Identifying and Validating Differentially Methylated Regions in Newly Diagnosed Patients with Graves' Disease.

This research used combined bioinformatic methods to identify differentially methylated regions (DMRs) in newly diagnosed patients with Graves' disease (GD). Peripheral blood from six GD patients and controls was collected and methyl-DNA immunoprecipitation (MeDIP), and NimbleGen Human DNA Methylation 3 × 720 K promoter plus CpG island microarrays were further analyzed. DMRs were categorized into low-methylated genes and high-methylated genes, which were mapped into a protein-protein interaction (PPI) network constructed by a dataset. Then, six candidate genes were validated in an expanded population with 32 GD patients and 30 controls using bisulfite amplicon sequencing. Top 10 hub genes revealed by PPI analysis were , , , , , , , , , and . Five CpG sites of (51436061), (94856657), (62422532 and 62422689), and (107979477) were validated, having significantly different methylation levels between GD patients and controls. Based on gender stratification, nine significant CpG sites of (51436061), (94855831), and (62422301, 62422327, 62422356, 62422365, 62422374, 62422532, and 62422689) were detected between female GD patients and controls. The methylation level of 62422532 of was significantly associated with levels of serum TGAb and TRAb. In addition, the methylation level of 62422689 of showed significant correlation with the age of GD patients. In the analysis of prediction of transcription factor binding at specific CpG sites in promoter region, paired box protein 5 () and CCAAT/enhancer-binding protein () might be under the influence of methylation at CpG sites 62422365 and 62422532, respectively. , , , and especially were potential aberrantly methylated genes related to GD. These findings might supply the latest information of DNA methylation in the GD disease.