MTHFD1 polymorphism as maternal risk for neural tube defects: a meta-analysis

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.

Folate Pathway Gene Single Nucleotide Polymorphisms and Neural Tube Defects: A Systematic Review and Meta-Analysis

Neural tube defects (NTDs) are congenital abnormalities in the central nervous system. The exact etiology of NTDs is still not determined, but several genetic and epigenetic factors have been studied. Folate supplementation during gestation is recommended to reduce the risk of NTDs. In this review we examine single nucleotide polymorphisms (SNPs) of the genes in the folate pathway associated with NTD. We reviewed the literature for all papers discussing both NTDs and SNPs in the folate pathway. Data were represented through five different genetic models. Quality assessment was performed using the Newcastle-Ottawa Scale (NOS) and Cohen's Kappa inter-rater coefficient assessed author agreement. Fifty-nine papers were included. SNPs in MTHFR, MTRR, RFC genes were found to be highly associated with NTD risk. NOS showed that high quality papers were selected, and Kappa Q-test was 0.86. Our combined results support the notion that SNPs significantly influence NTDs across the population, particularly in Asian ethnicity. Additional high-quality research from diverse ethnicities is needed and meta-regression analysis based on a range of criteria may provide a more complete understanding of the role of folate metabolism in NTDs.

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.

A Common Polymorphism in the MTHFD1 Gene Is a Modulator of Risk of Congenital Heart Disease

Several environmental and genetic factors may influence the risk of congenital heart defects (CHDs), which can have a substantial impact on pediatric morbidity and mortality. We investigated the association of polymorphisms in the genes of the folate and methionine pathways with CHDs using different strategies: a case–control, mother–child pair design, and a family-based association study. The polymorphism rs2236225 in the MTHFD1 was confirmed as an important modulator of CHD risk in both, whereas polymorphisms in MTRR, FPGS, and SLC19A1 were identified as risk factors in only one of the models. A strong synergistic effect on the development of CHDs was detected for MTHFD1 polymorphism and a lack of maternal folate supplementation during early pregnancy. A common polymorphism in the MTHFD1 is a genetic risk factor for the development of CHD, especially in the absence of folate supplementation in early pregnancy.

Association of Fetal MTHFR C677T Polymorphism with Susceptibility to Neural Tube Defects: A Systematic Review and Update Meta-Analysis

Background MTHFR gene may be a key epigenetic regulation-related factor crucial during embryogenesis. We performed a meta-analysis to determine the association of fetal MTHFR C677T polymorphism with neural tube defects (NTDs).Methods A comprehensive literature search of the PubMed, Embase, and CNKI database was performed up to April 10, 2020.Results A total of 19 case-control studies with 2,228 NTDs cases and 4,220 controls were identified. Pooled data revealed that the fetal MTHFR C677T polymorphism was significantly highly correlated with development of NTDs in the overall population. Stratified analysis showed a significant association among Caucasians and Asians, but not in mixed populations. There was a significant association between the MTHFR C677T polymorphism and spina bifida risk. No publication bias was found under any genetic model.Conclusions Our pooled data support the fetal MTHFR C677T polymorphism association with risk of NTDs, especially among Caucasians and Asians.

Understanding Choline Bioavailability and Utilization: First Step Toward Personalizing Choline Nutrition

Choline is an essential macronutrient involved in neurotransmitter synthesis, cell-membrane signaling, lipid transport, and methyl-group metabolism. Nevertheless, the vast majority are not meeting the recommended intake requirement. Choline deficiency is linked to nonalcoholic fatty liver disease, skeletal muscle atrophy, and neurodegenerative diseases. The conversion of dietary choline to trimethylamine by gut microbiota is known for its association with atherosclerosis and may contribute to choline deficiency. Choline-utilizing bacteria constitutes less than 1% of the gut community and is modulated by lifestyle interventions such as dietary patterns, antibiotics, and probiotics. In addition, choline utilization is also affected by genetic factors, further complicating the impact of choline on health. This review overviews the complex interplay between dietary intakes of choline, gut microbiota and genetic factors, and the subsequent impact on health. Understanding of gut microbiota metabolism of choline substrates and interindividual variability is warranted in the development of personalized choline nutrition.

Changes in maternal age and prevalence of congenital anomalies during the enactment of China's universal two-child policy (2013-2017) in Zhejiang Province, China: An observational study

BACKGROUND

China implemented a partial two-child policy (2013) followed by a universal two-child policy (2015), replacing the former one-child policy mandated by the government. The changes affect many aspects of China's population as well as maternal and infant health, but their potential impact on birth defects (BDs) remains unknown. In this study, we investigated the associations of these policy changes with BDs in Zhejiang Province, China.

METHODS AND FINDINGS

We used data from the BD surveillance system in Zhejiang Province, China, which covers 90 hospitals in 30 urban districts and rural counties, capturing one-third of the total births in this province. To fully consider the time interval between conception and delivery, we defined the one-child policy period as data from 2013 (births from October 2012 to September 2013), the partial two-child policy period as data from 2015 (births from October 2014 to September 2015), and the universal two-child policy period as data from 2017 (births from October 2016 to September 2017). Data from 2009 and 2011 were also used to show the changes in the proportion of births to women with advanced maternal age (35 years and older) prior to the policy changes. Main outcome measures were changes in the proportion of mothers with advanced maternal age, prevalence of BDs, rankings of BD subtypes by prevalence, prenatal diagnosis rate, and live birth rate of BDs over time. A total of 1,260,684 births (including live births, early fetal losses, stillbirths, and early neonatal deaths) were included in the analyses. Of these, 644,973 (51.16%) births were to women from urban areas, and 615,711 (48.84%) births were to women from rural areas. In total, 135,543 (10.75%) births were to women with advanced maternal age. The proportion increased by 85.68%, from 8.52% in 2013 to 15.82% in 2017. However, it had remained stable prior to policy changes. Overall, 23,095 BDs were identified over the policy changes (2013-2017). The prevalence of BDs during 2013, 2015, and 2017 was 245.95, 264.86, and 304.36 per 10,000 births, respectively. Trisomy 21 and other chromosomal defects increased in both risk and ranking from 2013 to 2017 (crude odds ratio [95% confidence interval] 2.13 [1.75-2.60], from ranking 10th to 5th, and 3.63 [2.84-4.69], from ranking 16th to 6th, respectively). The prenatal diagnosis rate increased by 3.63 (2.2-5.1) percentage points (P < 0.001), from 31.10% to 34.72%, and identification of BDs occurred 1.88 (1.81-1.95) weeks earlier (P < 0.001). The live birth rate for infants with BDs born before 28 gestational weeks increased from 1.29% to 11.45%. The major limitations of this observational study include an inability to establish causality and the possible existence of unknown confounding factors, some of which could contribute to BDs.

CONCLUSIONS

In this study, we observed significant increases in maternal age and the prevalence of total and age-related anomalies following China's new two-child policy. Increases in live birth rate for infants with BDs born before 28 gestational weeks suggest that healthcare for very preterm births with BDs may be warranted in the future, as well as updating the definition of perinatal period.

TRIM4 is associated with neural tube defects based on genome-wide DNA methylation analysis

BACKGROUND

Neural tube defects (NTDs) are complex abnormalities associated with gene-environment interactions. The underlying cause has not been determined.

METHODS

Spinal cord tissues from cases with NTDs and healthy controls were collected. Methylation patterns between cases and normal individuals were compared using 450K Infinium Methylation BeadChip Illumina. DNA methylation analysis by pyrosequencing (PyroMark Q96) and mRNA and protein expression were analyzed using real-time quantitative PCR and Western blotting, respectively. Next-generation and Sanger sequencing were used to determine genetic variants in the target genes.

RESULTS

Spinal cord tissues from cases with NTDs had more hypomethylated than hypermethylated genes. Further evaluation showed that the exon 1 region of TRIM4 was hypomethylated, and TRIM4 mRNA and protein levels were significantly increased in NTDs compared to controls. A rare missense variant (rs76665876) in TRIM4 was found in 3 of the 14 NTD cases but was not related to TRIM4 expression. TRIM4 mRNA levels were significantly increased in cases with hypomethylation and without the rs76665876 variant.

CONCLUSION

These findings suggest that spinal cord tissues in cases with NTDs had a different genome-wide methylation pattern compared to controls. Abnormal methylation patterns in TRIM4 in immunity pathways might be involved in NTD pathogenesis. Genetic variants in TRIM4 genes only slightly contribute to the etiology of human NTDs.

A unique methylation pattern co-segregates with neural tube defect statuses in Han Chinese pedigrees

Neural tube defects (NTDs) are a complex trait associated with gene-environment interactions. Folic acid deficiency and planar cell polarity gene mutations account for some NTD cases; however, the etiology of NTDs is still little understood. In this study, in three Han Chinese NTD pedigrees (two with multiple affected children), with no information on folic acid deficiency or supplement, we examined genome-wide methylation profiles of each individual in these families. We further compared methylation status among cases and normal individuals within the pedigrees. A unique methylation pattern co-segregated with affected status: NTD cases had more hypermethylated than hypomethylated CpG islands; genes with different methylations clustered in pathways associated with epithelial-to-mesenchymal transition (ZEB2, SMAD6, and CDH23), folic acid/homocysteine metabolism (MTHFD1L), transcription/nuclear factors (HDAC4, HOXB7, SOX18), cell migration/motility/adhesion, insulin and cell growth, and neuron/axon development. Although the genetics of NTD are likely complex, epigenetic changes may concentrate in certain key pathways.

Choline metabolites: gene by diet interactions

PURPOSE OF REVIEW

The review highlights recent advances in our understanding of the interactions between genetic polymorphisms in genes that metabolize choline and the dietary requirements of choline and how these interactions relate to human health and disease.

RECENT FINDINGS

The importance of choline as an essential nutrient has been well established, but our appreciation of the interaction between our underlying genetic architecture and dietary choline requirements is only beginning. It has been shown in both human and animal studies that choline deficiencies contribute to diseases such as nonalcoholic fatty liver disease and various neurodegenerative diseases. An adequate supply of dietary choline is important for optimum development, highlighted by the increased maternal requirements during fetal development and in breast-fed infants. We discuss recent studies investigating variants in PEMT and MTHFR1 that are associated with a variety of birth defects. In addition to genetic interactions, we discuss several recent studies that uncover changes in fetal global methylation patterns in response to maternal dietary choline intake that result in changes in gene expression in the offspring. In contrast to the developmental role of adequate choline, there is now an appreciation of the role choline has in cardiovascular disease through the gut microbiota-mediated metabolite trimethylamine N-oxide. This pathway highlights some of our understanding of how the microbiome affects nutrient processing and bioavailability. Finally, to better characterize the genetic architecture regulating choline requirements, we discuss recent results focused on identifying polymorphisms that regulate choline and its derivative products.

SUMMARY

Here we discuss recent studies that have advanced our understanding of how specific alleles in key choline metabolism genes are related to dietary choline requirements and human disease.