Two-dimensional electrophoresis for comparative proteomic analysis of human bile

Proteomic analysis of bile fluid holds promise as a method to identify biomarkers of bile tract diseases, especially for tumors. Two-dimensional electrophoresis (2-DE) is a popular and proven separation technique for proteome analysis, but using this strategy for bile fluid analysis is still not fully developed. This study was undertaken to (a) establish a reliable method for general clean-up to make bile fluid samples suitable for 2-DE; (b) obtain 2-D biliary maps with high reproducibility and resolution; and (c) identify protein patterns present in 2-D biliary maps for potential tumor biomarker discovery, with the intention of distinguishing malignant from benign causes of bile duct obstruction.

Bile fluid samples were obtained from two patients suffering from malignant and benign bile tract obstruction (one patient with cholangiocarcinoma as the experimental case, the other with cholelithiasis as control). A variety of sample preparation options, including delipidation, desalination and nucleic acid removal, were adopted to remove contaminants that affect 2-DE results. After that, each 350 microg purified sample was loaded onto nonlinear IPG strips (18 cm, pH 3-10 and pH 4-7) for first-dimension isoelectric focusing, and 12.5% SDS-PAGE electrophoresis for second dimension separation. Then 2-D maps were visualized after silver staining and analyzed with the Image Master 2-D software.

A large number of protein spots were separated in 2-D maps from the experimental and control groups, with means of 250 and 216 spots on pH 3-10 IPG strips, and 182 and 176 spots on pH 4-7 strips, respectively. Approximately 16 and 23 spots were differentially expressed in matched pairs from the experimental and control cases using pH 3-10 and pH 4-7 strips.

This study established a reliable sample preparation process suitable for 2-DE of bile fluid. By this method, 2-D biliary maps with high reproducibility and resolution were obtained. The differentially displayed proteomes in the 2-D biliary maps from the experimental and control groups indicated the potential application for bile fluid analysis to identify disease-associated biomarkers, especially for biliary tract tumors.