title: An integrated approach for comparative proteomic analysis of human bile reveals overexpressed cancer-associated proteins in malignant biliary stenosis.
abstract: Proteomics is a key tool in the identification of new bile biomarkers for differentiating malignant and nonmalignant biliary stenoses. Unfortunately, the complexity of bile and the presence of molecules interfering with protein analysis represent an obstacle for quantitative proteomic studies in bile samples. The simultaneous need to introduce purification steps and minimize the use of pre-fractionation methods inevitably leads to protein loss and limited quantifications. This dramatically reduces the chance of identifying new potential biomarkers. In the present study, we included differential centrifugation as a preliminary step in a quantitative proteomic workflow involving iTRAQ labeling, peptide fractionation by OFFGEL electrophoresis and LC-MS/MS, to compare protein expression in bile samples collected from patients with malignant or nonmalignant biliary stenoses. A total of 1267 proteins were identified, including a set of 322 newly described bile proteins, mainly belonging to high-density cellular fractions. The subsequent comparative analysis led to a 5-fold increase in the number of quantified proteins over previously published studies and highlighted 104 proteins overexpressed in malignant samples. Finally, immunoblot verifications performed on a cohort of 8 malignant (pancreatic adenocarcinoma, n=4; cholangiocarcinoma, n=4) and 5 nonmalignant samples (chronic pancreatitis, n=3; biliary stones, n=2) confirmed the results of proteomic analysis for three proteins: olfactomedin-4, syntenin-2 and Ras-related C3 botulinum toxin substrate 1. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
authors.affiliation: Biomedical Proteomics Research Group, Department of Human Protein Sciences, Geneva University, Geneva CH-1211, Switzerland.
authors.forename: Natalija
authors.initials: N
authors.lastname: Lukic
authors.affiliation: Biomedical Proteomics Research Group, Department of Human Protein Sciences, Geneva University, Geneva CH-1211, Switzerland.
authors.forename: Rémy
authors.initials: R
authors.lastname: Visentin
authors.affiliation: Department of Gastroenterology, Erasme Hospital, Free University of Brussels, Brussels BE-1070, Belgium.
authors.forename: Myriam
authors.initials: M
authors.lastname: Delhaye
authors.affiliation: Division of Gastroenterology and Hepatology, Geneva University Hospitals, Geneva CH-1211, Switzerland.
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Frossard
authors.affiliation: Biomedical Proteomics Research Group, Department of Human Protein Sciences, Geneva University, Geneva CH-1211, Switzerland; Clinical Proteomics Laboratory, Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva CH-1211, Switzerland.
authors.forename: Pierre
authors.initials: P
authors.lastname: Lescuyer
authors.affiliation: Division of Gastroenterology and Hepatology, Geneva University Hospitals, Geneva CH-1211, Switzerland.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Dumonceau
authors.affiliation: Biomedical Proteomics Research Group, Department of Human Protein Sciences, Geneva University, Geneva CH-1211, Switzerland. Electronic address: Annarita.Farina@unige.ch.
authors.forename: Annarita
authors.initials: A
authors.lastname: Farina
mesh_terms: D000230:Adenocarcinoma / Q000150:complications / Q000378:metabolism; D000368:Aged; D000369:Aged, 80 and over; D001650:Bile Duct Neoplasms / Q000150:complications* / Q000378:metabolism; D001653:Bile Ducts, Intrahepatic / Q000378:metabolism / Q000473:pathology; D014408:Biomarkers, Tumor / Q000378:metabolism*; D018281:Cholangiocarcinoma / Q000150:complications / Q000378:metabolism; D002779:Cholestasis / Q000175:diagnosis* / Q000209:etiology / Q000378:metabolism*; D002853:Chromatography, Liquid; D015331:Cohort Studies; D005260:Female; D006801:Humans; D015151:Immunoblotting; D008297:Male; D008875:Middle Aged; D010190:Pancreatic Neoplasms / Q000150:complications / Q000378:metabolism; D050500:Pancreatitis, Chronic / Q000150:complications / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry
chemical_list: D014408:Biomarkers, Tumor
keywords: Bile; Biomarker; Olfactomedin-4; Ras-related C3 botulinum toxin substrate 1; Syntenin-2; iTRAQ