Study on DNA methylation in three neural tube defects pedigrees / 中华实用儿科临床杂志

ABSTRACT

Objective To investigate the methylation alteration of genomic DNA (gDNA) and its significance in pedigree neural tube defects (NTDs).Methods Twelve subjects from 3 NTDs pedigrees were enrolled in this study.NTDs patients were served as the case group,and their family members with normal phenotype were served as the control group.Peripheral vein blood was extracted,then gDNA was extracted.The extracted gDNA was treated with sodium bisulfite propagated as DNA segments in the way of whole genome amplification,which was put in I11umina Infinium human methylation 450k bead chip to perform hybridization,elution,extension,and imaging.The chip was scanned by iScan.Genome Studio was used to read the outcome.Illumina methylation analyzer software was used to analyze the methylation data.Results Gene differential methylation analysis showed that differential methylation sites only accounted for 0.2％ of the detected CpG sites and there were 617 differential hypermethylation sites (P ＜ 0.05),and 63 of them represented significant difference(P ＜ 1 × 10-4),including zinc finger E-box binding homebox 2,5,10-methylenetetrahydrofolate dehydrogenase 1 etc;there were 104 differential hypomethylation sites (P ＜ 0.05),and 65 of them represented significant difference (P ＜ 0.01),including Homeobox B7 and runt-related transcription factor 3 etc.Clustering analysis indicated that the tendency of DNA hypermethylation was consistent with NTDs patients,but the tendency of DNA hypomethylation was consistent with the controls.Conclusion In NTDs pedigree,the abnormal DNA methylation alterations may be the risk factor for NTDs occurrence.