Bioinformatic analysis and validation of candidate genes in the eutopic endometrium reveal differential expressions in diffuse adenomyosis, endometrioma, and their co-existence

Abstract Background Adenomyosis and endometriosis are hormone-dependent benign gynecological disorders with overlapping features suggesting that they may share a common origin despite being considered distinct entities. This study compares the expression of candidate genes in the eutopic endometrium of diffuse adenomyosis, ovarian endometriosis, co-existent adenomyosis–endometriosis, and controls. Methods Publicly available transcriptomic datasets comprising endometrial tissue of women with adenomyosis, endometriosis, and women with healthy endometrium were analyzed, and overlapping differentially expressed genes (DEGs) were determined. Gene ontology and pathway enrichment analyses were performed to determine shared biological processes. A protein–protein interaction (PPI) network was constructed using the overlapping DEGs and the key genes identified. These genes and corresponding proteins were further validated in the patient population (25 women in each group of diffuse adenomyosis, ovarian endometrioma, co-existent adenomyosis–endometriosis). Thirty women with healthy endometrium having infertile male partners were recruited as controls for comparison purposes. Receiver operating characteristic (ROC) curves were generated for the key genes to evaluate their discriminatory accuracy in classifying isolated adenomyosis. Finally, the gene expressions were correlated with patient clinical characteristics. Results 23 significant DEGs (log2 fold-change > 1, p < 0.05) were found to be common between adenomyosis and endometriosis datasets, with serine-type endopeptidase activity emerging as the most enriched molecular function. PPI network analysis identified MMP7, MMP11, IGFBP5, SERPINA1, THBS1 as the hub genes. In addition, MMP9 and TIMP1 exhibited a strong association with the hub gene network. Experimental validation showed altered expression in adenomyosis as compared to controls and other disease groups. MMP9 and MMP7 showed strong discrimination for adenomyosis vs. endometriosis [area under the curve (AUC) = 0.93] and co-existent cases (AUC = 0.97), respectively. The expression of most of the genes in the co-existent group did not align with adenomyosis or endometriosis. MMP7 expression positively correlated with uterine volume in adenomyosis; MMP11 could be negatively associated with myometrial wall thickness ratio. Conclusions Distinct expression profiles were observed in diffuse adenomyosis versus ovarian endometriosis and co-existent phenotype. Expression of key genes indicated enhanced ECM remodeling in adenomyosis, with MMP7, MMP9, and MMP11 emerging as potential discriminatory markers. The divergent expressions in the co-existent phenotype suggest distinct molecular mechanisms that merit further study.