REPRODUCTIONRESEARCH PROOF ONLY High-throughput mRNA sequencing of stromal cells from endometriomas and endometrium Kadri Rekker1,2, Merli Saare1,2, Elo Eriste2, Tõnis Tasa3,4, Viktorija Kukuškina4,5, Anne Mari Roost2, Kristi Anderson2, Külli Samuel2, Helle Karro1,6, Andres Salumets1,2,7,8 and Maire Peters1,2 1Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia, 2Competence Centre on Health Technologies, Tartu, Estonia, 3Institute of Computer Science, University of Tartu, Tartu, Estonia, 4Estonian Genome Center, University of Tartu, Tartu, Estonia, 5Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia, 6Tartu University Hospital’s Women’s Clinic, Tartu, Estonia, 7Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia and 8Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland Correspondence should be addressed to K Rekker; Email:
[email protected] Abstract The aetiology of endometriosis is still unclear and to find mechanisms behind the disease development, it is important to study each cell type from endometrium and ectopic lesions independently. The objective of this study was to uncover complete mRNA profiles in uncultured stromal cells from paired samples of endometriomas and eutopic endometrium. High-throughput mRNA sequencing revealed over 1300 dysregulated genes in stromal cells from ectopic lesions, including several novel genes in the context of endometriosis. Functional annotation analysis of differentially expressed genes highlighted pathways related to cell adhesion, extracellular matrix–receptor interaction and complement and coagulation cascade. Most importantly, we found a simultaneous upregulation of complement system components and inhibitors, indicating major imbalances in complement regulation in ectopic stromal cells.