Abstract / Summary
Muscle-invasive bladder carcinoma (MIBC) has been classified into transcriptomic subtypes, but comprehensive proteomic characterization remains limited. In this study, we used data-independent acquisition mass spectrometry (DIA-MS) to characterize the proteomic landscape of MIBC and explore subtype-associated therapeutic opportunities. Proteins were extracted from 58 formalin-fixed, paraffin-embedded (FFPE) MIBC transurethral resection (TURBT) samples and analyzed by data-independent acquisition mass-spectrometry (DIA-MS). Proteomics data were processed using Perseus and analyzed by hierarchical clustering and network analysis with TMEV, gRapHD, and DAVID. Findings were validated using the TCGA MIBC cohort. By the analysis of TURBT samples, three proteomic clusters that recapitulate MIBC transcriptomic subtypes were identified: Luminal-papillary (high KRT20 expression, mitochondrial and metabolic activity), Basal-squamous (basal biomarkers, DNA replication, and glycosylation activity), and Luminal-infiltrated + Luminal (immune and extracellular matrix activity). Network analysis revealed subtype-specific biological processes that were supported by analyses of the Dressler’s and TCGA MIBC cohorts. Subtype-specific proteomic profiles suggested candidate therapeutic approaches. DIA-MS profiling of routine, pre-treatment FFPE TURBT specimens (the diagnostic material on which treatment decisions are made) reproduces the established transcriptomic classification at the protein level. These findings provide a proteomic framework for molecular subtype characterization in MIBC and support the investigation of subtype-informed therapeutic strategies.