Background: Endometriosis is a chronic, debilitating gynecological disorder characterized by the ectopic presence of endometrial-like tissue, often leading to pain and infertility. However, the role of mitochondrial dynamics, mitophagy, and mitochondrial-related complexes in the development of endometriosis—and their relationship with epithelial-mesenchymal transition (EMT)—remains unclear. Objective: This study aims to investigate the role of mitochondrial oxidative phosphorylation (OXPHOS) dysfunction and EMT in the pathogenesis and progression of endometriosis, and to explore how these molecular alterations correlate with disease severity. MaterialsandMethods: A total of 180 women with surgically confirmed endometriosis, categorized into minimal-mild (Stage I-II) and moderate-severe (Stage III-IV) groups, along with 180 healthy controls, were included. Clinical, hormonal, and demographic data were recorded. Endometrial tissue samples were analyzed using quantitative real-time PCR, flow cytometry, and phase-contrast microscopy. Gene expression profiling focused on OXPHOS components, mitochondrial dynamics (fission/fusion), mitophagy-related genes, hypoxia markers, EMT transcription factors, and mesenchymal cell surface markers. In vitro cultures of endometrial stromal cells were evaluated morphologically and molecularly to assess EMT progression. Results: Quantitative PCR and in vitro analyses revealed that advanced endometriosis is associated with significant downregulation of OXPHOS genes (ND1, ND6, CYTB, CO2, CO3, ATP6) and mitochondrial dynamics genes (DRP1, OPA1, MFN1/2, LCLAT1), along with decreased mitophagy markers (PINK1, PARKIN) and elevated hypoxia marker HIF-1α. EMT activation was confirmed by morphological transitions in cultured stromal cells, reduced E-cadherin, increased N-cadherin, and elevated expression of mesenchymal and EMT-related markers (CD73, CD90, CD105, TWIST, SNAIL, SLUG). These molecular alterations were most pronounced in advanced (Stage III-IV) disease, minimally evident in Stage I-II, and not significantly different from controls. Conclusion: Our findings demonstrate that mitochondrial dysfunction and EMT activation are interrelated processes contributing to the severity and persistence of endometriosis. The distinct alterations in gene expression associated with mitochondrial bioenergetics and cellular plasticity in advanced disease highlight their potential as biomarkers for diagnosis, disease staging, and as targets for novel therapeutic
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