Closing in on Mechanisms of Open Neural Tube Defects

Abstract

Neural tube defects (NTDs) represent a failure of the neural plate to complete the developmental transition to a neural tube. NTDs are the most common birth anomaly of the CNS. Following mandatory folic acid fortification of dietary grains, a dramatic reduction in the incidence of NTDs was observed in areas where the policy was implemented, yet the genetic drivers of NTDs in humans, and the mechanisms by which folic acid prevents disease, remain disputed. Here, we discuss current understanding of human NTD genetics, recent advances regarding potential mechanisms by which folic acid might modify risk through effects on the epigenome and transcriptome, and new approaches to study refined phenotypes for a greater appreciation of the developmental and genetic causes of NTDs.

Keywords: anencephaly; folate; folic acid; myelomeningocele; neural tube defect; spina bifida.

Figure 1.. Neural tube defects (NTDs) are likely to be impacted by many types of genetic variants.

These variants include coding and noncoding ones, structural ones, and chromosomal aneuploidy. Sources of variants include de novo, inherited, modifiers, somatic and combinations of these. Genetic variants are influenced by epigenetic factors and the environment to establish the NTD risk. Newborn image adopted from the CDC Public Library of Images.

Figure 2.. Estimation of cohort size for causative variants discovery.

Power calculation curve indicating estimated number of trios necessary to discover a given numbers of genes as recurrently mutated, assuming that there are 100 ‘discoverable’ genes for haploinsufficient neural tube defects (NTDs) in humans. The variable ‘v’ is defined as the ratio of the number of de novo loss-of-function (LoF) mutations in affected individuals divided by the number of de novo LoF mutations in unaffected individuals across the population. For these calculations, we estimate v as 1.5 or 2.5, meaning that subjects with NTD will have 1.5 or 2.5 as many de novo LoF mutations as controls. Assuming v=2.5, then a cohort of 1000 trios would discover 40 recurrently mutated genes with a false discovery rate of 10% (blue line). If on the other hand v = 1.5 then 1000 trios would only discover 10 recurrently mutated genes. These calculations are based upon the basal de novo mutation rate, and assumes a total of 20,000 human genes that can be mutated. Abbreviation: FDR, false discovery rate.

Figure 3.. Schematic of folate as a methyl group donor.

Either dietary folates or synthetic folic acid are incorporated into folate one-carbon metabolism pathway and serve as methyl group donors for various substrates including protein, DNA, RNA and lipids. Epigenetic regulation by DNA and histone methylation plays crucial roles in transcriptional regulation and embryonic development. DNMT, DNA methyltransferase; DHFR, dihydrofolate reductase; HMT, histone methyltransferase; K, lysine; mC, methylcytosine; MTHFR, methylenetetrahydrofolate reductase; MTR, methionine synthase; PRMT: protein arginine methyltransferase; R, arginine; SAH, S-adenosylhomocysteine; SAM, S-adenosylmethionine; SHMT, serine hydroxymethyltransferase; THF, tetrahydrofolate.

Figure 4.. A. Model of impact of folic acid (FA) supplementation on neural tube defect (NTD) incidence and severity.

In the absence of FA, a hypothetical gray curve represents the relationship between incidence and severity. FA supplementation may decrease NTD incidence (arrow 1, curve moves to left) or severity (arrow 2, curves moves down), or may impact both (arrow 3, curve moves both left and down). B. Cumulative NTD risk along y-axis and individual example risk profiles numbered at bottom. Yellow: genetic risk; green: environment risk attributed to FA deficiency or other factors. Individuals 1 and 2 have risk below the threshold. Individual 3 has cumulative risk above threshold for mild disease, but if exposed to folate, would fall below threshold for mild disease. Individuals 4 and 5 have cumulative risk above threshold for severe disease, but if exposed to folate, 4 would fall into mild disease and 5 would fall below mild disease threshold. Individual 6 has genetic risk above threshold for severe disease that is not modified by folate.