP signaling that involves in vertebrate bone formation. Single-cell transcriptomes reveal abnormal differentiation trajectories and transcriptional events in Pak2^-/- mouse embryos during neural tube development. Two nonsynonymous and one recurrent splice-site mutations in the PAK2 gene are identified in five human NTD fetuses, which exhibit attenuated PAK2 expression and upregulated BMP signaling in the brain. Mechanistically, PAK2 regulates Smad9 phosphorylation to inhibit BMP signaling and ultimately induce DLHP formation. Depletion of pak2a in zebrafish induces defects in the neural tube, which are partially rescued by the overexpression of wild-type, but not mutant PAK2. The findings demonstrate the conserved role of PAK2 in neurulation in multiple vertebrate species, highlighting the molecular pathogenesis of PAK2 mutations in NTDs.

Congenital malformations in the vertebral column: associations and possible embryologic origins

Cases of associations between random spinal congenital defects have previously been reported, yet several questions remain unanswered. Firstly, why are associations between what seems to be random combinations of vertebral malformations observed? Secondly, is there a common event or pattern that connects the associated defects? Therefore, this study aimed to identify congenital defects in the vertebral column and also to determine whether any associations, if present, between vertebral malformations exist. This article consequently discusses the possible embryological disruptions that may lead to the formation of various defects in the vertebral column. A random skeletal sample (n=187) was selected from the Pretoria Bone Collection housed in the Department of Anatomy, University of Pretoria (Ethics 678/2018). The sample was evaluated to determine the frequencies of spinal congenital defects in each set of remains. Identifiable congenital malformations were observed in 48.1% (n=90/187) of the sample. The results demonstrated a high probability of association between the different defects observed in the vertebral column. Findings are of value as they provide a reasonable explanation to why seemingly random cases of associations have been reported by several authors. This study is clinically relevant as severe spinal defects have been shown to have high morbidity in patients and mortality in infants.

CIC missense variants contribute to susceptibility for spina bifida

Neural tube defects (NTDs) are congenital malformations resulting from abnormal embryonic development of the brain, spine, or spinal column. The genetic etiology of human NTDs remains poorly understood despite intensive investigation. CIC, homolog of the Capicua transcription repressor, has been reported to interact with ataxin-1 (ATXN1) and participate in the pathogenesis of spinocerebellar ataxia type 1. Our previous study demonstrated that CIC loss of function (LoF) variants contributed to the cerebral folate deficiency syndrome by downregulating folate receptor 1 (FOLR1) expression. Given the importance of folate transport in neural tube formation, we hypothesized that CIC variants could contribute to increased risk for NTDs by depressing embryonic folate concentrations. In this study, we examined CIC variants from whole-genome sequencing (WGS) data of 140 isolated spina bifida cases and identified eight missense variants of CIC gene. We tested the pathogenicity of the observed variants through multiple in vitro experiments. We determined that CIC variants decreased the FOLR1 protein level and planar cell polarity (PCP) pathway signaling in a human cell line (HeLa). In a murine cell line (NIH3T3), CIC loss of function variants downregulated PCP signaling. Taken together, this study provides evidence supporting CIC as a risk gene for human NTD.

Pathogenesis of neural tube defects: The regulation and disruption of cellular processes underlying neural tube closure

Neural tube closure (NTC) is crucial for proper development of the brain and spinal cord and requires precise morphogenesis from a sheet of cells to an intact three-dimensional structure. NTC is dependent on successful regulation of hundreds of genes, a myriad of signaling pathways, concentration gradients, and is influenced by epigenetic and environmental cues. Failure of NTC is termed a neural tube defect (NTD) and is a leading class of congenital defects in the United States and worldwide. Though NTDs are all defined as incomplete closure of the neural tube, the pathogenesis of an NTD determines the type, severity, positioning, and accompanying phenotypes. In this review, we survey pathogenesis of NTDs relating to disruption of cellular processes arising from genetic mutations, altered epigenetic regulation, and environmental influences by micronutrients and maternal condition. This article is categorized under: Congenital Diseases > Genetics/Genomics/Epigenetics Neurological Diseases > Genetics/Genomics/Epigenetics Neurological Diseases > Stem Cells and Development.

Fetal Brain Development: Regulating Processes and Related Malformations

This paper describes the contemporary state of knowledge regarding processes that regulate normal development of the embryonic–fetal central nervous system (CNS). The processes are described according to the developmental timetable: dorsal induction, ventral induction, neurogenesis, neuronal migration, post-migration neuronal development, and cortical organization. We review the current literature on CNS malformations associated with these regulating processes. We specifically address neural tube defects, holoprosencephaly, malformations of cortical development (including microcephaly, megalencephaly, lissencephaly, cobblestone malformations, gray matter heterotopia, and polymicrogyria), disorders of the corpus callosum, and posterior fossa malformations. Fetal ventriculomegaly, which frequently accompanies these disorders, is also reviewed. Each malformation is described with reference to the etiology, genetic causes, prenatal sonographic imaging, associated anomalies, differential diagnosis, complimentary diagnostic studies, clinical interventions, neurodevelopmental outcome, and life quality.

Eph and Ephrin Variants in Malaysian Neural Tube Defect Families

Neural tube defects (NTDs) are common birth defects with a complex genetic etiology. Mouse genetic models have indicated a number of candidate genes, of which functional mutations in some have been found in human NTDs, usually in a heterozygous state. This study focuses on Ephs-ephrins as candidate genes of interest owing to growing evidence of the role of this gene family during neural tube closure in mouse models. Eph-ephrin genes were analyzed in 31 Malaysian individuals comprising seven individuals with sporadic spina bifida, 13 parents, one twin-sibling and 10 unrelated controls. Whole exome sequencing analysis and bioinformatic analysis were performed to identify variants in 22 known Eph-ephrin genes. We reported that three out of seven spina bifida probands and three out of thirteen family members carried a variant in either EPHA2 (rs147977279), EPHB6 (rs780569137) or EFNB1 (rs772228172). Analysis of public databases shows that these variants are rare. In exome datasets of the probands and parents of the probands with Eph-ephrin variants, the genotypes of spina bifida-related genes were compared to investigate the probability of the gene–gene interaction in relation to environmental risk factors. We report the presence of Eph-ephrin gene variants that are prevalent in a small cohort of spina bifida patients in Malaysian families.

Production of human spinal-cord organoids recapitulating neural-tube morphogenesis

Human spinal-cord-like tissues induced from human pluripotent stem cells are typically insufficiently mature and do not mimic the morphological features of neurulation. Here, we report a three-dimensional culture system and protocol for the production of human spinal-cord-like organoids (hSCOs) recapitulating the neurulation-like tube-forming morphogenesis of the early spinal cord. The hSCOs exhibited neurulation-like tube-forming morphogenesis, cellular differentiation into the major types of spinal-cord neurons as well as glial cells, and mature synaptic functional activities, among other features of the development of the spinal cord. We used the hSCOs to screen for antiepileptic drugs that can cause neural-tube defects. hSCOs may also facilitate the study of the development of the human spinal cord and the modelling of diseases associated with neural-tube defects.

MicroRNAs as Biomarkers for Birth Defects

It is estimated that 2-4% of live births will have a birth defect (BD). The availability of biomarkers for the prenatal detection of BDs will facilitate early risk assessment, prompt medical intervention and ameliorating disease severity. miRNA expression levels are often found to be altered in many diseases. There is, thus, a growing interest in determining whether miRNAs, particularly extracellular miRNAs, can predict, diagnose, or monitor BDs. These miRNAs, typically encapsulated in exosomes, are released by cells (including those of the fetus and placenta) into the extracellular milieu, such as blood, urine, saliva and cerebrospinal fluid, thereby enabling interaction with target cells. Exosomal miRNAs are stable, protected from degradation, and retain functionality. The observation that placental and fetal miRNAs can be detected in maternal serum, provides a strong rationale for adopting miRNAs as noninvasive prenatal biomarkers for BDs. In this mini-review, we examine the current state of research involving the use of miRNAs as prognostic and diagnostic biomarkers for BD.

Implication of Vestibular Hair Cell Loss of Planar Polarity for the Canal and Otolith-Dependent Vestibulo-Ocular Reflexes in Celsr1-/- Mice

Introduction: Vestibular sensory hair cells are precisely orientated according to planar cell polarity (PCP) and are key to enable mechanic-electrical transduction and normal vestibular function. PCP is found on different scales in the vestibular organs, ranging from correct hair bundle orientation, coordination of hair cell orientation with neighboring hair cells, and orientation around the striola in otolithic organs. Celsr1 is a PCP protein and a Celsr1 KO mouse model showed hair cell disorganization in all vestibular organs, especially in the canalar ampullae. The objective of this work was to assess to what extent the different vestibulo-ocular reflexes were impaired in Celsr1 KO mice.

Methods: Vestibular function was analyzed using non-invasive video-oculography. Semicircular canal function was assessed during sinusoidal rotation and during angular velocity steps. Otolithic function (mainly utricular) was assessed during off-vertical axis rotation (OVAR) and during static and dynamic head tilts.

Results: The vestibulo-ocular reflex of 10 Celsr1 KO and 10 control littermates was analyzed. All KO mice presented with spontaneous nystagmus or gaze instability in dark. Canalar function was reduced almost by half in KO mice. Compared to control mice, KO mice had reduced angular VOR gain in all tested frequencies (0.2–1.5 Hz), and abnormal phase at 0.2 and 0.5 Hz. Concerning horizontal steps, KO mice had reduced responses. Otolithic function was reduced by about a third in KO mice. Static ocular-counter roll gain and OVAR bias were both significantly reduced. These results demonstrate that canal- and otolith-dependent vestibulo-ocular reflexes are impaired in KO mice.

Conclusion: The major ampullar disorganization led to an important reduction but not to a complete loss of angular coding capacities. Mildly disorganized otolithic hair cells were associated with a significant loss of otolith-dependent function. These results suggest that the highly organized polarization of otolithic hair cells is a critical factor for the accurate encoding of the head movement and that the loss of a small fraction of the otolithic hair cells in pathological conditions is likely to have major functional consequences. Altogether, these results shed light on how partial loss of vestibular information encoding, as often encountered in pathological situations, translates into functional deficits.

miR-222-3p is involved in neural tube closure by directly targeting Ddit4 in RA induced NTDs mouse model

Previously our results showed miR-222-3p was significantly downregulated in retinoic acid-induced neural tube defect (NTD) mouse model through transcriptome. Down-regulation of miR-222-3p may be a causative biomarker in NTDs. In this study, RNA was extracted from mouse embryos at E8.5, E9.5 and E10.5, and the expression level of miR-222-3p was measured by quantitative real-time PCR analysis. The preliminary mechanism of miR-222-3p in NTDs involved in cell proliferation, apoptosis and migration was investigated in mouse HT-22 cell line. The expression of miR-222-3p was significantly decreased at E8.5, E9.5 and E10.5 developed in mouse embryos which were consistent with our transcriptome sequencing. Suppression of miR-222-3p in HT-22 cells resulted in the inhibition of cell proliferation and migration, cell cycle and apoptosis. Moreover, DNA damage transcript 4 (Ddit4) was identified as a direct and functional target of miR-222-3p. miR-222-3p is negatively regulated by Ddit4. The mutation of binding site of Ddit4 3'UTR abrogated the responsiveness of luciferase reporters to miR-222-3p and showed that Ddit4 expression partially attenuated the function of miR-222-3p. We preliminatively confirmed that low expression of miR-222-3p has reduced the expression of β-catenin, TCF4 and other related genes in the Wnt/β-catenin signaling pathway.Collectively, these results demonstrated that miR-222-3p regulates the Wnt/β-catenin signaling pathway through Ddit4 inhibition in HT-22 cells, resulted in cell proliferation and apoptosis imbalance, and thus led to neural tube defects.

Conserved and Divergent Principles of Planar Polarity Revealed by Hair Cell Development and Function

Planar polarity describes the organization and orientation of polarized cells or cellular structures within the plane of an epithelium. The sensory receptor hair cells of the vertebrate inner ear have been recognized as a preeminent vertebrate model system for studying planar polarity and its development. This is principally because planar polarity in the inner ear is structurally and molecularly apparent and therefore easy to visualize. Inner ear planar polarity is also functionally significant because hair cells are mechanosensors stimulated by sound or motion and planar polarity underlies the mechanosensory mechanism, thereby facilitating the auditory and vestibular functions of the ear. Structurally, hair cell planar polarity is evident in the organization of a polarized bundle of actin-based protrusions from the apical surface called stereocilia that is necessary for mechanosensation and when stereociliary bundle is disrupted auditory and vestibular behavioral deficits emerge. Hair cells are distributed between six sensory epithelia within the inner ear that have evolved unique patterns of planar polarity that facilitate auditory or vestibular function. Thus, specialized adaptations of planar polarity have occurred that distinguish auditory and vestibular hair cells and will be described throughout this review. There are also three levels of planar polarity organization that can be visualized within the vertebrate inner ear. These are the intrinsic polarity of individual hair cells, the planar cell polarity or coordinated orientation of cells within the epithelia, and planar bipolarity; an organization unique to a subset of vestibular hair cells in which the stereociliary bundles are oriented in opposite directions but remain aligned along a common polarity axis. The inner ear with its complement of auditory and vestibular sensory epithelia allows these levels, and the inter-relationships between them, to be studied using a single model organism. The purpose of this review is to introduce the functional significance of planar polarity in the auditory and vestibular systems and our contemporary understanding of the developmental mechanisms associated with organizing planar polarity at these three cellular levels.

Genetics and Molecular Pathogenesis of Human Hydrocephalus

Hydrocephalus is a neurological disorder with an incidence of 80-125 per 100,000 live births in the United States. The molecular pathogenesis of this multidimensional disorder is complex and has both genetic and environmental influences. This review aims to discuss the genetic and molecular alterations described in human hydrocephalus, from well-characterized, heritable forms of hydrocephalus (e.g., X-linked hydrocephalus from L1CAM variants) to those affecting cilia motility and other complex pathologies such as neural tube defects and Dandy-Walker syndrome. Ventricular zone disruption is one key pattern among congenital and acquired forms of hydrocephalus, with abnormalities in cadherins, which mediate neuroepithelium/ependymal cell junctions and contribute to the pathogenesis and severity of the disease. Given the relationship between hydrocephalus pathogenesis and neurodevelopment, future research should elucidate the genetic and molecular mechanisms that regulate ventricular zone integrity and stem cell biology.

Endoplasmic reticulum stress-related calcium imbalance plays an important role on Zinc oxide nanoparticles-induced failure of neural tube closure during embryogenesis

Zinc oxide nanoparticles (ZnO NPs) have been increasingly and widely utilized in various fields, such as agriculture, food and cosmetics. However, various levels of adverse impacts of ZnO NPs on the ecological environment and public health have been associated with each stage of their production, use and disposal. ZnO NPs can be ingested by pregnant women and transferred to developing embryos/foetus through the placental barrier, however, the potential toxicity of ZnO NPs to embryonic and foetal development is largely unclear. In this study, we discovered that ZnO NPs exposure caused growth proportional failure of neural tube closure in mouse and chicken embryos and a simultaneous increase in apoptosis in the developing neural tubes of chicken embryos, which was verified in an in vitro experiment using the SH-SY5Y cell line. Furthermore, removal of free Zn²⁺ ions with EDTA or inhibition of Zn²⁺ ion absorption by CaCl₂ partially alleviated the neurotoxicity induced by ZnO NPs, implying that ZnO NPs-induced developmental neurotoxicity is probably due to both ZnO NPs and the Zn²⁺ ions released from ZnO NPs. In addition, we found that ZnO NPs exposure caused endoplasmic reticulum stress-mediated apoptosis driven mainly by an increase in intracellular calcium (Ca²⁺) concentrations, rather than by the activation of three membrane protein receptors (ATF6, IRE-1 and PERK). Thus, Ca²⁺ imbalance-mediated apoptosis in the context of ZnO NPs exposure may lead to cellular dysfunctions in developing neural precursors, such as, abnormalities involved in neural tube closure, ultimately leading to neural tube defects (NTDs) during embryogenesis. In sum, our results revealed that ZnO NPs exposure greatly increases the risk of failure of neural tube closure through endoplasmic reticulum stress-mediated neural cell death in the developing embryos, which may further lead to the NTD in fetal stage, including failure of neural tube closure.

Clinico-epidemiological profile and outcomes of babies with neural tube defects in a tertiary care center in Northern India

INTRODUCTION

Neural tube defects constitute a major source of disability among children. Proper management requires accurate diagnosis, an assessment of the severity of the lesion, a decision whether intervention is warranted, the nature of the intervention, and educating the family of the need for lifelong medical care. But to do so, reliable data regarding presentation and outcome is very crucial.

AIM OF THE STUDY

To discuss the clinical epidemiological profile and outcome of babies admitted with neural tube defects (NTDs).

MATERIAL AND METHODS

Retrospective observational study was done by extracting data from case notes and follow-up files in Department of Neonatology, PGIMER and Dr. RML Hospital, New Delhi over a period from March 2015 to July 2020.

RESULTS

A total of 25 babies were included in the study. Majority of babies were born to mother at a median age group of 24 (19-36) yrs and nearly one-third of them were illiterate. The history of maternal periconceptional folic acid intake was seen in only five babies (21%). Two third of babies were male (64%) and the median age at admission was at 9 (1-27) days of life. Majority of the cases were open types of NTDs with most common type being meningomyelocele (88%) followed by occipital encephalocele (12%) and there was one case of closed type of neural tube defect having lipomeningomyelocele (4%). The most common associated anomaly was hydrocephalus (76%) followed by Arnold chiari malformation (56%). Motor weakness in form of paraparesis or paraplegia was present in 21 (84%) babies and sensory deficit was present in 44% babies. Bowel and bladder dysfuntion was present in 48% of cases. Ventriculitis was the most common associated morbidity (38%). Meningomyelocele (MMC) repair was the most commonly performed primary surgery (33%) followed by Ventriculo-peritoneal (VP) shunt repair (24%). Twelve babies (48%) were discharged while 2 (8%) expired and 11 (44%) babies left against medical advice.

CONCLUSION

Neural tube defect is a congenital disorder with significant morbidity. The clinical severity of the NTDs and the uncertainty in their cause makes this a priority for further research. National policies for prevention, in utero diagnosis, and early surgical intervention are required for a better prognosis.

Loss of Grhl3 is correlated with altered cellular protrusions in the non-neural ectoderm during neural tube closure

BACKGROUND

The transcription factor Grainyhead-like 3 (GRHL3) has multiple roles in a variety of tissues during development including epithelial patterning and actin cytoskeletal regulation. During neural tube closure (NTC) in the mouse embryo, GRHL3 is expressed and functions in the non-neural ectoderm (NNE). Two important functions of GRHL3 are regulating the actin cytoskeleton during NTC and regulating the boundary between the NNE and neural ectoderm. However, an open question that remains is whether these functions explain the caudally restricted neural tube defect (NTD) of spina bifida observed in Grhl3 mutants.

RESULTS

Using scanning electron microscopy and immunofluorescence based imaging on Grhl3 mutants and wildtype controls, we show that GRHL3 is dispensable for NNE identity or epithelial maintenance in the caudal NNE but is needed for regulation of cellular protrusions during NTC. Grhl3 mutants have decreased lamellipodia relative to wildtype embryos during caudal NTC, first observed at the onset of delays when lamellipodia become prominent in wildtype embryos. At the axial level of NTD, half of the mutants show increased and disorganized filopodia and half lack cellular protrusions.

CONCLUSION

These data suggest that altered cellular protrusions during NTC contribute to the etiology of NTD in Grhl3 mutants.

Birth prevalence of neural tube defects and associated risk factors in Africa: a systematic review and meta-analysis

Background

Neural tube defects are common congenital anomalies that result from early malformation in the development of the spinal cord and brain. It is related to substantial mortality, morbidity, disability, and psychological and economic costs. The aim of this review is to determine the pooled birth prevalence of neural tube defects and associated risk factors in Africa.

Methods

The first outcome of this review was the pooled birth prevalence of the neural tube defects and the second outcome was the pooled measure of association between neural tube defects and associated risk factors in Africa. We systematically searched PubMed, PubMed Central, Joanna Briggs Institute, Google Scopus, Cochrane Library, African Journals Online, Web of Science, Science Direct, Google Scholar, and Medline databases. The heterogeneity of studies was assessed using the Cochrane Q test statistic, I² test statistic, and, visually, using Forest and Galbraith’s plots. A random-effect model was applied to get the pooled birth prevalence of neural tube defects. Subgroup, sensitivity, meta-regression, time-trend, and meta-cumulative analyses were undertaken. The fixed-effect model was used to analyze the association between neural tube defects and associated risk factors.

Results

Forty-three studies with a total of 6086,384 participants were included in this systematic review and meta-analysis. The pooled birth prevalence of the neural tube defects was 21.42 (95% CI (Confidence Interval): 19.29, 23.56) per 10,000 births. A high pooled birth prevalence of neural tube defects was detected in Algeria 75 (95% CI: 64.98, 85.02), Ethiopia 61.43 (95% CI: 46.70, 76.16), Eritrea 39 (95% CI: 32.88, 45.12), and Nigeria 32.77 (95% CI: 21.94, 43.59) per 10,000 births. The prevalence of neural tube defects has increased over time. Taking folic acid during early pregnancy, consanguineous marriage, male sex, and substance abuse during pregnancy were assessed and none of them was significant.

Conclusions

The pooled birth prevalence of neural tube defects in Africa was found to be high. The risk factors evaluated were not found significant.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12887-021-02653-9.

Genetic Polymorphisms in DNA Repair Gene APE1/Ref-1 and the Risk of Neural Tube Defects in a High-Risk Area of China

Apurinic/apyrimidinic endonuclease 1/redox-factor 1 (APE1/Ref-1) gene encodes a multifunctional protein involved in the DNA base excision repair (BER) pathway, which initiates repair of apurinic/apyrimidinic (AP) sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone. APE1/Ref-1 polymorphisms are related to the occurrence of neural tube defects (NTDs), but the association between APE1/Ref-1 polymorphisms and NTDs is not reported in Chinese Han population. The aim of the present study was to evaluate the association of APE1/Ref-1 polymorphism and the risk of NTD occurrence for Han population in a high-risk area of China. APE1/Ref-1 genotypes were determined by iPLEX Gold SNP genotyping. AP sites and folate level of brain tissues were measured. The results showed that three polymorphisms (rs3136817, rs77794916, and rs1760944) of APE1/Ref-1 were statistically associated with NTD subtypes. Allele C of rs3136817, allele T of rs77794916, and allele G of rs1760944 were associated with an increased risk for encephalocele (OR = 2.52, 95% CI [1.25-5.07], P < 0.01; OR = 1.80, 95% CI [1.04-3.12], P = 0.04; and OR = 1.96, 95% CI [1.12-3.45], P = 0.02), compared with those harboring the alleles T, C, and T, respectively. The folate level in NTDs was lower than that in controls. DNA AP sites in the encephalocele were significantly higher than the control (P < 0.01). The three polymorphisms of APE1/Ref-1 were significantly related to NTD occurrence, which indicated that APE1/Ref-1 might be a potential genetic risk factor for encephalocele in a high-risk area of NTDs in China.

The Global Burden of Neural Tube Defects and Disparities in Neurosurgical Care

BACKGROUND

Despite the success of folic acid fortification programs, neural tube defects (NTDs) such as spina bifida, encephalocele, and anencephaly remain among the most substantial causes of childhood morbidity and mortality worldwide. Although these are complicated conditions that require an interdisciplinary approach to care, definitive treatment of survivable NTDs is often neurosurgical.

METHODS

Using Global Burden of Disease data, we examined the global burden of NTDs as related to a nation's wealth, health care quality, and access to neurosurgical care. We abstracted data for death by cause, years lived with disability (YLD), gross domestic product (GDP), United Nations geoscheme, Food Fortification Initiative participation, and Healthcare Access and Quality Index. We compared means using 1-way analysis of variance and proportions using Fisher exact tests, with statistical significance as α = 0.05.

RESULTS

Seventeen of 20 (85%) nations with the most deaths caused by NTDs (P < 0.0001) and 15/20 (75%) nations with the highest YLD (P < 0.0001) were in the lowest GDP quartile. Deaths and YLD were negatively correlated with increasing GDP and Healthcare Access and Quality Index (P < 0.0001). The nations with the highest disease burdens also had the fewest neurosurgeons per capita.

CONCLUSIONS

Despite the success of folic acid fortification programs, greater global public health efforts should be placed on improving access to neurosurgical care in low and middle-income nations through sustainable initiatives such as surgeon exchange programs and the establishment of neurosurgery residency training programs.

Perspectives on urological care in spina bifida patients

Spina bifida (SB) is a neurogenetic disorder with a complex etiology that involves genetic and environmental factors. SB can occur in two major forms of open SB or SB aperta and closed SB or SB occulta. Myelomeningocele (MMC), the most common neural tube defects (NTDs), occurs in approximately 1 in 1,000 births. Considering non-genetic factors, diminished folate status is the best-known factor influencing NTD risk. The methylenetetrahydrofolate reductase (MTHFR) gene has been implicated as a risk factor for NTDs. The primary disorder in the pathogenesis of MMC is failed neural tube closure in the embryonic spinal region. The clinical manifestation of SB depends on clinical type and severity. SB can be detected in the second trimester using ultrasound which will reveal specific cranial signs. The management of MMC traditionally involves surgery within 48 h of birth. Prenatal repair of MMC is recommended for fetuses who meet maternal and fetal Management of Myelomeningocele Study (MOMS) specified criteria. Urological manifestations of SB include urinary incontinence, urolithiasis, sexual dysfunction, renal dysfunction, and urinary tract infection. Renal failure is among the most severe complications of SB. The most important role of the urologist is the management of neurogenic bladder. Medical management with clean intermittent catheterization and anticholinergic treatment is generally considered the gold standard of therapy. However, when this therapy fails surgical reconstruction become the only remaining option. This review will summarize the pathogenesis, risk factors, genetic contribution, diagnostic test, and management of SB. Lastly, the urologic outcomes and therapies are reviewed.

Loss-of-function or gain-of-function variations in VINCULIN (VCL) are risk factors of human neural tube defects

Background

Neural tube defects (NTDs) are severe birth defects resulting from the failure of neural tube closure during embryogenesis. Both genetic and environmental factors contribute to the occurrence of NTDs and the heritability of NTDs is approximately 70%. As a key component of focal adhesions, Vinculin (VCL) plays pivotal roles in cell skeleton remodeling and signal transduction. Vcl deficient mice displayed NTD, but how VCL variants contribute to human NTDs has not been addressed yet.

Methods

We screened VCL variants in a Chinese cohort of 387 NTDs and 244 controls by targeted next‐generation sequencing.

Results

We identified four case‐specific VCL variations (p.M209L, p.D256fs, p.L555V and p.R586Q). VCL p.D256fs and p.L555V are novel variations that have never been reported. Our analysis revealed that p.D256fs is a loss‐of‐function variant, while p.L555V showed a gain of function in planner cell polarity (PCP) pathway regulation and cell migration, probably due to its enhanced protein stability.

Conclusion

Our study reports human NTD specific novel variations in VCL and provides the functional evaluation of VCL variants related to the etiology of human NTDs.

Myelomeningocele genotype-phenotype correlation findings in cilia, HH, PCP, and WNT signaling pathways

BACKGROUND

Myelomeningocele (MMC) is the most severe and frequent type of spina bifida. Its etiology remains poorly understood. The Hedgehog (Hh), Wnt, and planar cell polarity (PCP) signaling pathways are essential for normal tube closure, needing a structural-functional cilium for its adequate function. The present study aimed to investigate the impact of different gene variants (GV) from those pathways on MMC genotype-subphenotype correlations.

METHODS

The study comprised 500 MMC trios and 500 controls, from 16 Telethon centers of 16 Mexican states. Thirty-four GVs of 29 genes from cilia, Hh, PCP, and Wnt pathways, were analyzed, by an Illumina on design microarray. The total sample (T-MMC) was stratified in High-MMC (H-MMC) when thoracic and Low-MMC (L-MMC) when lumbar-sacral vertebrae affected. STATA/SE-12.1 and PLINK software were used for allelic association, TDT, and gene-gene interaction (GGI) analyses, considering p value <.01 as statistically significant differences (SSD).

RESULTS

Association analysis showed SSD for COBL-rs10230120, DVL2-rs2074216, PLCB4-rs6077510 GVs in T-MMC and L-MMC, and VANGL2-rs120886448 in T-MMC and H-MMC, and INVS-rs7024375 exclusively in L-MMC. TDT assay showed SSD preferential transmissions of C2CD3-rs826058 in H-MMC, and LRP5-rs3736228, and BBS2-rs1373 in L-MMC. Statistically significant GGI was observed in four in T-MMC, four completely different in L-MMC, and one in H-MMC. Interestingly, no one repeated in subphenotypes.

CONCLUSIONS

Our results support an association of GVs in Hh, Wnt, PCP, and cilia pathways, with MMC occurrence location, although further validation is needed. Furthermore, present results show a distinctive panel of gene-variants in H-MMC and LMMC subphenotypes, suggesting a feasible genotype-phenotype correlation.

Landscape of Pediatric Biobanking: Challenges and Current Efforts

Diseases that manifest themselves in the pediatric age group frequently have a more diverse spectrum of abnormalities and a greater rarity than diseases that are primarily seen in adults. The complexity and the relatively small populations with specific diseases are factors that have hindered progress in the treatment of pediatric disorders. Personalized medical therapies that are specifically tailored for individuals with unusual or unique problems have great potential to assist in overcoming these factors that have been a bottleneck to pediatric medical success. Personalization of therapies will necessarily be data driven and will require delineation of the proteomic, genomic, epigenomic, and immune characteristics of patients in comparison to the general population. It follows that there is a need to provide researchers with accessible high-quality pediatric tissue collections to facilitate the acquisition of the molecular information needed to support personalized medicine. Because of the unusual nature of many pediatric diseases, sample pools from individual institutions are often too small to adequately power definitive studies. Thus, etiological and translational research in this area are increasingly relying on biobanking networks to provide investigators with adequate numbers of tissue samples. Several pediatric biobanking networks have been formed, which are aimed at increasing the power of research studies and desired pools of high-quality samples. However, despite the concerted efforts, these multicenter networks and collaborations have met with mixed outcomes owing to increasing complexities and heterogeneity in the biobanking arena. While there have been challenges and roadblocks, there also have been some positive outcomes that have had paradigm impacts on diagnosis, study, and treatment of specific diseases. This article highlights the need for establishing pediatric biobanks, how current efforts in pediatric biobanking are influencing the pediatric research landscape, and attempts to identify practical impediments that continue to hamper advancements for the future.

Neural Tube Defects and Associated Anomalies before and after Folic Acid Fortification

OBJECTIVE

To examine the prevalence and types of neural tube defects and the types of anomalies co-occurring with neural tube defects in 6 years before fortification of cereal grain flour with folic acid (1992-1998) and 20 years after fortification (1999-2018) in South Carolina, a state with a historically high prevalence of these birth defects.

STUDY DESIGN

The prevalence of neural tube defects was determined by active and passive surveillance methods in South Carolina since 1992. The types of neural tube defects and co-occurring malformations were determined by prenatal ultrasound and post-delivery examination.

RESULTS

In the 6 prefortification years, 363 neural tube defects were identified among 279 163 live births and fetal deaths (1/769), 305 (84%) of which were isolated defects of the calvaria or spine. In the 20 fortification years, there were significant reductions in the prevalence and percentage of isolated defects: 938 neural tube defects were identified among 1 165 134 live births and fetal deaths (1/1242), 696 (74.2%) of which were isolated. The current prevalence of neural tube defects in South Carolina (0.56/1000 live births and fetal deaths) is comparable with that nationwide.

CONCLUSIONS

The continued occurrence of neural tube defects, the majority of which are isolated, after folic acid fortification of cereal grain flours suggests that additional prevention measures are necessary to reduce further the prevalence of these serious defects of the brain and spine.

Maternal Inositol Status and Neural Tube Defects: A Role for the Human Yolk Sac in Embryonic Inositol Delivery?

Supplementation with myo-inositol during the periconceptional period of pregnancy may ameliorate the recurrence risk of having a fetus affected by a neural tube defect (NTD; e.g., spina bifida). This could be of particular importance in providing a means for preventing NTDs that are unresponsive to folic acid. This review highlights the characteristics of inositol and describes the role of myo-inositol in the prevention of NTDs in rodent studies and the evidence for its efficacy in reducing NTD risk in human pregnancy. The possible reduction in NTD risk by maternal myo-inositol implies functional and developmentally important maternal-embryonic inositol interrelationships and also suggests that embryonic uptake of myo-inositol is crucial for embryonic development. The establishment of active myo-inositol cellular uptake mechanisms in the embryonic stages of human pregnancy, when the neural tube is closing, is likely to be an important determinant of normal development. We draw attention to the generation of materno-fetal inositol concentration gradients and relationships, and outline a transport pathway by which myo-inositol may be delivered to the early developing human embryo. These considerations provide novel insights into the mechanisms that may underpin inositol's ability to confer embryonic developmental benefit.

Exploring Neuronal Vulnerability to Head Trauma Using a Whole Exome Approach

Brain injuries are associated with oxidative stress and a need to restore neuronal homeostasis. Mutations in ion channel genes, in particular CACNA1A, have been implicated in familial hemiplegic migraine (FHM) and in the development of concussion-related symptoms in response to trivial head trauma. The aim of this study was to explore the potential role of variants in other ion channel genes in the development of such responses. We conducted whole exome sequencing (WES) on16 individuals who developed a range of neurological and concussion-related symptoms following minor or trivial head injuries. All individuals were initially tested and shown to be negative for mutations in known FHM genes. Variants identified from the WES results were filtered to identify rare variants (minor allele frequency [MAF] <0.01) in genes related to neural processes as well as genes highly expressed in the brain using a combination of in silico prediction tools (SIFT, PolyPhen, PredictSNP, Mutation Taster, and Mutation Assessor). Rare (MAF <0.001) or novel heterozygous variants in 7 ion channel genes were identified in 37.5% (6/16) of the cases (CACNA1I, CACNA1C, ATP10A, ATP7B, KCNAB1, KCNJ10, and SLC26A4), rare variants in neurotransmitter genes were found in 2 cases (GABRG1 and GRIK1), and rare variants in 3 ubiquitin-related genes identified in 4 cases (SQSTM1, TRIM2, and HECTD1). In this study, the largest proportion of potentially pathogenic variants in individuals with severe responses to minor head trauma were identified in genes previously implicated in migraine and seizure-related autosomal recessive neurological disorders. Together with results implicating variants in the hemiplegic migraine genes, CACNA1A and ATP1A2, in severe head trauma response, our results support a role for heterozygous deleterious mutations in genes implicated in neurological dysfunction and potentially increasing the risk of poor response to trivial head trauma.

Structural insight into the effect of polymorphic variation on the functional dynamics of methionine synthase reductase: Implications in neural tube defects

Neural tube defects (NTDs), one of the most common birth defects, are strongly associated with the variations of several single nucleotide polymorphisms (SNPs) in the MTRR gene. The gene codes a key enzyme that is involved in the rejuvenation of methionine synthase activity. An allelic variant of the protein leads to missense mutation at 49th position from isoleucine to methionine (I49M) is associated with higher disease prevalence in different populations. Here, extensive molecular dynamics simulations and interaction network analysis reveal that the 49th isoleucine is a crucial residue that allosterically regulates the dynamics between the flavin mononucleotide (FMN) and NADP(H) binding domains. I49M variation alters the functional dynamics in a way that might impede the electron transport chain along the NADP(H) → flavin adenine dinucleotide → FMN pathway. The present study provides functional insights into the effect of the genetic variations of the MTRR gene on the NTDs disease pathogenesis.

De Novo Transcriptome Assembly and Gene Expression Profiling of the Copepod Calanus helgolandicus Feeding on the PUA-Producing Diatom Skeletonema marinoi

Diatoms are the dominant component of the marine phytoplankton. Several diatoms produce secondary metabolites, namely oxylipins, with teratogenic effects on their main predators, crustacean copepods. Our study reports the de novo assembled transcriptome of the calanoid copepod Calanus helgolandicus feeding on the oxylipin-producing diatom Skeletonema marinoi. Differential expression analysis was also performed between copepod females exposed to the diatom and the control flagellate Prorocentrum minimum, which does not produce oxylipins. Our results showed that transcripts involved in carbohydrate, amino acid, folate and methionine metabolism, embryogenesis, and response to stimulus were differentially expressed in the two conditions. Expression of 27 selected genes belonging to these functional categories was also analyzed by RT-qPCR in C. helgolandicus females exposed to a mixed solution of the oxylipins heptadienal and octadienal at the concentration of 10 µM, 15 µM, and 20 µM. The results confirmed differential expression analysis, with up-regulation of genes involved in stress response and down-regulation of genes associated with folate and methionine metabolism, embryogenesis, and signaling. Overall, we offer new insights on the mechanism of action of oxylipins on maternally-induced embryo abnormality. Our results may also help identify biomarker genes associated with diatom-related reproductive failure in the natural copepod population at sea.

Association between rare variants in specific functional pathways and human neural tube defects multiple subphenotypes

BACKGROUND

Neural tube defects (NTDs) are failure of neural tube closure, which includes multiple central nervous system phenotypes. More than 300 mouse mutant strains exhibits NTDs phenotypes and give us some clues to establish association between biological functions and subphenotypes. However, the knowledge about association in human remains still very poor.

METHODS

High throughput targeted genome DNA sequencing were performed on 280 neural tube closure-related genes in 355 NTDs cases and 225 ethnicity matched controls, RESULTS: We explored that potential damaging rare variants in genes functioning in chromatin modification, apoptosis, retinoid metabolism and lipid metabolism are associated with human NTDs. Importantly, our data indicate that except for planar cell polarity pathway, craniorachischisis is also genetically related with chromatin modification and retinoid metabolism. Furthermore, single phenotype in cranial or spinal regions displays significant association with specific biological function, such as anencephaly is associated with potentially damaging rare variants in genes functioning in chromatin modification, encephalocele is associated with apoptosis, retinoid metabolism and one carbon metabolism, spina bifida aperta and spina bifida cystica are associated with apoptosis; lumbar sacral spina bifida aperta and spina bifida occulta are associated with lipid metabolism. By contrast, complex phenotypes in both cranial and spinal regions display association with various biological functions given the different phenotypes.

CONCLUSIONS

Our study links genetic variant to subphenotypes of human NTDs and provides a preliminary but direct clue to investigate pathogenic mechanism for human NTDs.

Understanding the Mothers of Children with Spina Bifida and Hydrocephalus in Tanzania

OBJECTIVE

To identify if there are cultural, medical, educational, economic, nutritional and geographic barriers to the prevention and treatment of spina bifida and hydrocephalus.

METHODS

The mothers of infants with spina bifida and hydrocephalus admitted to Muhimbilli Orthopaedic Institute, Dar Es Salaam, Tanzania, between 2013 and 2014 were asked to complete a questionnaire. A total of 299 infants were identified: 65 with myelomeningoceles, 19 with encephaloceles, and 215 with isolated hydrocephalus. The questionnaire was completed by 294 of the mothers.

RESULTS

There was a high variation in the geographic origin of the mothers. Approximately 85% traveled from outside of Dar Es Salaam. The mean age was 29 (15-45) years old with a parity of 3 (1-10). The rates of consanguinity, obesity, antiepileptic medication, HIV seropositivity, and family history were 2%, 13%, 0%, 2%, and 2%, respectively. A maize-based diet was found in 84%, and only 3% of woman took folic acid supplementation, despite 61% of mothers stating that they wished to conceive another baby. Unemployment was high (77%), a low level of education was common (76% not attended any school or obtaining a primary level only), and 20% were single mothers. Hospital only was the preferred method of treatment for 94% of the mothers, and 85% of the babies were born in a hospital.

CONCLUSIONS

Our study highlights some of the cultural, educational, geographic, nutritional, and economic difficulties in the prevention and management of spina bifida and hydrocephalus in Tanzania.

Approaches to studying the genomic architecture of complex birth defects

Every year nearly 6 percent of children worldwide are born with a serious congenital malformation, resulting in death or lifelong disability. In the United States, birth defects remain one of the leading causes of infant mortality. Among the common structural congenital defects are conditions known as neural tube defects (NTDs). These are a class of malformation of the brain and spinal cord where the neural tube fails to close during the neurulation. Although NTDs remain among the most pervasive and debilitating of all human developmental anomalies, there is insufficient understanding of their etiology. Previous studies have proposed that complex birth defects like NTDs are likely omnigenic, involving interconnected gene regulatory networks with associated signals throughout the genome. Advances in technologies have allowed researchers to more critically investigate regulatory gene networks in ever increasing detail, informing our understanding of the genetic basis of NTDs. Employing a systematic analysis of these complex birth defects using massively parallel DNA sequencing with stringent bioinformatic algorithms, it is possible to approach a greater level of understanding of the genomic architecture underlying NTDs. Herein, we present a brief overview of different approaches undertaken in our laboratory to dissect out the genetics of susceptibility to NTDs. This involves the use of mouse models to identify candidate genes, as well as large scale whole genome/whole exome (WGS/WES) studies to interrogate the genomic landscape of NTDs. The goal of this research is to elucidate the gene-environment interactions contributing to NTDs, thus encouraging global research efforts in their prevention.

DVL mutations identified from human neural tube defects and Dandy-Walker malformation obstruct the Wnt signaling pathway

Wnt signaling pathways, including the canonical Wnt/β-catenin pathway, planar cell polarity pathway, and Wnt/Ca²⁺ signaling pathway, play important roles in neural development during embryonic stages. The DVL genes encode the hub proteins for Wnt signaling pathways. The mutations in DVL2 and DVL3 were identified from patients with neural tube defects (NTDs), but their functions in the pathogenesis of human neural diseases remain elusive. Here, we sequenced the coding regions of three DVL genes in 176 stillborn or miscarried fetuses with NTDs or Dandy-Walker malformation (DWM) and 480 adult controls from a Han Chinese population. Four rare mutations were identified: DVL1 p.R558H, DVL1 p.R606C, DVL2 p.R633W, and DVL3 p.R222Q. To assess the effect of these mutations on NTDs and DWM, various functional analyses such as luciferase reporter assay, stress fiber formation, and in vivo teratogenic assay were performed. The results showed that the DVL2 p.R633W mutation destabilized DVL2 protein and upregulated activities for all three Wnt signalings (Wnt/β-catenin signaling, Wnt/planar cell polarity signaling, and Wnt/Ca²⁺ signaling) in mammalian cells. In contrast, DVL1 mutants (DVL1 p.R558H and DVL1 p.R606C) decreased canonical Wnt/β-catenin signaling but increased the activity of Wnt/Ca²⁺ signaling, and DVL3 p.R222Q only decreased the activity of Wnt/Ca²⁺ signaling. We also found that only the DVL2 p.R633W mutant displayed more severe teratogenicity in zebrafish embryos than wild-type DVL2. Our study demonstrates that these four rare DVL mutations, especially DVL2 p.R633W, may contribute to human neural diseases such as NTDs and DWM by obstructing Wnt signaling pathways.

Rare copy number variations of planar cell polarity genes are associated with human neural tube defects

Select single-nucleotide variants in planar cell polarity (PCP) genes are associated with increased risk for neural tube defects (NTDs). However, whether copy number variants (CNVs) in PCP genes contribute to NTDs is unknown. Considering that CNVs are implicated in several human developmental disorders, we hypothesized that CNVs in PCP genes may be causative factors to human NTDs. DNA from umbilical cord tissues of NTD-affected fetuses and parental venous blood samples were collected. We performed a quantitative analysis of copy numbers of all exon regions in the VANGL1, VANGL2, CELSR1, SCRIB, DVL2, DVL3, and PTK7 genes using a CNVplex assay. Quantitative real-time PCR (qPCR) was carried out to confirm the results of CNV analysis. As a result, 16 CNVs were identified among the NTDs. Of these CNVs, 5 loci were identified in 11 NTD probands with CNVs involving DVL2 (exons 1-15), VANGL1 (exons 1-7, exon 8), and VANGL2 (exons 5-8, exons 7 and 8). One CNV (DVL2 exons 1-15) was a duplication and the remaining 15 CNVs were deletions. Eleven CNVs were confirmed by qPCR. One de novo CNV in VANGL1 and one DVL2 were detected from two cases. Compared with unaffected control populations in 1000 Genome, ExAC, MARRVEL, DGV, and dbVar databases, the frequencies of de novo deletion in VANGL1 (1.14%) and de novo duplication in DVL2 (0.57%) were significantly higher in our NTD subjects (p < 0.05). This study demonstrates that de novo CNVs in PCP genes, notably deletions in VANGL1 and gains in DVL2, could contribute to the risk of NTDs.

Somatic mutations in planar cell polarity genes in neural tissue from human fetuses with neural tube defects

Extensive studies that have sought causative mutation(s) for neural tube defects (NTDs) have yielded limited positive findings to date. One possible reason for this is that many studies have been confined to analyses of germline mutations and so may have missed other, non-germline mutations in NTD cases. We hypothesize that somatic mutations of planar polarity pathway (PCP) genes may play a role in the development of NTDs. Torrent™ Personal Genome Machine™ (PGM) sequencing was designed for selected PCP genes in paired DNA samples extracted from the tissues of lesion sites and umbilical cord from 48 cases. Sanger sequencing was used to validate the detected mutations. The source and distribution of the validated mutations in tissues from different germ layers were investigated. Subcellular location, western blotting, and luciferase assays were performed to better understand the effects of the mutations on protein localization, protein level, and pathway signaling. ix somatic mutations were identified and validated, which showed diverse distributions in different tissues. Three somatic mutations were novel/rare: CELSR1 p.Gln2125His, FZD6 p.Gln88Glu, and VANGL1 p.Arg374His. FZD6 p.Gln88Glu caused mislocalization of its protein from the cytoplasm to the nucleus, and disrupted the colocalization of CELSR1 and FZD6. This mutation affected non-canonical WNT signaling in luciferase assays. VANGL1 p.Arg374His impaired the co-localization of CELSR1 and VANGL1, increased the protein levels of VANGL1, and influenced cell migration. In all, 7/48 (14.5%) of the studied NTD cases contained somatic PCP mutations. Somatic mutations in PCP genes (e.g., FZD6 and VANGL1) are associated with human NTDs, and they may occur in different stages and regions during embryonic development, resulting in a varied distribution in fetal tissues/organs.

Klippel-Feil Syndrome with Cervical Diastematomyelia in an Adult with Extensive Cervicothoracic Fusions: Case Report and Review of the Literature

Split cord malformation (SCM) is a developmental disorder that is usually symptomatic and diagnosed in childhood. The majority of these lesions are in the thoracic and lumbar spine, with only 1%-3% of cases found in the cervical spine. This is a case report of a 55-year-old female patient with an unremarkable medical history who presented with neck pain. Upon workup, she was found to have extensive developmental anomalies throughout her cervical and thoracic spine, including an incidentally found type 2 SCM and multiple autofused vertebrae. There are only 6 similar studies published in the literature. There was extensive facet degeneration in her cervical spine, which was suspected to be the etiology of her neck pain. This case illustrates the rare finding of asymptomatic adult cervical SCM and the likely significance of her autofused vertebrae causing accelerated symptomatic facet spondylosis.

Mouse Models of Neural Tube Defects

During embryonic development, the central nervous system forms as the neural plate and then rolls into a tube in a complex morphogenetic process known as neurulation. Neural tube defects (NTDs) occur when neurulation fails and are among the most common structural birth defects in humans. The frequency of NTDs varies greatly anywhere from 0.5 to 10 in 1000 live births, depending on the genetic background of the population, as well as a variety of environmental factors. The prognosis varies depending on the size and placement of the lesion and ranges from death to severe or moderate disability, and some NTDs are asymptomatic. This chapter reviews how mouse models have contributed to the elucidation of the genetic, molecular, and cellular basis of neural tube closure, as well as to our understanding of the causes and prevention of this devastating birth defect.