Biomarker potential of ST6GALNAC3 and ZNF660 promoter hypermethylation in prostate cancer tissue and liquid biopsies

Abstract

Current diagnostic and prognostic tools for prostate cancer (PC) are suboptimal, leading to overdiagnosis and overtreatment. Aberrant promoter hypermethylation of specific genes has been suggested as novel candidate biomarkers for PC that may improve diagnosis and prognosis. We here analyzed ST6GALNAC3 and ZNF660 promoter methylation in prostate tissues, and ST6GALNAC3,ZNF660,CCDC181, and HAPLN3 promoter methylation in liquid biopsies. First, using four independent patient sample sets, including a total of 110 nonmalignant (NM) and 705 PC tissue samples, analyzed by methylation‐specific qPCR or methylation array, we found that hypermethylation of ST6GALNAC3 and ZNF660 was highly cancer‐specific with areas under the curve (AUC) of receiver operating characteristic (ROC) curve analysis of 0.917–0.995 and 0.846–0.903, respectively. Furthermore, ZNF660 hypermethylation was significantly associated with biochemical recurrence in two radical prostatectomy (RP) cohorts of 158 and 392 patients and remained significant also in the subsets of patients with Gleason score ≤7 (univariate Cox regression and log‐rank tests, P < 0.05), suggesting that ZNF660 methylation analysis can potentially help to stratify low‐/intermediate‐grade PCs into indolent vs. more aggressive subtypes. Notably, ZNF660 hypermethylation was also significantly associated with poor overall and PC‐specific survival in the RP cohort (n = 158) with long clinical follow‐up available. Moreover, as proof of principle, we successfully detected highly PC‐specific hypermethylated circulating tumor DNA (ctDNA) for ST6GALNAC3,ZNF660,HAPLN3, and CCDC181 in liquid biopsies (serum) from 27 patients with PC vs. 10 patients with BPH, using droplet digital methylation‐specific PCR analysis. Finally, we generated a three‐gene (ST6GALNAC3/CCDC181/HAPLN3) ctDNA hypermethylation model, which detected PC with 100% specificity and 67% sensitivity. In conclusion, we here for the first time demonstrate diagnostic biomarker potential of ST6GALNAC3 and ZNF660 methylation, as well as prognostic biomarker potential of ZNF660. Furthermore, we show that hypermethylation of four genes can be detected in ctDNA in liquid biopsies (serum) from patients with PC.

Identification of key DNA methylation-driven genes in prostate adenocarcinoma: an integrative analysis of TCGA methylation data

“…Previous studies reveals that DNA methylation plays an important role in the development of prostate cancer and associates with adverse clinical outcomes. The methylation state of promoters of specific genes were also involved in the development of prostate cancer [11, 18, 19]. Larsen et al [20] reported that DNA-methylation analysis of urine cells captured by microfiltration provides a novel tool for noninvasive detection of high-grade prostate cancer.…”

DNA Methylation-Based Testing in Liquid Biopsies as Detection and Prognostic Biomarkers for the Four Major Cancer Types

“…Likewise, ZNF660 me , CCDC181 me , ST6GALNAC3 me and HAPLN3 me in serum displayed 22%, 26%, 31% and 44% sensitivity, respectively, and 100% specificity for PCa. Remarkably, the best gene panel (ST6GALNAC3 me , CCDC181 me and HAPLN3 me ) increased sensitivity to 67%, keeping 100% specificity [178].…”

Advances in Prognostic Methylation Biomarkers for Prostate Cancer

“…SERPINB5 and AIM1 , the only markers found to have significant associations with progression [ 95 ] and overall survival [ 85 ] have only been investigated in two small independent studies each thus far, and require further validation in larger cohorts. And finally, new candidate genes from different biological pathways have been explored recently (e.g., PD1− , PD-L1 , CDO1 , TFF3 , ZNF660 ) [ 108 , 109 , 110 , 111 , 112 ] and also require further validation.…”