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. In vitro reconstitution confirmed the phase separation capacity of the PDGFRB intrinsically disordered region. PDGFRB knockdown impaired cell proliferation and migration, and induced ferroptosis as demonstrated by mitochondrial damage, elevated lipid peroxidation, and rescue by Ferrostatin-1. Immune infiltration analysis showed that the five genes, particularly PDGFRB and FLNA, were significantly associated with immune and stromal scores.

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.