Epigenetic Analysis of Circulating Tumor DNA in Localized and Metastatic Prostate Cancer: Evaluation of Clinical Biomarker Potential

Abstract

Novel and minimally-invasive prostate cancer (PCa)-specific biomarkers are needed to improve diagnosis and risk stratification. Here, we investigated the biomarker potential in localized and de novo metastatic PCa (mPCa) of methylated circulating tumor DNA (ctDNA) in plasma. Using the Marmal-aid database and in-house datasets, we identified three top candidates specifically hypermethylated in PCa tissue: DOCK2, HAPLN3, and FBXO30 (specificity/sensitivity: 80%–100%/75–94%). These candidates were further analyzed in plasma samples from 36 healthy controls, 61 benign prostatic hyperplasia (BPH), 102 localized PCa, and 65 de novo mPCa patients using methylation-specific droplet digital PCR. Methylated ctDNA for DOCK2/HAPLN3/FBXO30 was generally not detected in healthy controls, BPH patients, nor in patients with localized PCa despite a positive signal in 98%–100% of matched radical prostatectomy tissue samples. However, ctDNA methylation of DOCK2, HAPLN3, and/or FBXO30 was detected in 61.5% (40/65) of de novo mPCa patients and markedly increased in high- compared to low-volume mPCa (89.3% (25/28) vs. 32.1% (10/31), p < 0.001). Moreover, detection of methylated ctDNA was associated with significantly shorter time to progression to metastatic castration resistant PCa, independent of tumor-volume. These results indicate that methylated ctDNA (DOCK2/HAPLN3/FBXO30) may be potentially useful for identification of hormone-naïve mPCa patients who could benefit from intensified treatment.

Pan-Cancer DNA Methylation Analysis and Tumor Origin Identification of Carcinoma of Unknown Primary Site Based on Multi-Omics

“…difference between groups was greater than 0.2 (adjusted p-value < 0.05 and |△β| > 0.2) (Bjerre et al, 2020).…”

“…The CpG sites with more than 50% missing values were excluded, and the remaining missing values were imputed based on K-Nearest Neighbor algorithm ( Wu et al, 2020 ). The CpG sites were identified as statistically significantly different between tumor tissues and matched adjacent normal tissues with adjusted p -value < 0.05, and the absolute value of the mean β value difference between groups was greater than 0.2 (adjusted p -value < 0.05 and |△ β | > 0.2) ( Bjerre et al, 2020 ).…”

Insights from DOCK2 in cell function and pathophysiology

“…Plasma from 36 healthy subjects, 61 patients with benign prostatic hyperplasia (BPH), 102 patients with limited prostate cancer and 65 patients with early metastatic PCa (MPCA) were examined, and hypermethylated DOCK2 was detected in the plasma of MPCA patients. It was also found that the levels of DOCK2 methylation also increased positively with increasing tumor volume, revealing that hypermethylated DOCK2 may be an independent predictor of MPCA progression ( Bjerre et al, 2020 ). Furthermore, high levels of DOCK2 hypermethylation were significantly associated with disease recurrence rates after radical prostatectomy ( Bjerre et al, 2019 ).…”

Detection and relevance of epigenetic markers on ctDNA: recent advances and future outlook

“…In localized and de novo metastatic prostate cancer, three genes, DOCK2, HAPLN3, and FBXO30, were found to be specifically hypermethylated in prostate cancer tissues using MS-ddPCR [44]. In plasma cfDNA, methylation of these three genes was detected in 61.5% of metastatic prostate cancer patients and was associated with significantly shorter time to progression to metastatic castration-resistant prostate cancer (mCRPC), indicating a potential usefulness for the identification of hormone-na€ ıve metastatic prostate cancer patients who could benefit from intensified treatment [44]. It was also recently reported that DNA methylation in regions of chromosome 8q24 may be associated with the risk of developing prostate cancer [45].…”