Locus-Specific Bisulfate NGS Sequencing of GSTP1, RNF219, and KIAA1539 Genes in the Total Pool of Cell-Free and Cell-Surface-Bound DNA in Prostate Cancer: A Novel Approach for Prostate Cancer Diagnostics

SIMPLE SUMMARY: Prostate cancer (PCa) is a global problem in the modern world. PCa has an almost 100% five-year relative survival rate at localized and regional stages and 31% at the appearance of distant metastases. Tumor development is always accompanied by a violation of DNA methylation, which could be detected even at the earliest stages of tumor development, not only in tumor tissue but also in cell-free DNA circulating in blood. The article describes a liquid biopsy approach for differential PCa diagnostics based on the data on locus-specific methylation of the two genes (GSTP1, RNF219) obtained with NGS of the total pool of blood cell-free DNA, including cell-free DNA from plasma and cell-surface-bound DNA, of PCa patients and healthy individuals. We offer a diagnostic approach that allowed a complete separation of cancer patients from healthy donors. ABSTRACT: The locus-specific methylation of three genes (GSTP1, RNF219, and KIAA1539, also known as FAM214B) in the total pool of blood cell-free DNA, including cell-free DNA from plasma and cell-surface-bound DNA, of patients with prostate cancer and healthy donors was studied on the MiSeq platform. Our study found a higher methylation index of loci for total cell-free DNA compared with cell-free DNA. For total cell-free DNA, the methylation of GSTP1 in each of the 11 positions provided a complete separation of cancer patients from healthy donors, whereas for cell-free DNA, there were no positions in the three genes allowing for such separation. Among the prostate cancer patients, the minimum proportion of GSTP1 genes methylated in any of the 17 positions was 12.1% of the total circulated DNA fragments, and the minimum proportion of GSTP1 genes methylated in any of the 11 diagnostically specific positions was 8.4%. Total cell-free DNA was shown to be more convenient and informative as a source of methylated DNA molecules circulating in the blood than cell-free DNA.