Epigenetic alterations, particularly DNA methylation changes, are key drivers of tumorigenesis and progression in urological cancers. While prostate cancer (PCa) overdiagnosis highlights the need for better biomarkers, bladder cancer (BlCa) relies on invasive procedures for diagnosis and follow-up, and kidney cancer (KCa) remains challenging due to its histological heterogeneity and resistance to conventional therapies. DNA methylation profiling holds promise for biomarker discovery and therapeutic targeting. This study aimed to characterize the DNA methylation landscape of PCa, BlCa and KCa, integrating findings with The Cancer Genome Atlas (TCGA) datasets to identify shared and cancer-specific DNA methylation signatures with functional relevance.

DNA methylation profiles of 72 fresh-frozen tissues (25 PCa, 5 normal prostate, 14 BlCa, 5 normal bladder, 17 KCa, and 6 normal kidney) were analyzed using the HumanMethylation450 BeadChip (Illumina). All samples were classified by an expert uropathologist and staged using the AJCC 8th Edition. Ethical approval was obtained (CES-IPOPFG-EPE 205/2013). Differentially methylated CpG sites were identified and integrated with TCGA datasets [RNAseq and DNA methylation (450k)] to evaluate their impact on gene expression. Gene ontology (GO) analysis was performed to identify affected biological pathways.

Distinct methylation landscapes were observed across urological cancers. BlCa and KCa exhibited genome-wide hypomethylation, whereas PCa was characterized by predominant promoter hypermethylation. Hypermethylation-associated gene silencing was a common feature in PCa and BlCa, particularly affecting genes involved in DNA repair, oxidative stress regulation, epithelial-mesenchymal transition (EMT), and immune evasion. Cancer-specific analyses revealed that PCa hypermethylation predominantly impacted metabolic and detoxification pathways, whereas in BlCa, it affected genes regulating cell fate and tissue organization, likely contributing to stem-like phenotypes and EMT dysregulation. These findings highlight both shared and unique epigenetic alterations that may drive cancer-specific pathways.

This study provides new insights into the epigenetic heterogeneity of urological cancers, reinforcing the critical role of DNA methylation in tumor-specific biology. The identification of both shared and cancer-specific methylation patterns underscores their potential as biomarkers for early detection and disease monitoring, and therapeutic targeting. These findings support the development of epigenetic therapies and companion biomarkers tailored to the unique vulnerabilities of urological malignancies, highlighting the relevance of precision oncology approaches in these cancers.