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Endometriosis is a benign, chronic, gynaecological disorder defined as the growth of endometrial-like tissue outside the uterus. The disease is highly prevalent, affecting about 10% of women of reproductive age and up to 50% of women with pelvic pain and/or infertility. Understanding the pathogenesis of endometriosis and finding a non-invasive diagnosis have been identified as research priorities. The most common theory on the origin of endometriosis states that during menstruation endometrial cells and tissue fragments flow backwards through the oviducts into the peritoneal cavity where they can implant, grow and develop into endometriotic lesions. We detected endometrial cells in the peritoneal fluid of some but not all women regardless of the presence of endometriosis (Chapter 2), indicating that other factors besides retrograde menstruation must be involved in the pathogenesis of this complex disease. It has been postulated that endometrial stem cells are the true instigators of the disease. We investigated the transcriptome of endometrial mesenchymal stem cells of women with and without endometriosis and found differences in gene expression conferring an increased survival capacity in endometriosis (Chapter 3). Till today, the gold standard of diagnosis is through laparoscopic surgery with histological confirmation of endometrial glands and stroma in excised lesions. The lack of a non-invasive diagnosis contributes to a diagnostic delay of approximately 10 years. To reduce this delay, we aimed to validate previously reported biomarkers for the development of a semi- or non-invasive diagnostic test in endometrium or peripheral blood plasma, respectively. We could not confirm the previously reported high diagnostic value of PGP9.5-positive endometrial nerve fibers (Chapter 4), nor of the previously developed prediction models containing CA-125, VEGF, Annexin V and glycodelin or sICAM-1 (Chapter 5). Validation of biomarkers for endometriosis remains challenging due to the existing patient heterogeneity, pre-analytical variability in sample collection and storage, analytical/technical variability of research immunoassays and differences in data interpretation and statistical analysis. For biomarker discovery we used the proteomic mass spectrometry method Orbitrap LC-MS as hypothesis-generating tool for untargeted biomarker discovery and identified 15 putative endometriosis biomarkers that warrant further validation (Chapter 6.1). We used antibody arrays as a hypothesis-driven approach in which up to 1000 of pre-specified proteins can be identified in one reaction (Chapter 6.2). However, our results were not repeatable nor reproducible and therefore, we could not identify any new biomarker candidates. Finally, the single marker myeloperoxidase was investigated as an endometriosis biomarker because of its role as a marker of inflammation. There was no difference in specific myeloperoxidase levels between women with endometriosis and women with other benign gynecological conditions, rendering this marker ineffective as endometriosis biomarker (Chapter 6.3). In conclusion, endometriosis is a complex disease with an unclear pathogenesis. Biomarkers for endometriosis have remained elusive due to heterogeneity in assay methodology and patient characteristics. Initiatives to stimulate collaboration between research groups can contribute to collecting larger numbers of well-defined patient samples in order to increase the quality of biomarker research.