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

Epigenetic changes and modifications are a crucial component of initiation and progression of tumorigenesis [14]. DNA methylation has been most studied and hypermethylaiton is associated with a silencing effect on tumor suppressor genes. Previous studies [15‐17] reported that the modification of the methylation status of specific genes has been associated with worse prognosis, which demonstrated that the modification of epigenetics may be involved in the progression of tumorigenesis.

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.

The novel genes involved in the epigenetic regulation of prostate cancer could be identified by using high-throughput arrays [7, 9, 18]. We aimed to elucidate the role and importance of DNA methylation in prostate cancer by analyzing The Cancer Genome Atlas Project. In this study, a model-based tool (MethyMix) was used to identify key genes with aberrant methylation and gene expression was linked to aberrant methylation. In this study, the top 3 hypermethylated genes were demonstrated including HIST1H2BH, FAM200A, and ZFP36L2 and the top 3 hypomethylated genes were also demonstrated including TAF1D, TMEM87A, and KLK2.

The GO term analysis revealed that the differentially expressed DNA methylation driven genes were involved in oxidation–reduction process, extracellular exosome, electron carrier activity, response to reactive oxygen species, and aldehyde dehydrogenase [NAD(P)+] activity. Furthermore, the enriched KEGG pathway of the differentially expressed DNA methylation driven genes including drug metabolism—cytochrome P450, phenylalanine metabolism, histidine metabolism, glutathione metabolism, and tyrosine metabolism. PPI analysis demonstrated that hub genes were IFITM1, RTP4, ACSF2, GSTM2, GSTM1, ACOX2, COL4A6, ITGA2, AKR1B1, NPY, CFTR, GPX7, ALDH3A1, CRYZ, ALDH2, MAOB, GSTP1, GPX3, XAF1, and BST2, which might play important roles in DNA methylation in prostate cancer patients. We then overlapped the differentially methylated genes and identified a common list of 6 methylated genes including AKR1B1, RTP4, MAOB, GSTM2, GPX3, and COL4A6.

In terms of GSTM2, Angulo et al. [21] revealed that GSTM2 hypermethylation could be used to predict biochemical recurrence after radical prostatectomy, which suggested that epigenetic silencing of GSTM2 played an important role in involving biochemical recurrence. Plus, Ashour et al. [22] demonstrated that GSTM2 was hypermethylated in PCa and was simultaneously methylated in 40.9% if the PCa, which revealed that epigenetic silencing of GSTM2 is a common event in PCa. Maldonado et al. [23] revealed that GPX3 was aberrantly methylated and silenced in PCa tissues and had tumor suppressor activity in PCa cell lines. Plus, Lin et al. [24] revealed that GPX3, as a DNA methylation-silenced tumor suppressor gene, was hypermethylated in PCa. Strand et al. [25] stated that hypermethylation of COL4A6 could be treated as a frequent target in PCa. Ikeda et al. [26] demonstrated that hypermethylation of COL4A5 was one of the events that was responsible for the development of colorectal cancer.

With respect to AKR1B1, Theresa et al. [27] stated that AKR1B1 promoter methylation proved to be commonly methylated in breast cancer. Also, Wei et al. [28] demonstrated that AKR1B1 could be potential screening markers of colorectal carcinoma. However, the relationship between AKR1B1 methylation and PCa has not been elucidated yet. To the best of our knowledge, RTP4 and MAOB have not been reported to be associated with DNA methylation in the occurrence and development of cancer, which means RTP4 and MAOB could be regarded as potential targets for the new therapeutic managements in prostate cancer. The Human Protein Atlas validated the staining and intensity of RTP4 and MAOB in PCa tissue, the results were consistent with bioinformatic analysis that MAOB and RTP4 may be novel biomarkers in PCa.

In this study, GO term enrichment analysis showed that extracellular exosome was associated with DNA methylation in prostate cancer. Huang et al. [29] demonstrated that extracellular exosomes, especially plasma exosomes, containing miR-1290 and miR-375 may serves as promising prognostic biomarkers for castration-resistant prostate cancer (CRPC). Bryzgunova et al. [30] also demonstrated that extracellular vesicles founded from urine showed a high specificity and sensitivity in distinguishing prostate cancer patients from healthy donors. GO term enrichment analysis also revealed that oxidation–reduction process was also involved in DNA methylation of prostate cancer. Schlaepfer et al. [31] revealed that inhibition of lipid oxidation plays a crucial role in elevating glucose metabolism of PCa cells. Liu et al. [32] also demonstrated that oxidation–reduction reactions was associated with mitochondria and mitochondrial damage in DU145 and PC3 prostate cancer cell lines.

In this study, KEGG pathway enrichment analysis showed that cytochrome P450 pathway was involved in the methylation process in PCa. Chen et al. [33] demonstrated that cytochrome P450 (CYP) enzymes including CYP2R1, CYP27B1 and CYP24A1 were involved in the development and progression of PCa and were treated as promising targets in the treatment of PCa. Mandić et al. [34] also revealed that CYP1A1 can bind to DNA and induced the carcinogenesis of prostate cancer via involving in the various endogenous and environmental reactive compounds. The phenylalanine metabolism was also found to be participant in the methylation process in PCa. Gueron et al. [35] reported that the concomitant resistance (CR) phenomenon occurs in murine prostate cancer accompanied with ROS-damaged phenylalanine and the CR phenomenon was reversed when the phenylalanine were injected into mice. Lapek et al. demonstrated that the histidine-phosphorylated proteins with diverse functions including metabolism, protein folding, and motility play important roles in the development and progression of PCa.