Profiling the potential biomarkers for cell differentiation of pancreatic cancer using iTRAQ and 2-D LC-MS/MS

Pancreatic cancer is a highly lethal disease that is difficult to diagnose at early stage and even more difficult to cure. SW1990 and PANC-1 represent the two cancer cell lines, which are both derived from pancreatic duct, but at different cell differentiation stages. In this study, we applied the iTRAQ-labeling technology and 2-D strong cation exchange/reversed phase liquid chromatography - LC-MS/MS) to profile the secreted proteins of SW1990 and PANC-1 cells in a conditioned cell culture medium. A total of 401 proteins were identified by MS/MS and protein database searching, the percentages of these proteins predicted in the categories of plasma membrane, intracellular and secreted proteins were 29.2, 32.7 and 38.2%, respectively. Fifty six proteins were identified with unknown functions and 19 proteins were quantified with significant level changes between the two cancer cell lines under the specific cell condition with 12 proteins being up-regulated (>1.3-fold change) in PANC-1 (e.g. FLJ31222 protein, 97 kDa protein, type IV collagenase precursor, 38 kDa protein and centaurin) and seven proteins being up-regulated in SW1990 (e.g. fibroblast growth factor receptor substrate 2, putative p150, hypothetical protein LOC 654463 and LOC 55701). The proteins with significant level changes may provide a baseline to investigate mechanisms underlying the differentiation of two cell lines and can be further screened for better protein biomarkers in pancreatic cancer.