Abstract A34: Longitudinal analysis of personal DNA methylome patterns in metastatic prostate cancer
Authors: Silva Romina , Moran Bruce , Gallagher William M. , Brennan Donal J. , Perry Antoinette S. 
Published: June 2020

Background: Epigenetic modifications, in particular DNA methylation, are centrally involved in initiation and progression of prostate cancer (PCa). Yet, it is still unknown how these events unfold during acquired drug resistance in advanced PCa. One reason for this knowledge gap is the inherent difficulty in accessing metastatic tumor deposits for study. The advent of liquid biopsies has emerged as a useful method that allows to not only overcome the challenges of tissue biopsies but also to study tumor dynamics by use of serial sampling. The aim of this study is to understand how the methylome evolves over time, during clinical progression and acquired drug resistance in metastatic PCa (mPCa), on an individual level.

Methods: 48 serial samples of peripheral blood plasma, taken at baseline and multiple therapeutic intervals, were collected from mPCa patients (n=9) involved in the iPROSPECT study. Samples were collected every 4 months and subjects were followed for 13-21 months. Cell-free DNA was isolated using the QIAamp Circulating Nucleic Acid kit. Epigenome-wide methylation measurements were performed with the Infinium® MethylationEPIC BeadChip. Raw data were preprocessed with minfi. QC was performed, with all 48 samples and 801,849 probes retained for analysis. To study differential methylation over time, the standard deviation (SD) was calculated for each probe longitudinally. Within each subject, the top 5% most variable probes were selected for further analysis. Probe patterns across time-points were compared using TSdist to identify congruent changes between probes. Gene ontology was performed with probes displaying similar patterns.

Results: Evaluation of temporal variability in CpG methylation showed that most probes remained relatively stable (SD&lt;0.1) across different treatments, indicating a low intrasubject variation in methylation of cfDNA. The top 5% most variable probes (n=40,092) in each subject were selected and filtered for 5’-regulatory probes. Analysis suggests coordinate dysregulation of DNA methylation at gene promoters, with specific patterns observed at clinically relevant time-points. For example, in one individual, de novo hypermethylation of GSTP1 with concurrent hypomethylation of the AR gene emerged at biochemical (PSA) evidence of cabazitaxel resistance. Work is ongoing to further identify coordinate epigenetic changes in cfDNA and the corresponding genes involved during disease progression and treatment resistance.

Conclusions: Early analysis of this longitudinal study of mPCa patients, at an individual level, indicates correlation of dynamic methylation changes with clinical events. Further examination will determine the potential use of these specific molecular signatures in precision medicine.

Citation Format: Romina Silva, Bruce Moran, William M. Gallagher, Donal J. Brennan, Antoinette S. Perry. Longitudinal analysis of personal DNA methylome patterns in metastatic prostate cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A34.