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The messenger RNA and long non-coding RNA expression profiles in ectopic and eutopic endometrium provide novel insights into endometriosis

Objective: To establish the messenger RNA (mRNA) and long non-coding RNA (lncRNA) expression profiles in ectopic and eutopic endometrium and provide novel insights into endometriosis. Methods: The mRNA and lncRNA expression profiles were tested using high-throughput sequencing technology in ectopic and eutopic endometrium with endometriosis and normal endometrium without endometriosis. The potential targeted lncRNAs were annotated by analyzing the correlation between lncRNA and mRNA expression to better understand the pathogenesis of endometriosis. Results: In ectopic compared with normal endometrium, a total of 2,188 mRNAs and 1,200 lncRNAs were differentially expressed with a fold-change (FC) ≥2.5. In eutopic compared with normal endometrium, a total of 2,324 mRNAs and 695 lncRNAs were differentially expressed with an FC ≥1.5. In ectopic compared with eutopic endometrium, a total of 2,223 mRNAs and 511 lncRNAs were differentially expressed with an FC ≥2. Bioinformatic analysis indicated that the differentially expressed mRNAs were enriched in the biological processes and signaling pathways involved in endometriosis. In addition, we constructed a gene coexpression network based on the dysregulated lncRNAs in both ectopic endometrium and eutopic endometrium, combined with their coexpressed mRNAs to simulate the complex interactions. Conclusions: This study describes the first-to-integrate analysis of the differential expression profiles of mRNAs and lncRNAs, including analyses between ectopic and normal endometrium, eutopic and normal endometrium, and ectopic and eutopic endometrium, which provides new insights to investigate the pathogenesis of endometriosis and explore novel diagnostic biomarkers and therapeutic targets.