Objective The objective of this study was to determine the genes that may be associated with malignant transformation of ovarian endometrioma.

Methods Endometriotic epithelial cells were isolated from tissues derived from chocolate cyst linings by laser capture microdissection. A Gene Chip Human Genome U133 Plus 2.0 Array was applied to evaluate levels of gene expression in 3 different groups of epithelial cells: epithelial cells of endometrioma, epithelial cells of endometrioma adjacent to clear cell carcinoma, and epithelial cells of clear cell carcinoma. As a validation assay, real-time reverse transcriptase–polymerase chain reaction and immunohistochemical analyses were performed.

Results Gene expression analysis identified differential expressions among the 3 groups of epithelial cells. Using the classification of a signaling pathways database, 9 genes (12 gene probes) were selected from among 39 up-regulated genes indicating more than 2-fold higher expression between any comparisons of the 3 groups in the comprehensive microarray. Enhancement of fibroblast growth factor receptor 2 (FGFR2) gene expression was detected by microarray using 3 distinct probes. Gene and protein expression of FGFR2 differed significantly between epithelial cells of endometrioma and the epithelial component of clear cell carcinoma.

Conclusions We demonstrated that FGFR2 may play a significant role in the carcinogenesis of endometriosis and thus represents a potential therapeutic target.