Exploring prognostic DNA methylation genes in bladder cancer: a comprehensive analysis.

ABSTRACT

The current study aimed to investigate the status of genes with prognostic DNA methylation sites in bladder cancer (BLCA). We obtained bulk transcriptome sequencing data, methylation data, and single-cell sequencing data of BLCA from public databases. Initially, Cox survival analysis was conducted for each methylation site, and genes with more than 10 methylation sites demonstrating prognostic significance were identified to form the BLCA prognostic methylation gene set. Subsequently, the intersection of marker genes associated with epithelial cells in single-cell sequencing analysis was obtained to acquire epithelial cell prognostic methylation genes. Utilizing ten machine learning algorithms for multiple combinations, we selected key genes (METRNL, SYT8, COL18A1, TAP1, MEST, AHNAK, RPP21, AKAP13, RNH1) based on the C-index from multiple validation sets. Single-factor and multi-factor Cox analyses were conducted incorporating clinical characteristics and model genes to identify independent prognostic factors (AHNAK, RNH1, TAP1, Age, and Stage) for constructing a Nomogram model, which was validated for its good diagnostic efficacy, prognostic prediction ability, and clinical decision-making benefits. Expression patterns of model genes varied among different clinical features. Seven immune cell infiltration prediction algorithms were used to assess the correlation between immune cell scores and Nomogram scores. Finally, drug sensitivity analysis of Nomogram model genes was conducted based on the CMap database, followed by molecular docking experiments. Our research offers a reference and theoretical basis for prognostic evaluation, drug selection, and understanding the impact of DNA methylation changes on the prognosis of BLCA.