A Comprehensive Genome-wide DNA Methylation Analysis in Blood Reveals Differentially Methylated Regions Associated with Immune Response and Steroidogenesis Pathways in Women with Polycystic Ovary Syndrome: A cross sectional study

Background: Polycystic ovary syndrome (PCOS) is a complex endocrine disorder with a multifactorial aetiology, including genetic and epigenetic components. Despite increasing evidence highlighting the role of epigenetic modifications in PCOS, their contribution to disease progression remains unclear. Aim: This study aimed to investigate the role of DNA methylation in the aetiology of PCOS. Settings and Design: This is a hospital-based observational study. Materials and Methods: The materials and methods of this study were to examine the role of DNA methylation in PCOS. Genomic DNA was isolated using the QIAamp DNA Mini Kit, and DNA methylation profiling was performed using the Infinium Human Methylation 850K (EPIC) array in 43 PCOS cases compared with controls. Statistical Analysis Used: The Student’s t -test (two-tailed) was used to compare the means and derive statistical significance from the independent groups. The ChAMP software package was used for methylation analysis on the R interface v4.2.0. Results: Differential methylation analysis identified 243 differentially methylated CpG sites within 26 differentially methylated regions (DMRs) (|Δβ| > 0.1, P < 0.05). Notably, most DMRs were located in promoter regions near CpG islands and shores, with a significant proportion (23.07%) mapping to chromosome 6. The majority (76.9%) of DMRs exhibited hypomethylation, whereas the top two DMRs were hypermethylated. Functional enrichment analysis revealed that differentially methylated genes were associated with key pathways, including Th17 cell differentiation, steroid biosynthesis and autoimmune thyroid disease. Gene ontology analysis highlighted enrichment in immune-related biological processes, MHC protein complexes and molecular functions, including prenyltransferase and transaminase activities. Conclusion: Our findings underscore the potential contribution of epigenetic modifications to PCOS pathogenesis, particularly through immune regulation and steroid metabolism. Further studies with larger cohorts and functional validation are warranted to establish the role of these epigenetic changes in PCOS.