Epidemiology and genetics of neural tube defects: an application of the Utah Genealogical Data Base

Identification and functional analysis of rare HECTD1 missense variants in human neural tube defects

Neural tube defects (NTDs) are severe malformations of the central nervous system that arise from failure of neural tube closure. HECTD1 is an E3 ubiquitin ligase required for cranial neural tube closure in mouse models. NTDs in the Hectd1 mutant mouse model are due to the failure of cranial mesenchyme morphogenesis during neural fold elevation. Our earlier research has linked increased extracellular heat shock protein 90 (eHSP90) secretion to aberrant cranial mesenchyme morphogenesis in the Hectd1 model. Furthermore, overexpression of HECTD1 suppresses stress-induced eHSP90 secretion in cell lines. In this study, we report the identification of five rare HECTD1 missense sequence variants in NTD cases. The variants were found through targeted next-generation sequencing in a Chinese cohort of 352 NTD cases and 224 ethnically matched controls. We present data showing that HECTD1 is a highly conserved gene, extremely intolerant to loss-of-function mutations and missense changes. To evaluate the functional consequences of NTD-associated missense variants, functional assays in HEK293T cells were performed to examine protein expression and the ability of HECTD1 sequence variants to suppress eHSP90 secretion. One NTD-associated variant (A1084T) had significantly reduced expression in HEK293T cells. All five NTD-associated variants (p.M392V, p.T801I, p.I906V, p.A1084T, and p.P1835L) reduced regulation of eHSP90 secretion by HECTD1, while a putative benign variant (p.P2474L) did not. These findings are the first association of HECTD1 sequence variation with NTDs in humans.

Identification and Functional Analysis of Rare HECTD1 Missense Variants in Human Neural Tube Defects

Neural tube defects (NTDs) are severe malformations of the central nervous system that arise from failure of neural tube closure. HECTD1 is an E3 ubiquitin ligase required for cranial neural tube closure in mouse models. NTDs in the Hectd1 mutant mouse model are due to the failure of cranial mesenchyme morphogenesis during neural fold elevation. Our earlier research has linked increased secretion of extracellular heat shock protein 90 (eHSP90) to aberrant cranial mesenchyme morphogenesis in the Hectd1 model. Furthermore, overexpression of HECTD1 suppresses stress-induced eHSP90 secretion in cell lines. In this study, we report the identification of five rare HECTD1 missense sequence variants in NTD cases. The variants were found through targeted next-generation sequencing in a Chinese cohort of 352 NTD cases and 224 ethnically matched controls. We present data showing that HECTD1 is a highly conserved gene, extremely intolerant to loss-of-function mutations and missense changes. To evaluate the functional consequences of NTD-associated missense variants, functional assays in HEK293T cells were performed to examine protein expression and the ability of HECTD1 sequence variants to suppress eHSP90 secretion. One NTD-associated variant (A1084T) had significantly reduced expression in HEK293T cells. All five NTD-associated variants (p.M392V, p.T801I, p.I906V, p.A1084T, and p.P1835L) reduced regulation of eHSP90 secretion by HECTD1, while a putative benign variant (p.P2474L) did not. These findings are the first association of HECTD1 sequence variation with human disease and suggest that sequence variation in HECTD1 may play a role in the etiology of human NTDs.

Folic acid prescription practice for high-risk prevention of spina bifida at a tertiary care hospital in Addis Ababa, Ethiopia

PURPOSE

Mothers who have had a pregnancy affected by spina bifida are advised to take 4-5 mg/day folic acid pills to prevent recurrence. The folic acid prescription pattern was examined for high-risk mothers whose children received spina bifida surgery in an urban Ethiopian hospital.

METHODS

Data were analyzed from a large Ethiopian urban tertiary care hospital that provided spina bifida care. General practitioners recorded 5 mg/day folic acid prescriptions administered to mothers of infants with spina bifida born between January 2019 and June 2022.

RESULTS

Among 500 baby-mother pairs, 340 (68%) received a 120-day prescription for 5 mg/day folic acid pills. Of these 340 mothers, 331 (97%) received their folic acid prescription at their child's first or second patient encounter. Almost all mothers (94%) had documentation of only one prescription for the study duration. The percentage of mothers receiving at least one prescription varied by the baby's year of birth (2019:75%; 2020:92%; 2021:46%; Jan 2022 -June 2022:79%).

CONCLUSION

This prioritization of spina bifida recurrence prevention demonstrates feasibility for other healthcare centers in low-income countries. Sustained funds to provide women with free folic acid pills can favor high compliance and uptake of this prevention intervention.

Systems biology analysis of human genomes points to key pathways conferring spina bifida risk

Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids much of the bias inherent in candidate gene searches that are pervasive in the field. We examine both protein coding and noncoding regions of whole genomes to analyze sequence variants, collapsed by gene or regulatory region, and apply machine learning, gene enrichment, and pathway analyses to elucidate molecular pathways and genes contributing to human SB.

Spina bifida (SB) is a debilitating birth defect caused by multiple gene and environment interactions. Though SB shows non-Mendelian inheritance, genetic factors contribute to an estimated 70% of cases. Nevertheless, identifying human mutations conferring SB risk is challenging due to its relative rarity, genetic heterogeneity, incomplete penetrance, and environmental influences that hamper genome-wide association studies approaches to untargeted discovery. Thus, SB genetic studies may suffer from population substructure and/or selection bias introduced by typical candidate gene searches. We report a population based, ancestry-matched whole-genome sequence analysis of SB genetic predisposition using a systems biology strategy to interrogate 298 case-control subject genomes (149 pairs). Genes that were enriched in likely gene disrupting (LGD), rare protein-coding variants were subjected to machine learning analysis to identify genes in which LGD variants occur with a different frequency in cases versus controls and so discriminate between these groups. Those genes with high discriminatory potential for SB significantly enriched pathways pertaining to carbon metabolism, inflammation, innate immunity, cytoskeletal regulation, and essential transcriptional regulation consistent with their having impact on the pathogenesis of human SB. Additionally, an interrogation of conserved noncoding sequences identified robust variant enrichment in regulatory regions of several transcription factors critical to embryonic development. This genome-wide perspective offers an effective approach to the interrogation of coding and noncoding sequence variant contributions to rare complex genetic disorders.

Unraveling the complex genetics of neural tube defects: From biological models to human genomics and back

Neural tube defects (NTDs) are a classic example of preventable birth defects for which there is a proven-effective intervention, folic acid (FA); however, further methods of prevention remain unrealized. In the decades following implementation of FA nutritional fortification programs throughout at least 87 nations, it has become apparent that not all NTDs can be prevented by FA. In the United States, FA fortification only reduced NTD rates by 28-35% (Williams et al., 2015). As such, it is imperative that further work is performed to understand the risk factors associated with NTDs and their underlying mechanisms so that alternative prevention strategies can be developed. However, this is complicated by the sheer number of genes associated with neural tube development, the heterogeneity of observable phenotypes in human cases, the rareness of the disease, and the myriad of environmental factors associated with NTD risk. Given the complex genetic architecture underlying NTD pathology and the way in which that architecture interacts dynamically with environmental factors, further prevention initiatives will undoubtedly require precision medicine strategies that utilize the power of human genomics and modern tools for assessing genetic risk factors. Herein, we review recent advances in genomic strategies for discovering genetic variants associated with these defects, and new ways in which biological models, such as mice and cell culture-derived organoids, are leveraged to assess mechanistic functionality, the way these variants interact with other genetic or environmental factors, and their ultimate contribution to human NTD risk.

Periconceptional folic acid and risk for neural tube defects among higher risk pregnancies

BACKGROUND

Women with a previous neural tube defect (NTD)-affected pregnancy are recommended to consume 4,000 μg daily folic acid (FA) for prevention (10 times the general-population recommendation). Protection from doses between 400 and 4,000 μg for this and other higher risk groups is unclear.

METHODS

In the case-control Slone Birth Defects Study (1988-2015), we examined the associations between periconceptional FA doses and NTDs among four higher risk groups: NTD family history, periconceptional antiepileptic drug exposure (AED), pregestational diabetes, and prepregnancy obesity. Mothers completed standardized interviews about pregnancy events and exposures. FA categorizations were based on (a) supplements only and (b) supplements and diet ("total folate"). We estimated odds ratios (ORs) and 95% confidence intervals (CIs) (adjusted for age and study center) using logistic regression.

RESULTS

Cases and controls included: 45 and 119 with family history, 25 and 108 with AED exposure, 12 and 63 with pregestational diabetes, 111 and 1,243 with obesity. Daily FA supplementation was associated with lower NTD risk compared to no supplementation (adjusted ORs were 0.33 [95% CI 0.13, 0.76] for family history, 0.31 [0.09, 0.95] for AED exposure, 0.25 [0.04, 1.05] for pregestational diabetes, 0.65 [0.40, 1.04] for obesity). Though estimates were imprecise, as total folate increased stronger point estimates were observed, notably among family history. No mothers with a prior NTD-affected pregnancy supplemented with 4,000 μg.

CONCLUSIONS

Our findings reinforce that all women of childbearing potential should consume at least 400 μg FA/day to protect against NTDs. Higher risk groups may benefit from higher doses.

Proportion of neural tube defects attributable to known risk factors

BACKGROUND

Recognized risk factors for neural tube defects (NTDs) poorly predict population-level NTD risk. However, the proportion of NTDs that can be attributed to these risk factors is uncertain.

METHODS

To determine the proportion of NTD cases that is attributable to known or suspected risk factors (i.e., female infant sex, family history of NTDs, and maternal Hispanic ethnicity, obesity, pregestational diabetes, gestational diabetes, low dietary folate intake, lack of folic acid supplementation, anticonvulsant use, and hot tub or sauna use), we estimated the adjusted population attributable fraction (aAF) for each factor, using the method of Eide and Geffler and data from the National Birth Defects Prevention Study.

RESULTS

Our analyses of these data indicate that the proportion of cases of spina bifida and anencephaly that can be attributed to known risk factors is 28% and 44%, respectively. For spina bifida, the factor with the greatest attributable fraction was maternal obesity (aAF, 10%), whereas for anencephaly it was Hispanic ethnicity (aAF, 15%).

CONCLUSION

Our analyses indicate that known risk factors account for <50% of NTD cases. Hence, the majority of NTD cases are attributable to, as yet, unidentified factors. These findings highlight the need for continued research to identify genetic and additional nongenetic risk factors for NTDs. Further, these findings suggest that strategies that aim to reduce the risk of NTDs associated with maternal Hispanic ethnicity and obesity may have the greatest impact on the population prevalence of these conditions.

Genetic and environmental factors in complex neurodevelopmental disorders

Complex neurodevelopmental disorders, such as schizophrenia, autism, attention deficit (hyperactivity) disorder, (manic) depressive illness and addiction, are thought to result from an interaction between genetic and environmental factors. Association studies on candidate genes and genome-wide linkage analyses have identified many susceptibility chromosomal regions and genes, but considerable efforts to replicate association have been surprisingly often disappointing. Here, we summarize the current knowledge of the genetic contribution to complex neurodevelopmental disorders, focusing on the findings from association and linkage studies. Furthermore, the contribution of the interaction of the genetic with environmental and epigenetic factors to the aetiology of complex neurodevelopmental disorders as well as suggestions for future research are discussed.

Spina bifida: a diagnostic dilemma in paleopathology

This article provides information regarding the etiology, pathogenesis, and skeletal manifestation of spina bifida or spinal dysraphisms. On the basis of a review of the medical literature, it addresses discrepancies in documentation and interpretation of spina bifida in paleopathology. Furthermore, it offers suggestions for use of universal terminology and highlights the difficulties in the specific diagnosis of dysraphisms in skeletal remains. In addition, the necessity of examining the entire skeleton for abnormalities to distinguish simple delay/failure of fusion of the posterior neural arches from other occult spinal dysraphisms is emphasized, as it is the need for stratification of the sample by age and sex when reporting frequencies of sacral spina bifida occulta.

A reproductive history of mothers with spina bifida offspring--a new look at old issues

Background

Spina bifida is a disorder of the cerebrospinal fluid system associated with failure of neural tube closure in the fetus. Reproductive history studies of mothers with spina bifida offspring have often been conducted shortly after the affected child's birth. In this study, a large group of community-based mothers were studied after most had completed their families. The aims were to present a more comprehensive reproductive history and to test several hypotheses regarding the nature of spina bifida.

Methods

Data from 271 mothers was collected by interview 18.3 mean years after the affected child's birth. Data analysis was by χ-square, Fisher exact test and t test with a p value less than 0.05 considered significant.

Results

Females made up 56.5% of affected offspring (probands) and 53.1% of unaffected offspring. The spina bifida and anencephaly recurrence rate was 4.0%. The twinning rate was 8.6/1000 live births. 24.4% of mothers had a history of spontaneous abortion and the rate varied by pregnancy order from 87 to 185/1000 live births. Duration of pregnancies subsequent to probands was shorter for female than male probands. Mean birth weight of probands with high lesions exceeded those with low lesions. A spontaneous abortion preceded female probands more often than males as compared to live births. Affected males with high lesions conceived by white mothers were at greater risk to be spontaneously aborted. Previous inter-gestational interval for mothers with no history of spontaneous abortion was longer for probands than unaffected offspring but not for mothers with a history of spontaneous abortion.

Conclusion

Overall, and for every major subgroup of these mothers, more affected and unaffected female than male offspring were born. Differences by gender and lesion level among probands and between probands and unaffected offspring were consistent with an etiology of unknown genetic factors, hormonal and/or immune system factors.

Neural tube defects

Defects of development of the neural tube can result in a number of seemingly different malformations. Understanding the abnormal embryology helps one understand the malformations and their surgical treatments. The clinical presentations and the follow-up of these patients require attention to various end organs besides the nervous system. For most of these conditions, long-term follow-up is necessary regardless of initial treatment. A decline in function is not a part of the natural history of these malformations and requires prompt evaluation and treatment.

A genealogical study of Alzheimer disease in the Saguenay region of Quebec

We performed an analysis of inbreeding and kinship among the ascending genealogies of 205 autopsy-confirmed Alzheimer disease (AD) subjects recruited in the Saguenay area of Québec. We hypothesized that if some traits pertaining to the disease were determined by inherited factors, and if the corresponding genes were not too frequent in the population, it might be possible to detect some clusters of patients related to common ancestors and presenting a level of kinship and/or inbreeding higher than is observed in the unaffected population of the same age. In view of the heterogeneity of the disease, we also verified if some of the factors investigated could be associated more specifically with subsets of cases based on age of onset and on apolipoprotein E (APOE) genotype. Results were compared with those obtained on 205 controls matched for gender, place and year of birth. We found that late-onset AD cases with an APOE-epsilon 4 were significantly more inbred than controls and that this increase was explained by the high level of inbreeding of a few cases whose parents were related at the first-cousin level. This could possibly indicate the implication of a recessive element in a small subset of AD cases in the Saguenay population. We also found that late-onset epsilon 4+ cases were significantly more closely related among themselves than with controls. This increase in kinship may be attributable to the presence of the epsilon 4 allele or to some other unidentified genetic factor possibly acting in conjunction with APOE-epsilon 4.

Epidemiology of congenital hydrocephalus in Utah, 1940-1979: report of an iatrogenically related "epidemic"

As part of an epidemiological study of congenital hydrocephalus in Utah, we focused on the effect of ascertainment sources and temporal variability to further delineate the causes of this relatively common, handicapping birth defect. The incidence and distribution of 934 reported cases diagnosed prior to age 6 months, and born to Utah residents from 1940 to 1979, were analyzed. Data were ascertained by examination of multiple sources, e.g., 982,066 birth, 11,161 fetal death, and 248,208 death certificates, and selected hospital and clinic records. Of the 934 reported cases, 700 met our selection criteria for congenital hydrocephalus, which results in a crude incidence of 0.70 per 1,000 live and stillbirths. Seventy-one cases (10.1%) had additional, multiple congenital anomalies. The male/female sex ratios of the 619 cases of isolated congenital hydrocephalus (occurring as a single entity or in the absence of other reported or known birth defects) and those with multiple congenital anomalies (71 cases) were virtually identical, being 1.45 and 1.48, respectively. A significant 85% increase in the rate of reported cases was observed for the period 1966 to 1970. However, examination of patients' records from 1966 to 1975 in the hospital responsible for almost all of this increase suggests that this was an iatrogenically related "epidemic" caused by several factors: the introduction and possible misinterpretation of pneumoencephalograms (PEG) in the diagnosis of hydrocephalus (PEG was replaced by CAT scanning in the early 1970s), inappropriate diagnosis, and incorrect recording of age at time of diagnosis.

Acalvaria: a unique congenital anomaly

Acalvaria is a rare malformation usually regarded as a postneurulation defect. It consists of absence of the calvarial bones, dura mater and associated muscles in the presence of a normal skull base and normal facial bones. The condition is frequently confused by prenatal ultrasonography with anencephaly or an encephalocele. Whereas the cerebral hemispheres are absent in anencephaly, the cranial contents in acalvaria are generally complete, though some neuropathological abnormality is often present. The presumed pathogenesis of acalvaria is faulty migration of the membranous neurocranium with normal placement of the embryonic ectoderm, resulting in absence of the calvaria but an intact layer of skin over the brain parenchyma. We describe 2 cases of acalvaria, one misdiagnosed ultrasonographically as an occipital encephalocele prenatally. The brain in one fetus demonstrated semilobar holoprosencephaly and micropolygyria, but in the other, was structurally and histologically normal with the exception of hydrocephalus.

Neural tube defects after infertility treatment: a review

OBJECTIVE

To investigate whether an association exists between ovulation induction and neural tube defects (NTDs).

MATERIALS AND METHODS

Risk estimations in the medical literature were identified through Medline, and validity and power were assessed. Large in vitro fertilization-embryo transfer (IVF-ET) registries represent another source of information. The total number of NTDs and the total number of fetuses were computed from five registries. These data were expressed as proportions and compared with data from the general population.

RESULTS

Only one study could be identified as both valid and powerful, through literature review. This case-control study concluded there was no association between ovulation induction and NTDs. The pool of IVF-ET registry data represents another powerful epidemiologic tool. Analysis of the registry data confirms the findings of the case-control study.

CONCLUSIONS

Ovulation induction does not seem to represent a risk factor for NTDs in the offspring.

Genetic epidemiology of Down's syndrome in Shetland

Pedigrees of all known cases, on Shetland, of Down's syndrome, cytogenetically confirmed as trisomy 21, and of a control for each patient matched by birth date, sex and birth place, were traced over a minimum of eight generations. Mean kinship coefficients in all pairs of Down's syndrome patients and in all pairs of controls were similar. The kinship between the father and mother of each case shows that the parents are more closely related than the general level of relationship in the population, suggesting some recessive element in the etiology. It is argued that the effect of the resulting increased homozygosity would be to prevent the loss of the conceptus that occurs in the majority of trisomy 21 conceptions.

Consanguinity and multiple sclerosis in Orkney

For all patients with multiple sclerosis in Orkney who were alive in 1974 or who had died during 1958 to 1974, pedigree data were analysed. The relationship between their parents, expressed by kinship coefficients, was compared with that between parents of matched controls. The closer relationship between parents of patients suggests that it is the genes that are shared by a patient's parents, and that he inherits from both, that influence his susceptibility to multiple sclerosis.

The UCLA-University of Utah epidemiologic survey of autism: genealogical analysis of familial aggregation

To assess familial aggregation of autism, 86 autistic subjects were linked to the Utah Genealogical Database. Kinship coefficients were estimated for all possible pairs of autistic subjects and then averaged. Fifty replicate sets of matched control subjects (86 members in each set) were drawn randomly from the database, and the average kinship coefficient was computed for all possible pairs of individuals in each set. The average kinship coefficient for the autistic subjects was approximately 1/1,000, while the average kinship coefficients for the 50 control groups ranged from 4/100,000 to 1.6./10,000. These results indicate a strong tendency for autism to cluster in families. When kinship was analyzed by specific degrees of relationship, it was shown that the familial aggregation of autism is confined exclusively to sib pairs and does not extend to more remote degrees of relationship. This finding indicates that a single-gene model is unlikely to account for most cases of autism.

Severe neural tube defect syndrome from the Early Archaic of Florida

The Early Archaic Windover site is on the east coast of mid-peninsular Florida. A subadult skeleton (about 15 years old at time of death) was recovered with multiple pathologies related to spina bifida aperta of the neural arch at the L3-S2 level of the spine. Other evidence indicates s.b. cystica, although the degree of severity of the dysraphic neural tube syndrome cannot be directly determined. In addition to spina bifida, the lumbar region is scoliotic from malformation of zygapophyses. The defect is accompanied by severe infection of the right tibia and fibula, and disuse atrophy of long bones. It is hypothesized the NTD (neural tube defect) led to progressive sensory deprivation, which in turn led to increased loss of mobility, ulceration, and risk of serious infections. Other "minor" anomalies such as cone-shaped epiphyses, enlarged nutrient foramina, and vental vertebral cavitation are also discussed. The chronic nature of these defects provide insight on the high level of long-term care and attention provided a severely handicapped individual 7,500 years ago.

Inbreeding in the Utah Mormons: an evaluation of estimates based on pedigrees, isonymy, and migration matrices

Using a computerized genealogical database, inbreeding coefficients were calculated for a sample of 435777 Utah Mormons. The population was divided into ten ten-year birth cohorts (1846-1945) and 22 geographic subdivisions in order to assess temporal and spatial variation in inbreeding. The average inbreeding coefficient for this population is 0.000 106. The average within-groups random kinship coefficient is 0.000 312, reflecting consanguinity avoidance. Random kinship matrices were formed by estimating the average kinship within each spatial subdivision and between all pairs of subdivisions. These matrices were compared statistically with kinship matrices previously estimated using migration matrices and isonymy data. The isonymy approach consistently overestimates random and total inbreeding as well as Wright's Fst. This can be attributed primarily to the assumption of monophyletic origin of surnames. The migration matrix method underestimates random inbreeding and Fst. This is due mainly to the assumption that outside immigrants are derived from a genetically homogeneous population. While the absolute values of the kinship coefficients estimated by each method differ substantially, the patterns of between-groups kinship coefficients given by each method are highly congruent. Logistic and linear regression analyses of 85,235 marriages demonstrate that consanguinity is significantly dependent upon year of marriage, geographic distance between husband's and wife's birthplaces, and the population size of husband's and wife's birthplaces.

A statistical test for detection of ancestral genetic contributions to disease occurrence in finite populations

We have been investigating cancer patterns in the Hutterites, a religious isolate residing on communal farms [Martin et al, 1980a,b,c]. Advantages of this population include extensive and accurate genealogies, essentially complete case ascertainment, and relatively uniform environmental background with regard to geographic location, lifestyle, and diet. However, application of the common epidemiological approach to familial risk assessment based on incidence in relatives of index cases [Haenszel, 1959] posed difficulties because all cases are probands. We also planned to employ matching to control for important confounders and thus had to deal with the problems of the matching of cases and controls as well as the existence of complex inbreeding [Hauck and Martin, 1982]. Our basic approach was to compare coefficients of kinship (Fm, a measure of coancestry) of cases with each other to coefficients between cases and matched controls drawn from the same population. We have developed a paired t-type statistic to assess the significance of observed differences. We present, as examples, application of our methods to the analysis of Hutterite data on neurofibromatosis, known to be inherited in autosomal dominant fashion, and on cancer. Neurofibromatosis showed significant familial aggregation, as expected. Breast, colon-rectal, and stomach cancer did not. We then show how to evaluate power and to determine appropriate sample sizes for detecting specified increases in kinship.