Integrated ovary-specific DNA methylation profiling and transcriptome reveals novel regulatory features in polycystic ovary syndrome

Abstract

Polycystic ovary syndrome (PCOS) is one of the most common endocrine disorders in women. However, to date, little is known about epigenomics, especially the DNA methylation profiles in the pathophysiology of PCOS. Differentially methylated and expressed profiling were analyzed by the Infinium HumanMethylation450 BeadChip and Affymetrix Human Genome U133 Plus 2.0 Array, respectively. Fresh ovarian tissue was obtained from cervical cancer patients at the follicular phase, with regular menstrual cycles and younger than 40 years, who underwent radical hysterectomy and pelvic lymphadenectomy for cervical cancer. Fresh ovarian tissue was obtained from PCOS patients at the follicular phase, with irregular menstrual cycle and younger than 40 years, who underwent laparoscopic wedge resection. PCOS was defined according to the 2003 Rotterdam criteria. DNA methylation profiling data were processed by the Methylation Module of GenomeStudio v1.9 software using default parameters. Expression profiling data were assessed using the Affymetrix GeneChip Operating Software. Here, combining the DNA methylation profiling together with transcriptome analysis, we showed that (i) there were 7929 differentially methylated CpG sites (b> 0.1, P < 0.05) and 650 differential transcripts (fold change > 1.5, P < 0.005) in PCOS compared to normal ovaries; (ii) 54 genes were identified with methylated levels that were correlated with gene transcription in PCOS, and these genes were further verified by pyrosequencing. Notably, PCOS ovarian tissues exhibit a significant differences of methylation status of DDB2, KCNMA1, CCL2, fibrillin 1 gene (unpublished data), and TNIK gene (published data). In addition, our previous study suggests that several significant pathways, including the type I diabetes mellitus pathway, p53 signaling pathway and NOD-like receptor signaling pathway, may be involved in PCOS development. However, recent studies further indicated that the functional significance of type I diabetes mellitus pathway, may play an essential and nonredundant role in PCOS (unpublished data). These results suggested that differences in genome-wide DNA methylation and expression patterns exist between PCOS ovaries and normal ovaries; epigenetic mechanisms may in part be responsible for the different gene expression and PCOS phenotype.