The development of a blood-based test of DNA methylation for the earlier detection of high-grade serous tubo-ovarian cancer

Abstract

Background High grade serous carcinoma (HGSC) is the most common and most aggressive subtype of epithelial ovarian cancer (OC). The majority of patients present in the advanced stage with poor prognosis. If diagnosed in the earliest stage (stage I) survival is greatly improved; however, there is currently no effective screening method for OC. Strong pathological evidence supports the theory that the distal fallopian tube is the origin of HGSC and a precursor lesion known as serous tubal epithelial carcinoma (STIC) has been identified. DNA methylation (DNAme) aberrations occur as an early event in carcinogenesis. The use of minimally invasive blood sampling, or ‘liquid biopsies’ is a fast-emerging area of cancer diagnostics. Identifying and developing novel DNAme markers for the detection of HGSC in blood samples will fulfil an unmet clinical need in a poor outcome cancer. Methodology A short list of 20 differentially hypermethylated DNA regions were identified following DNAme array profiling (on the Illumina® Infinium 450K platform). Pyrosequencing analysis, probe-based quantitative PCR and digital PCR were employed to analyse a selection of candidate DNAme markers. The most promising DNAme marker was analysed in a cohort of matched tissue and plasma samples using an optimised methylation-sensitive restriction enzyme PCR (MSRE qPCR) protocol. Results Results Of the 20 regions analysed using pyrosequencing, seven showed statistically significant hypermethylation (p<0.0001) from NFT-STIC-HGSC FFPE tissue samples. Diagnostic accuracy was improved compared to CA125 in two markers. Statistically significant hypermethylation (p=0.009) was detected using MSRE qPCR in plasma cell free DNA (cfDNA) for one marker. Conclusions This study has provided a proof-of-principle for the identification of novel DNAme biomarker for HGSC. A unique biomarker discovery pipeline has been established and optimised to use in the development of potential DNAme blood-based biomarkers in HGSC.

Date of Award	Jul 2020
Original language	English
Awarding Institution	Queen's University Belfast
Supervisor	Paul Mullan (Supervisor), Manuel Salto-Tellez (Supervisor) & James Patrick Beirne (Supervisor)