Women with PCOS had atypical skeletal muscle gene expression and DNA methylation changes; IR was found to be linked to transcriptional dysregulation; KLF10 expression was upregulated in PCOS muscle cells and influenced by insulin. Testosterone downregulated COL1A1 and MAP2K6 expression in muscle cells. Epigenetic modifications contributed to altered immune system pathways in PCOS. Here, COL1A1 is linked to polycystic ovary syndrome.