title: In-depth proteomic analysis of six types of exudative pleural effusions for nonsmall cell lung cancer biomarker discovery.
abstract: Pleural effusion (PE), a tumor-proximal body fluid, may be a promising source for biomarker discovery in human cancers. Because a variety of pathological conditions can lead to PE, characterization of the relative PE proteomic profiles from different types of PEs would accelerate discovery of potential PE biomarkers specifically used to diagnose pulmonary disorders. Using quantitative proteomic approaches, we identified 772 nonredundant proteins from six types of exudative PEs, including three malignant PEs (MPE, from lung, breast, and gastric cancers), one lung cancer paramalignant PE, and two benign diseases (tuberculosis and pneumonia). Spectral counting was utilized to semiquantify PE protein levels. Principal component analysis, hierarchical clustering, and Gene Ontology of cellular process analyses revealed differential levels and functional profiling of proteins in each type of PE. We identified 30 candidate proteins with twofold higher levels (q<0.05) in lung cancer MPEs than in the two benign PEs. Three potential markers, MET, DPP4, and PTPRF, were further verified by ELISA using 345 PE samples. The protein levels of these potential biomarkers were significantly higher in lung cancer MPE than in benign diseases or lung cancer paramalignant PE. The area under the receiver-operator characteristic curve for three combined biomarkers in discriminating lung cancer MPE from benign diseases was 0.903. We also observed that the PE protein levels were more clearly discriminated in effusions in which the cytological examination was positive and that they would be useful in rescuing the false negative of cytological examination in diagnosis of nonsmall cell lung cancer-MPE. Western blotting analysis further demonstrated that MET overexpression in lung cancer cells would contribute to the elevation of soluble MET in MPE. Our results collectively demonstrate the utility of label-free quantitative proteomic approaches in establishing differential PE proteomes and provide a new database of proteins that can be used to facilitate identification of pulmonary disorder-related biomarkers.
authors: From the ‡Graduate Institute of Biomedical Sciences.
authors: Pei-Jun
authors: PJ
authors: Liu
authors: From the ‡Graduate Institute of Biomedical Sciences, **Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan;
authors: Chi-De
authors: CD
authors: Chen
authors: §School of Medicine, ‡‡Division of Pulmonary Oncology and Interventional Bronchoscopy, Department of Thoracic Medicine.
authors: Chih-Liang
authors: CL
authors: Wang
authors: §§Department of Thoracic Surgery, Chang Gung Memorial Hospital, Linkou, Tao-Yuan, Taiwan.
authors: Yi-Cheng
authors: YC
authors: Wu
authors: From the ‡Graduate Institute of Biomedical Sciences, **Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan;
authors: Chia-Wei
authors: CW
authors: Hsu
authors: From the ‡Graduate Institute of Biomedical Sciences.
authors: Chien-Wei
authors: CW
authors: Lee
authors: From the ‡Graduate Institute of Biomedical Sciences.
authors: Lien-Hung
authors: LH
authors: Huang
authors: From the ‡Graduate Institute of Biomedical Sciences, ¶Department of Cell and Molecular Biology, and **Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan;
authors: Jau-Song
authors: JS
authors: Yu
authors: From the ‡Graduate Institute of Biomedical Sciences, **Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan;
authors: Yu-Sun
authors: YS
authors: Chang
authors: **Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan; yucj1124@mail.cgu.edu.tw luckywu@mail.cgu.edu.tw.
authors: Chih-Ching
authors: CC
authors: Wu
authors: From the ‡Graduate Institute of Biomedical Sciences, ¶Department of Cell and Molecular Biology, and yucj1124@mail.cgu.edu.tw luckywu@mail.cgu.edu.tw.
authors: Chia-Jung
authors: CJ
authors: Yu
mesh_terms: D019540:Area Under Curve; D014408:Biomarkers, Tumor / Q000378:metabolism*; D015153:Blotting, Western; D002289:Carcinoma, Non-Small-Cell Lung / Q000378:metabolism*; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D004797:Enzyme-Linked Immunosorbent Assay; D005260:Female; D006801:Humans; D008175:Lung Neoplasms / Q000378:metabolism*; D008297:Male; D008875:Middle Aged; D015999:Multivariate Analysis; D009363:Neoplasm Proteins / Q000378:metabolism*; D035422:Pleural Cavity / Q000378:metabolism / Q000473:pathology; D010996:Pleural Effusion / Q000175:diagnosis / Q000378:metabolism*; D010997:Pleural Neoplasms / Q000556:secondary; D025341:Principal Component Analysis; D040901:Proteomics / Q000379:methods*; D019859:Proto-Oncogene Proteins c-met / Q000378:metabolism; D015203:Reproducibility of Results
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D019859:Proto-Oncogene Proteins c-met
references: Development. 2013 Aug;140(16):3413-22
references: 23863482
references: Curr Opin Oncol. 2013 Mar;25(2):130-6
references: 23385860
references: J Mol Diagn. 2003 May;5(2):73-81
references: 12707371
references: J Thorac Oncol. 2012 Feb;7(2):459-67
references: 22237263
references: Thorax. 2003 May;58 Suppl 2:ii8-17
references: 12728146
references: Radiology. 1983 Sep;148(3):839-43
references: 6878708
references: Eur Respir J. 1997 Feb;10(2):476-81
references: 9042652
references: BMC Genomics. 2007;8:140
references: 17540040
references: Am J Pathol. 2005 Dec;167(6):1763-75
references: 16314486
references: Nature. 1989 May 11;339(6220):155-6
references: 2541345
references: Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13790-5
references: 11707567
references: Am Fam Physician. 2006 Apr 1;73(7):1211-20
references: 16623208
references: Int J Clin Exp Pathol. 2013;6(4):598-612
references: 23573306
references: Cell Res. 2005 Jan;15(1):49-51
references: 15686627
references: J Exp Med. 1999 Aug 2;190(3):301-6
references: 10430618
references: Biochim Biophys Acta. 2013 Nov;1834(11):2242-58
references: 23376433
references: Genome Res. 2012 Jul;22(7):1197-211
references: 22613842
references: Histochem J. 1985 Jan;17(1):23-31
references: 2859262
references: Breast Cancer Res Treat. 2000 Nov;64(2):221-8
references: 11194458
references: World J Clin Oncol. 2011 Jun 10;2(6):245-61
references: 21773075
references: J Proteome Res. 2011 Oct 7;10(10):4671-82
references: 21806062
references: Nat Rev Mol Cell Biol. 2003 Dec;4(12):915-25
references: 14685170
references: PLoS One. 2013;8(4):e62304
references: 23638030
references: Semin Oncol. 2009 Apr;36(2 Suppl 1):S52-8
references: 19393836
references: Curr Opin Cell Biol. 1996 Apr;8(2):182-8
references: 8791415
references: Mol Cell Proteomics. 2014 Mar;13(3):701-15
references: 24361865
references: Nat Med. 2002 Aug;8(8):816-24
references: 12118244
references: Cancer. 1950 Jan;3(1):32-5
references: 15405679
references: Neoplasia. 2004 Jan-Feb;6(1):1-6
references: 15068665
references: Immunol Today. 1999 Aug;20(8):367-75
references: 10431157
references: Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5
references: 12883005
references: Int J Cancer. 1986 Apr 15;37(4):479-85
references: 3957458
references: Clin Chem. 1988 Nov;34(11):2299-301
references: 2902942
references: Cell Signal. 2011 Jun;23(6):1050-6
references: 21300149
references: Respirology. 2004 Jun;9(2):148-56
references: 15182263
references: Clin Cancer Res. 2006 Jul 15;12(14 Pt 1):4154-62
references: 16857786
references: Oncol Rep. 2011 Dec;26(6):1369-75
references: 21894438
references: Singapore Med J. 2000 Jan;41(1):19-23
references: 10783675
references: Am J Respir Cell Mol Biol. 1997 Sep;17(3):353-60
references: 9308922
references: Anticancer Agents Med Chem. 2011 Jan;11(1):133-40
references: 21235433
references: Science. 1991 Feb 15;251(4995):802-4
references: 1846706
references: Mol Cell Proteomics. 2005 Dec;4(12):2010-21
references: 16249172
references: Am J Respir Cell Mol Biol. 2004 Jul;31(1):114-21
references: 14975938
references: Clin Cancer Res. 2003 Oct 15;9(13):4695-704
references: 14581339
references: J Clin Oncol. 2013 Mar 10;31(8):1089-96
references: 23401458
references: Mol Cell Biol. 1991 Dec;11(12):5954-62
references: 1944272
references: Anticancer Res. 1986 Sep-Oct;6(5):983-8
references: 2879510
references: Br J Cancer. 2000 Nov;83(9):1139-46
references: 11027426
references: Biochem Pharmacol. 1995 Sep 28;50(7):959-66
references: 7575680
references: Eur Respir J. 1997 Aug;10(8):1907-13
references: 9272937
references: Biochim Biophys Acta. 2012 Apr;1824(4):692-700
references: 22326748
references: Mol Cell Biol. 2005 Nov;25(21):9632-45
references: 16227611
references: Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13784-9
references: 11707590
references: J Proteome Res. 2009 Oct;8(10):4428-40
references: 19655816
references: J Proteome Res. 2012 May 4;11(5):2653-65
references: 22494190
references: PLoS One. 2010;5(4):e10312
references: 20421987
references: Biomarkers. 2013 Mar;18(2):126-35
references: 23410046
references: Int J Cancer. 2013 May 1;132(9):2148-56
references: 23001699
references: Cancer Res. 2012 Jan 1;72(1):100-11
references: 22080568
references: J Proteome Res. 2012 Dec 7;11(12):6277-81
references: 23140350
references: Ann Pharmacother. 1994 Jul-Aug;28(7-8):894-903
references: 7524816
references: Oncogene. 1989 Nov;4(11):1383-8
references: 2554238
references: Cancer. 1985 Aug 15;56(4):905-9
references: 4016683
references: PLoS One. 2008;3(2):e1651
references: 18297132