Transcriptomic Analyses of Ovarian Clear-Cell Carcinoma with Concurrent Endometriosis

Endometriosis, a benign inflammatory disease whereby endometrial-like tissue grows outside the uterus, is a risk factor for endometriosis-associated ovarian cancers. In particular, ovarian endometriomas, cystic lesions of deeply invasive endometriosis, are considered the precursor lesion for ovarian clear-cell carcinoma (OCCC). To explore the transcriptomic landscape, OCCC from women with pathology-proven concurrent endometriosis (n = 4) were compared to benign endometriomas (n = 4) by bulk RNA and small-RNA sequencing. Overall design: RNA-seq was performed on 8 primary tissue samples (OCCC from women with pathology-proven concurrent endometriosis (n = 4) were compared to benign endometriomas (n = 4)). RNA samples were sequenced on Illumina NextSeq 500 (Illumina, San Diego, CA). The resulting reads were mapped to the reference genome (Homo sapiens, ensemble, GRCh38) using MiRDeep2. Differential expression analysis for bulk RNA and miRNA was performed using the DESeq2 package (version 1.36.0) in R/Bioconductor (R version 4.2.0)