Genome-wide DNA methylation landscapes in gallbladder carcinoma: revealing shared and distinct epigenetic signatures across subtypes.

BACKGROUND: Gallbladder cancer is an aggressive malignancy with poor survival rates, there are biologically distinct subtypes, yet genome-wide epigenetic differences remain poorly understood. This study was designed as an exploratory investigation of subtype-specific DNA methylation patterns. METHODS: The study included sixteen gallbladder tissue sample (adenocarcinoma, n = 6; ICPN with invasion, n = 6; controls, n = 4). Genome-wide DNA methylation profiling was performed using the Illumina Infinium MethylationEPIC (850K) array. Differential methylation was assessed using Δβ ≥ 0.2 and FDR < 0.05, with emphasis on effect sizes. Chromosomal distribution, CpG island annotation, Gene Ontology enrichment, protein-protein interaction networks, and promoter-specific methylation patterns were examined. RESULTS: GBC demonstrated predominant global hypomethylation, with adenocarcinoma showing marked promoter hypomethylation (79.2%), compared with ICPN (54.7%). Adenocarcinoma exhibited enrichment of transcriptional and proliferative pathways whereas ICPN showed stress-response, autophagy, and apoptotic pathway enrichment. A set of 543 consensus genes displayed recurrent methylation changes across all comparisons, suggesting shared epigenetic remodeling duringndisease progression. CONCLUSIONS: This exploratory study identifies distinct and shared epigenetic signatures across gallbladder carcinoma subtypes, highlighting subtype-specific promoter remodeling. These findings provide a foundation for future large-scale validation studies integrating methylation, transcriptomic, and clinical outcome.