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Magali Court

Urinary proteome: Characterization and interest for the discovery of biomarker

Published on 20 June 2014
Thesis presented June 20, 2014

Abstract :
Bladder cancer is the 4th type of cancer causing man death in Europe. In most cases, primary tumors can be easily removed by resection but in 60% of the cases, the tumors regrowth in more aggressive forms. Therefore, it is essential to detect early recurrence of bladder cancer. To date, the gold standard for the diagnosis of bladder cancer is cystoscopy. It allows the examination of the inside of the bladder using an optical system which is inserted in the urethra. This method is sensitive and specific but extremely uncomfortable and invasive for the patient. Therefore, it is crucial to find new diagnosis and monitoring methods for bladder tumor more comfortable for the patient, in a cost efficient way. The search for clinically useful protein biomarkers in the urine is a major alternative for the diagnosis, the prognostic and the therapeutic treatment of patients with urea-genital pathologies. In the specific case of the bladder cancer, the bladder contains the cells left by the tumor, and subsequently urine becomes the ideal fluid for biomarker investigation as a “proximal fluid”. In the last few years, the search for protein biomarkers has benefited of significant progress in the field of mass spectrometry and bio-chemistry, allowing the detection of a wide variety of proteins in a large dynamic range of concentrations. In addition, new approaches of quantitative proteomic, such as the “Accurate Mass and Time (AMT) tags” approach, coupled with the “label free” quantification, allows the comparison of proteomes from distinct physiological state by measuring protein abundances. During this thesis, we developed an experimental protocol covering the whole process of discovering new biomarkers associated to bladder cancer in urines, i.e., from the collection and preparation of urine samples, to the evaluation of the best fractioning method to define the urinary proteome using quantitative approaches and dedicated statistical methodologies. This work enables the population of a database containing 2014 urinary proteins. Abundance variations were measured for more tha​n the half through a cohort of 98 healthy and bladder cancer patients. A final list of 97 biomarker candidates has been established. This list holds a significant number of exosomal proteins that are potentially secreted by the tumor​.


Keywords:
Urinary proteome, mass spectrometry, AMT