子宮內膜異位相關卵巢癌（EAOC）主要包括子宮內膜樣卵巢癌與透明細胞卵巢癌（CCOC），屬於上皮性卵巢癌中臨床與分子特徵獨特的亞型。本研究進行轉錄體比較分析，以探討EAOC及其透明細胞亞型（CCOC）的分子特徵、外泌體生物標記及治療弱點。透過公共RNA定序資料，我們分別針對EAOC及CCOC分別與良性子宮內膜異位囊腫樣本進行差異表現基因（DEGs）分析。GO與KEGG路徑富集分析顯示，相關DEGs涉及多項腫瘤進程路徑，如細胞黏附、免疫調節與PI3K/AKT/mTOR訊號軸。LINCS資料庫分析預測出多種潛在治療藥物，包括mTOR、MEK、TKI與HDAC抑制劑，尤其對CCOC具臨床治療潛力。此外，結合外泌體資料庫（ExoCarta與Vesiclepedia），我們鑑定出數種來源於外泌體的microRNA，可望成為無創液態活檢的診斷標記。研究結果提供EAOC致病機制之新見解，突顯其CCOC亞型的特異分子特性，並有助於未來發展亞型特異性的診療策略。

Endometriosis-associated ovarian cancer (EAOC), primarily comprising endometrioid and clear cell ovarian carcinomas, represents a distinct clinical and molecular subset of epithelial ovarian cancers. In this study, we performed a comparative transcriptomic analysis to investigate molecular features, exosomal biomarkers, and therapeutic vulnerabilities of EAOC, with a specific focus on its clear cell subtype (CCOC), which is known for chemoresistance and poor prognosis. Using publicly available RNA-seq datasets, we identified differentially expressed genes (DEGs) in EAOC and CCOC, respectively, each compared to endometriosis-related benign ovarian tissues. Gene ontology (GO) and KEGG pathway analyses of DEGs revealed key biological processes and signaling pathways implicated in tumor progression, including cell adhesion, immune modulation, and the PI3K/AKT/mTOR axis. LINCS-based drug repurposing analysis predicted candidate compounds such as mTOR, MEK, TKI, and HDAC inhibitors, with potential clinical relevance, especially in CCOC. Furthermore, integration with exosomal gene repositories (ExoCarta and Vesiclepedia) identified several exosome-derived microRNAs (e.g., MIR23A, MIR27A, MIR145, MIR30C1) as promising biomarkers for non-invasive liquid biopsy approaches. These findings offer new insights into EAOC pathogenesis, highlight distinct molecular features of its CCOC subtype, and support future development of subtype-specific diagnostic and therapeutic strategies.

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