Pancreatic cancer is one of the leading causes of
cancer-related deaths, for which serological
biomarkers are urgently needed. Most discovery-phase studies focus on the use of one biological source for analysis. The present study details the combined mining of
pancreatic cancer-related cell line
conditioned media and pancreatic juice for identification of putative diagnostic leads. Using strong
cation exchange chromatography, followed by LC-MS/MS on an LTQ-Orbitrap mass spectrometer, we extensively characterized the
proteomes of
conditioned media from six
pancreatic cancer cell lines (BxPc3, MIA-PaCa2, PANC1, CAPAN1, CFPAC1, and SU.86.86), the normal human pancreatic ductal epithelial cell line HPDE, and two pools of six pancreatic juice samples from ductal
adenocarcinoma patients. All samples were analyzed in triplicate. Between 1261 and 2171
proteins were identified with two or more
peptides in each of the cell lines, and an average of 521
proteins were identified in the pancreatic juice pools. In total, 3479 nonredundant
proteins were identified with high confidence, of which ∼ 40% were extracellular or cell membrane-bound based on Genome Ontology classifications. Three strategies were employed for identification of candidate
biomarkers: (1) examination of differential
protein expression between the
cancer and normal cell lines using label-free
protein quantification, (2) integrative analysis, focusing on the overlap of
proteins among the multiple biological fluids, and (3) tissue specificity analysis through mining of publically available databases. Preliminary verification of anterior gradient homolog 2,
syncollin, olfactomedin-4,
polymeric immunoglobulin receptor, and
collagen alpha-1(VI) chain in plasma samples from
pancreatic cancer patients and healthy controls using ELISA, showed a significant increase (p < 0.01) of these
proteins in plasma from
pancreatic cancer patients. The combination of these five
proteins showed an improved area under the receiver operating characteristic curve to CA19.9 alone. Further validation of these
proteins is warranted, as is the investigation of the remaining group of candidates.