title: Integrated proteomic profiling of cell line conditioned media and pancreatic juice for the identification of pancreatic cancer biomarkers.
abstract: 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.
authors.affiliation: Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Shalini
authors.initials: S
authors.lastname: Makawita
authors.forename: Chris
authors.initials: C
authors.lastname: Smith
authors.forename: Ihor
authors.initials: I
authors.lastname: Batruch
authors.forename: Yingye
authors.initials: Y
authors.lastname: Zheng
authors.forename: Felix
authors.initials: F
authors.lastname: Rückert
authors.forename: Robert
authors.initials: R
authors.lastname: Grützmann
authors.forename: Christian
authors.initials: C
authors.lastname: Pilarsky
authors.forename: Steven
authors.initials: S
authors.lastname: Gallinger
authors.forename: Eleftherios P
authors.initials: EP
authors.lastname: Diamandis
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis*; D021441:Carcinoma, Pancreatic Ductal / Q000235:genetics / Q000378:metabolism*; D002352:Carrier Proteins / Q000097:blood; D045744:Cell Line, Tumor; D024141:Collagen Type IV / Q000097:blood; D017077:Culture Media, Conditioned / Q000032:analysis* / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic; D016179:Granulocyte Colony-Stimulating Factor / Q000097:blood; D006801:Humans; D008565:Membrane Proteins / Q000097:blood; D009088:Mucoproteins; D015513:Oncogene Proteins; D010189:Pancreatic Juice / Q000737:chemistry* / Q000378:metabolism; D010190:Pancreatic Neoplasms / Q000175:diagnosis* / Q000235:genetics / Q000378:metabolism; D011506:Proteins / Q000378:metabolism; D020543:Proteome / Q000032:analysis* / Q000378:metabolism; D012372:ROC Curve; D019056:Receptors, Polymeric Immunoglobulin / Q000097:blood
chemical_list: C502296:AGR2 protein, human; D014408:Biomarkers, Tumor; D002352:Carrier Proteins; D024141:Collagen Type IV; D017077:Culture Media, Conditioned; D008565:Membrane Proteins; D009088:Mucoproteins; C454127:OLFM4 protein, human; D015513:Oncogene Proteins; D011506:Proteins; D020543:Proteome; D019056:Receptors, Polymeric Immunoglobulin; C107454:Sycn protein, rat; D016179:Granulocyte Colony-Stimulating Factor