Discovery and Evaluation of Urothelial Bladder Cancer Protein Biomarker Candidates in Urine

High throughput proteomics measurements enable comparisons of clinical samples from large populations of patients and controls. This represents a formidable opportunity for the discovery of early diagnostic or prognostic biomarkers, i.e. molecular indicators of a pathological state or its probable evolution that are present before the onset of specific clinical symptoms. New challenges lie in the integration of these technologies in the discovery and the evaluation of novel biomarkers, to translate initial findings into manageable lists of candidates for the design of new clinical assays. The DECanBio project aimed at (i) developing reliable analytical protocols and strategies for the generation of robust quantitative proteomics data, (ii) using them for the discovery and evaluation of new candidate biomarkers of bladder cancer in urine.

Among proteomics technologies, two methods emerged with a high potential for integration: the Accurate Mass and retention Time (AMT) tag method used for global sample profiling [Pasa-Tolic et al. Biotechniques, 2004, 37:621-624] and the Selected Reaction Monitoring approach used for targeted candidate evaluation [Lange et al. Mol. Sys. Biol., 2008, 4: 222-235]. Importantly, both methods could rely on the same sample type and standardized preparation method [M. Court et al. Proteomics, 2011, 11:1160-1171]. Using the AMT tag approach on a 98 patients cohort (cancer vs. healthy controls), among 1,180 proteins, statistical analysis yielded a list of 97 candidates. SRM was used to evaluate a selection of candidates originating from our AMT results, but also from other sources (literature mining, 2DE study, transcriptomics of bladder tumor biopsies). This evaluation entailed estimating differential concentrations of 134 candidates in 121 urine samples from patients with a suspicion of bladder cancer (confirmed or discarded through pathological examination), 108 could be accurately monitored in urine, and 71 showed potential for diagnosis or prognosis of bladder cancer incidence or recurrence.