Liquid-liquid phase separation-associated gene networks link EMT and ferroptosis to define a PDGFRB-centered prognostic signature in bladder cancer.

Introduction: Bladder cancer (BLCA) remains a formidable clinical challenge due to its high recurrence rate and complex molecular landscape. The integrated roles of liquid-liquid phase separation (LLPS), epithelial-mesenchymal transition (EMT), and ferroptosis in BLCA progression remain largely unresolved. Methods: We integrated bulk RNA-seq, single-cell RNA sequencing (scRNA-seq), and spatial transcriptomics to develop a 5-gene prognostic signature. Functional experiments including Western blot, transmission electron microscopy, lipid peroxidation assays, and Ferrostatin-1 rescue were performed in T24 bladder cancer cells. Tissue validation was conducted in clinical specimens and a mouse orthotopic model. Results: We identified a 5-gene signature (PDGFRB, FLNA, JUN, SNAI2, and ITGB1) that effectively stratifies BLCA patients into distinct risk groups. PDGFRB-positive epithelial subsets were characterized by high LLPS-associated gene expression and dispersed spatial localization. Immunofluorescence revealed endogenous PDGFRB condensate-like puncta in both human and mouse bladder cancer tissues. Discussion: These findings define a PDGFRB-centered prognostic signature that serves as a transcriptomic framework linking LLPS-associated gene networks with EMT and ferroptosis vulnerability. The study provides experimental evidence supporting PDGFRB as a potential therapeutic target and suggests implications for the tumor immune microenvironment in bladder cancer.