We identified robust transcriptomic differences in PCOS endometrial, epithelial and stromal subclusters, with upregulated genes involved in cell adhesion, ECM and integrin signaling (ITGAV, ITGA2, ITGA3, ITGB6, ITGB8, CD44 and ADAMTS9), particularly in SOX9+LGR5+ and AR+ subclusters. Here, SOX9 is linked to polycystic ovary syndrome.