Development of a liquid biopsy for bladder cancer using a mutant protein panel in urinary extracellular vesicles

Non-muscle invasive bladder cancer often relapses after cystoscopic surgery, necessitating rigorous monitoring for recurrence through invasive and painful cystoscopy. To develop a novel non-invasive and cancer-specific diagnostic method, somatic mutant proteins in urinary extracellular vesicles (EVs) were for the first time investigated using a proteogenomics pipeline consisting of whole exome sequencing and LC/MS. The analysis of bladder cancer tissues, cultured tissue-derived EVs, and urinary EVs from five patients identified 11,207, 9,809, and 5,828 unique proteins, respectively. Notably, 39, 32, and 4 mutant proteins were found in each of the sample sets. Furthermore, mass spectrometric absolute quantification measurements were conducted using prospectively collected urine samples, revealing that the levels of all monitored mutant proteins (LCP1_D321H, TKT_K102N, and PLCD1_R639H) exhibited a clear correlation with the cystoscopic tumor burden. Therefore, the presence of mutant proteins in Evs presents an ideal approach for liquid biopsy, serving as a non-invasive urine test for bladder cancer.