Comparison of membrane-associated proteins in human cholangiocarcinoma and hepatocellular carcinoma cell lines.

Cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC) occur with relatively high incidence in Thailand. Cell line models, originating from Thai patients, are available for both diseases, including the human bile duct epithelial carcinoma cell line (HuCCA-1) and the HCC cell line HCC-S102. Here, we have prepared subproteomes enriched in membrane proteins or in cytosolic proteins from the HuCCA-1 and the HCC-S102 cell lines. Study of differential protein expression by 2-DE and LC/MS/MS showed 195 proteins expressed in the two cell lines, including both membrane-associated and cytosolic proteins. Eighteen proteins were found in both membrane and cytosolic fractions of HuCCA-1, but not in HCC-S102, while nine proteins were found in both membrane and cytosolic fractions of HCC-S102, but not in HuCCA-1. Ten membrane proteins were found in HuCCA-1 but not in HCC-S102, including integrin alpha-6 precursor, ezrin, hippocalcin-like protein 1, mitogen-activated protein kinase kinase kinase 2 (MAPK/ERK kinase kinase 2), and calgizzarin. Proteins showing increased expression in the membrane fraction of HuCCA-1 were mainly cytoskeletal proteins (40.9%), while proteins showing increased expression in the membrane fraction of HCC-S102 were mainly metabolic proteins (39.4%). The subproteomic approach used here facilitates detection of potential biomarkers undetected by regular proteomic methods.