Integrating whole-genome bisulfite sequencing and TCGA data reveals methylation patterns associated with the MTHFR 677 C > T Variant

This study investigated the influence of the methylenetetrahydrofolate reductase (MTHFR) 677C > T polymorphism on bladder urothelial carcinoma (BLCA) using whole-genome bisulfite sequencing (WGBS) and The Cancer Genome Atlas (TCGA) data. The TT genotype was associated with reduced global DNA methylation, thereby altering the molecular landscape of BLCA. Differential methylation analysis identified three molecular subtypes of BLCA. Subtype 2, characterized by the lowest methylation levels, was associated with favorable prognosis, earlier disease stage, and a higher frequency of FGFR3 mutations, along with increased infiltration of plasma cells, memory B cells, and naive CD4 + T cells. In contrast, Subtype 3 exhibited increased neutrophil infiltration and upregulation of immune checkpoint molecules, including PD-L1 and CTLA-4. Transcriptomic analysis indicated that low methylation and high expression of TRIM27 in Subtype 2 were associated with improved prognosis, whereas high methylation and low expression of RASSF1 in Subtype 3 were associated with poorer outcomes. Metabolic pathways were enriched in Subtype 2, whereas cell cycle-related genes were overexpressed in Subtype 3. These findings indicate that the MTHFR 677C > T polymorphism modulates DNA methylation and significantly influences the molecular characteristics, immune microenvironment, and prognosis of BLCA. Methylation-based subtyping may provide biomarkers for precise diagnosis and therapeutic stratification in BLCA.