Abstract
BackgroundNeural tube defects (NTDs) are severe congenital malformations that arise from failure of neurulation during early embryonic development. The molecular basis underlying most human NTDs still remains largely unknown. Based on the hypothesis that folic acid prevents NTDs by stimulating methylation reactions, DNA methylation changes could play a role in NTDs. We performed a methylome analysis for patients with myelomeningocele (MMC). Using a candidate CpG analysis for HOX genes, a significant association between HOXB7 hypomethylation and MMC was found.MethodsIn the current study, we analyzed leukocyte methylome data of ten patients with MMC and six controls using Illumina Methylation Analyzer and WateRmelon R-packages and performed validation studies using larger MMC and control cohorts with Sequenom EpiTYPER.ResultsThe methylome analysis showed 75 CpGs in 45 genes that are significantly differentially methylated in MMC patients. CpG-specific methylation differences were next replicated for the top six candidate genes ABAT, CNTNAP1, SLC1A6, SNED1, SOX18, and TEPP but only for the SOX18 locus a significant overall hypomethylation was observed (P value = 0.0003). Chemically induced DNA demethylation in HEK cells resulted in SOX18 hypomethylation and increased expression. Injection of sox18 mRNA in zebrafish resulted in abnormal neural tube formation. Quantification of DNA methylation for the SOX18 locus was also determined for five families where parents had normal methylation values compared to significant lower values for both the MMC as their non-affected child. SOX18 methylation studies were performed for a MMC patient with a paternally inherited chromosomal deletion that includes BMP4. The patient showed extreme SOX18 hypomethylation similar to his healthy mother while his father had normal methylation values.ConclusionsThis is the first genome-wide methylation study in leukocytes for patients with NTDs. We report SOX18 as a novel MMC risk gene but our findings also suggest that SOX18 hypomethylation must interplay with environmental and (epi)genetic factors to cause NTDs. Further studies are needed that combine methylome data with next-generation sequencing approaches to unravel NTD etiology.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-016-0272-8) contains supplementary material, which is available to authorized users.
Highlights
Neural tube defects (NTDs) are severe congenital malformations that arise from failure of neurulation during early embryonic development
Investigation of DNA methylation of the candidate genes folate receptor α (FOLR1), proton-coupled folate transporter (PCFT), and reduced folate carrier 1 (RFC1) genes did not show significantly differences between patients and controls, though some minor differences were observed according to RFC1 80G>A genotype [9]
A study by Kok et al found that DNA methylation of HOXB7 in particular and of the majority of the other HOX genes tend to be increased after folic acid and vitamin
Summary
Neural tube defects (NTDs) are severe congenital malformations that arise from failure of neurulation during early embryonic development. The only well-characterized genetic risk factor for human NTDs is the 677C>T change in the 5,10-methylene tetrahydrofolate reductase (MTHFR) gene This variant is known to lead to hyperhomocysteinemia and global DNA hypomethylation [2,3,4]. This association led to the hypothesis that folic acid prevents NTDs by stimulating DNA methylation [2, 5]. We performed a genome-wide DNA methylation study using the HumanMethylation 450K BeadChip (HM450k) and leukocyte DNA from ten patients with myelomeningocele (MMC) and six unrelated healthy controls We analyzed these data using a candidate-gene approach for the Homeobox (HOX) genes [11]. A study by Kok et al found that DNA methylation of HOXB7 in particular and of the majority of the other HOX genes tend to be increased after folic acid and vitamin
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
