PO-045 Evaluating liquid biopsies for methylomic profiling of prostate cancer

Abstract

IntroductionEpigenetic modifications, particularly DNA methylation, are centrally involved in prostate cancer (PCa) initiation and progression. Yet, how these alterations unfold and interplay in the progression to the lethal castration resistant phenotype is poorly understood. One reason for this is the difficulty in accessing metastatic tumour deposits for study. Recently, the analysis of liquid biopsies has emerged as a useful and minimally invasive method to study tumour characteristics. The aim of this study is to explore and compare how accurately the DNA methylation patterns of liquid biopsies reflect those of the primary tumour.Material and methodsWe identified 4 metastatic treatment-naïve PCa patients for whom matched biopsy cores (tumour and histologically matched normal), pre-biopsy urine (≤50 ml), and peripheral blood plasma (3 ml) were available. DNA was isolated from all sample types and quantified using the Qubit Fluorometer. DNA methylation was profiled using the Infinium MethylationEPIC BeadChip (Illumina), and analysed using RnBeads software. Absolute β-values were used to filter the data into probes of interest, with cut-offs for hyper- and hypo-methylation of >0.8,<0.2, respectively.Results and discussionsWe first considered whether matched normal tissue was epigenetically distinct from tumour by comparing the methylation patterns of several genes (i.e. RARB), for which hypermethylation is considered a hallmark of PCa. Focusing next on the methylation extremes (β >0.8 or β <0.2), we observed that hypermethylation was consistently more prevalent than hypomethylation in both tissue and liquid biopsies. Enumerating these methylation extreme probes revealed that the liquid biopsies contained a higher absolute abundance of hypo- and hypermethylation than the tissue biopsies. We also found that we could detect more hyper- and hypomethylated tumour-specific probes in urine than in plasma (80% vs. 62% and 69% vs. 64%, respectively).ConclusionLiquid biopsies are excellent surrogates for profiling tumour-specific DNA methylation, with urine demonstrating superior sensitivity over blood. Further analysis of differentially methylated regions in the liquid and tissue biopsies, and their relevance is PCa biology, is underway.