Allele-specific methylation of the PSA promoter in prostate cells: a new translational marker for the differential diagnosis of prostate cancer

Abstract

Abstract Background DNA methylation is one of the mechanisms of epigenetic control of gene expression and a change in the intrinsic pattern can lead to various diseases and disorders. At the same time, this makes DNA methylation a disease-specific biomarker. Here, we show that the acquisition of biallelic methylation status or even biallelic lack of methylation by the PSA promoter is a characteristic feature of cancer cells, while the monoallelic distribution of CpG\CCWGG methylation in the PSA promoter is a hallmark of non-cancerous conditions. Methods We performed PCR bisulfite sequencing analysis of the proximal PSA promoter, which has six potential CpG and five CCWGG methylation marks that are targets of DNMTs and therefore have the ability to epigenetically influence gene expression and be a disease-specific biomarker. SNP G-158A, located in the AREI of the PSA promoter, was taken into account when genotyping prostate cell lines for allele-specific methylation analysis. To clarify the differences in PSA promoter methylation we applied RT-qPCR to estimate the level expression of the DNMTs by comparing that with data of gene expression in 54 tissues from GTEx RNA-seq of donors. A PCR cloning sequencing approach and detection of SNPs in exon 3 were used to identify biallelic expression of PSA in the LNCaP cell line. Results According to our study of prostate cancer cell lines, the CG/CCWGG methylation in PSA promoter has a great translational ability to be a disease-specific biomarker. Elevated PSA level along with monoallelic promoter methylation would reflect BPH or other non-malignant conditions, whereas a significantly elevated PSA level due to biallelic PSA expression and status of the unmethylated PSA promoter will be consistent with the PCa. The detection of biallelic PSA promoter methylation at the given PSA level will indicate the aggressive PCa. We propose that the CCWGG motif represents an allele-specific methylation signal, which is a novel functionality for this mark involved in the allele-specific methylation mechanism and/or imprinting, as well as its possible role in regulating monoallelic gene expression. Significance According to our study in prostate cell line models, the determination of allele-specific methylation in the PSA promoter can be translated into a disease-specific state and can refine PSA-based PCa testing.