Genetic Association Analyses of Nitric Oxide Synthase Genes and Neural Tube Defects Vary by Phenotype

Abstract

Neural tube defects (NTDs) are caused by improper neural tube closure during the early stages of embryonic development. NTDs are hypothesized to have a complex genetic origin and numerous candidate genes have been proposed. The nitric oxide synthase 3 (NOS3) G594T polymorphism has been implicated in risk for spina bifida, and interactions between that single nucleotide polymorphism (SNP) and the methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism have also been observed. To evaluate other genetic variation in the NO pathway in the development of NTDs, we examined all three NOS genes: NOS1, NOS2, and NOS3. Using 3109 Caucasian samples in 745 families, we evaluated association in the overall dataset and within specific phenotypic subsets. Haplotype tagging SNPs in the NOS genes were tested for genetic association with NTD subtypes, both for main effects as well as for the presence of interactions with the MTHFR C677T polymorphism. Nominal main effect associations were found with all subtypes, across all three NOS genes, and interactions were observed between SNPs in all three NOS genes and MTHFR C677T. Unlike the previous report, the most significant associations in our dataset were with cranial subtypes and the AG genotype of rs4795067 in NOS2 (p = 0.0014) and the interaction between the rs9658490 G allele in NOS1 and MTHFR 677TT genotype (p = 0.0014). Our data extend the previous findings by implicating a role for all three NOS genes, independently and through interactions with MTHFR, in risk not only for spina bifida, but all NTD subtypes.

A targeted sequencing panel identifies rare damaging variants in multiple genes in the cranial neural tube defect, anencephaly

“…In ExAC, 20 LoF variants are reported in NOS2 with a pLI = 0, suggesting tolerance of LoF and low confidence of causal effect. However, NOS2 has been previously associated with a cranial NTD phenotype where A/G genotype of the rs4795067 SNP within NOS2 was shown to be associated specifically with increased cranial NTD risk …”

“…However, NOS2 has been previously associated with a cranial NTD phenotype where A/G genotype of the rs4795067 SNP within NOS2 was shown to be associated specifically with increased cranial NTD risk. 37 One individual (283F06) was heterozygous for a novel missense variant in the catalytic N-terminal domain of the methylenetetrahydrofolate reductase (MTHFR) gene (c.601C>T; p.His201Tyr) ( Figure 2D), which was predicted to be damaging by all 6 mutation predictors tested (Table 1) Figure 2E, Table S2 in Appendix S3). Heterozygous missense mutations in CELSR1 gene have previously been reported in a number of NTD patients.…”

The TFAP2A–IRF6–GRHL3 genetic pathway is conserved in neurulation

“…Cases were diagnosed with myelomeningocele, a severe form of spina bifida. We also performed association studies on two family-based cohorts, a 500 case/parent trio population from the HBNTD study (29) and a 284 case/parent trio population recruited by researchers from the University of Texas-Houston (39). In these three populations, we focused on three variants; rs642961 in MCS9.7 that impacts AP-2a binding, rs17371411 in MCS21 that altered mRNA stability and rs76145088.…”

“…Samples from 425 cases and 451 matched controls from the CBDMP were genotyped and analyzed as described previously (30). Samples from 500 case/parent trios from the HBNTD were genotyped and analyzed as described previously (29). Samples from 284 case/parent trios from the University of Texas-Houston trios were genotyped on the Infinium HumanExome BeadChip v1.1 (Illumina, San Diego, CA).…”