Integrating High-throughput Technologies for the Identification and Validation of Novel Ovarian Cancer Biomarkers

Ovarian cancer is the most lethal gynaecological malignancy in North America. Although survival rates are high when the disease is diagnosed at an early stage, this decreases significantly in late-stage diagnoses. The majority of cases are of epithelial origin, which can be classified into four major subtypes: serous, mucinous, endometrioid and clear cell carcinoma. Unfortunately, the clinically-approved markers for ovarian cancer - CA125 and HE4 alone - perform poorly for the mucinous, endometrioid and clear cell subtypes and thus, diagnosis of these subtypes remains a significant challenge. To this end, an integrated approach to ovarian cancer biomarker discovery was developed in this study through combining proteomics with other high-throughput platforms. Using proteomic analyses of ascites fluid from women with ovarian cancer and conditioned media of ovarian cancer cell lines, 15 high-priority candidates were identified as putative novel biomarkers using said integrated approach. Serum validation revealed two markers - folate receptor 1 and kallikrein 6 - to have comparable diagnostic ability to the clinically-approved markers, albeit with similar limitations in their ability to detect patients of the non-serous histotypes as well. Fortunately, the validation of the two in-house markers served as proof-of-principle of our integrated approach to biomarker discovery. As a result, the approach was employed on non-serous ovarian cancer tissues to identify novel markers specific to the mucinous, endometrioid and clear cell subtypes of ovarian cancer. Over 9000 unique proteins were identified in this exercise and with the use of an unbiased filtering algorithm based on transcriptomics and bioinformatics, a list of high-priority candidates for each subtype was generated. Several of the high-priority candidates have shown strong biological and molecular relevance to their respective subtypes, demonstrating the robustness and utility of the integrated approach. Future studies will need to investigate these candidates in independent serum cohorts to truly assess for their ability to diagnose their respective subtypes.Ph.D.2017-11-30 00:00:0