SWATH™- and iTRAQ-based quantitative proteomic analyses reveal an overexpression and biological relevance of CD109 in advanced NSCLC

Journal of Proteomics

Volumn 102, Issue , 2014, Pages 125-136

  Zhang, Fanglin ^a   Lin, Hechun ^b   Gu, Aiqin ^c   Li, Jing ^b   Liu, Lei ^b   Yu, Tao ^b   Cui, Yongqi ^b   Deng, Wei ^b   Yan, Mingxia ^b   Li, Jinjun ^b   Yao, Ming ^b  

^a FUDAN UNIVERSITY   (China)

^b SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

^c SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

CD109; ITRAQ; Metastasis; Non small cell lung cancer (NSCLC); Secretome; SWATH

Indexed keywords

CADMIUM 109; EXOSTOSIN 1; INTERSTITIAL COLLAGENASE; LAMININ; LAMININ SUBUNIT BETA 3; PROTEIN; PROTEIN 14 3 3; SOMATOMEDIN BINDING PROTEIN 3; UNCLASSIFIED DRUG; CD109 PROTEIN, HUMAN; CULTURE MEDIUM; GLYCOSYLPHOSPHATIDYLINOSITOL ANCHORED PROTEIN; LEUKOCYTE ANTIGEN; TUMOR MARKER; TUMOR PROTEIN;

ADULT; ADVANCED CANCER; ANALYTIC METHOD; ARTICLE; BLOOD SAMPLING; CANCER CELL CULTURE; CANCER PATIENT; CANCER STAGING; CELL CYCLE PHASE; CELL FUNCTION; CELL GROWTH; CELL PROLIFERATION; CELL VIABILITY; CLINICAL ARTICLE; CONTROLLED STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; FEMALE; HUMAN; HUMAN CELL; HUMAN TISSUE; ISOBARIC TAG IN A RELATIVE AND ABSOLUTE QUANTITATION; LUNG NON SMALL CELL CANCER; MALE; MIDDLE AGED; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL; PROTEIN EXPRESSION; PROTEOMICS; QUANTITATIVE ANALYSIS; WESTERN BLOTTING; AGED; ALGORITHM; CELL CYCLE; CELL MOTION; CHEMISTRY; CULTURE MEDIUM; DISEASE COURSE; GENE EXPRESSION REGULATION; LUNG TUMOR; METABOLISM; METASTASIS; NON SMALL CELL LUNG CANCER; PHENOTYPE; PROCEDURES; TUMOR CELL LINE; TUMOR INVASION; WOUND HEALING;

AGED; ALGORITHMS; ANTIGENS, CD; CARCINOMA, NON-SMALL-CELL LUNG; CELL CYCLE; CELL LINE, TUMOR; CELL MOVEMENT; CELL PROLIFERATION; CULTURE MEDIA, CONDITIONED; DISEASE PROGRESSION; ENZYME-LINKED IMMUNOSORBENT ASSAY; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; GPI-LINKED PROTEINS; HUMANS; LUNG NEOPLASMS; MALE; MIDDLE AGED; NEOPLASM INVASIVENESS; NEOPLASM METASTASIS; NEOPLASM PROTEINS; PHENOTYPE; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL; WOUND HEALING;

EID: 84897536608     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2014.03.007     Document Type: Article

References (59)

1. Siegel R., Naishadham D., Jemal A. Cancer statistics for Hispanics/Latinos, 2012. CA Cancer J Clin 2012, 62:283-298.
2. Baltayiannis N., Chandrinos M., Anagnostopoulos D., Zarogoulidis P., Tsakiridis K., Mpakas A., et al. Lung cancer surgery: an up to date. J Thorac Dis 2013, 5:S425-S439.
3. Fischer B., Lassen U., Mortensen J., Larsen S., Loft A., Bertelsen A., et al. Preoperative staging of lung cancer with combined PET-CT. N Engl J Med 2009, 361:32-39.
4. Reck M., Heigener D.F., Mok T., Soria J.C., Rabe K.F. Management of non-small-cell lung cancer: recent developments. Lancet 2013, 382:709-719.
5. Ceteci F., Ceteci S., Karreman C., Kramer B.W., Asan E., Gotz R., et al. Disruption of tumor cell adhesion promotes angiogenic switch and progression to micrometastasis in RAF-driven murine lung cancer. Cancer Cell 2007, 12:145-159.
6. Herbst R.S., Yano S., Kuniyasu H., Khuri F.R., Bucana C.D., Guo F., et al. Differential expression of E-cadherin and type IV collagenase genes predicts outcome in patients with stage I non-small cell lung carcinoma. Clin Cancer Res 2000, 6:790-797.
7. Indovina P., Marcelli E., Pentimalli F., Tanganelli P., Tarro G., Giordano A. Mass spectrometry-based proteomics: the road to lung cancer biomarker discovery. Mass Spectrom Rev 2013, 32:129-142.
8. Carretero J., Shimamura T., Rikova K., Jackson A.L., Wilkerson M.D., Borgman C.L., et al. Integrative genomic and proteomic analyses identify targets for Lkb1-deficient metastatic lung tumors. Cancer Cell 2010, 17:547-559.
9. Ghosh D., Li Z., Tan X.F., Lim T.K., Mao Y., Lin Q. iTRAQ based quantitative proteomics approach validated the role of calcyclin binding protein (CacyBP) in promoting colorectal cancer metastasis. Mol Cell Proteomics 2013, 12:1865-1880.
10. Olsson N., Carlsson P., James P., Hansson K., Waldemarson S., Malmstrom P., et al. Grading breast cancer tissues using molecular portraits. Mol Cell Proteomics 2013, 12:3612-3623.
11. Hao J., Li W., Dan J., Ye X., Wang F., Zeng X., et al. Reprogramming- and pluripotency-associated membrane proteins in mouse stem cells revealed by label-free quantitative proteomics. J Proteomics 2013, 86:70-84.
12. Jeppesen D.K., Nawrocki A., Jensen S.G., Thorsen K., Whitehead B., Howard K.A., et al. Quantitative proteomics of fractionated membrane and lumen exosome proteins from isogenic metastatic and non-metastatic bladder cancer cells reveal differential expression of EMT factors. Proteomics 2013, 10.1002/pmic.201300452.
13. Kristensen L.P., Larsen M.R., Mickley H., Saaby L., Diederichsen A.C., Lambrechtsen J., et al. Plasma proteome profiling of atherosclerotic disease manifestations reveals elevated levels of the cytoskeletal protein vinculin. J Proteomics 2013, S1874-S3919.
14. Tate S., Larsen B., Bonner R., Gingras A.C. Label-free quantitative proteomics trends for protein-protein interactions. J Proteomics 2013, 81:91-101.
15. Gillet L.C., Navarro P., Tate S., Rost H., Selevsek N., Reiter L., et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 2012, 11:O111-O016717.
16. Lambert J.P., Ivosev G., Couzens A.L., Larsen B., Taipale M., Lin Z.Y., et al. Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition. Nat Methods 2013, 10:1239-1245.
17. Collins B.C., Gillet L.C., Rosenberger G., Rost H.L., Vichalkovski A., Gstaiger M., et al. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat Methods 2013, 10:1246-1253.
18. Makridakis M., Vlahou A. Secretome proteomics for discovery of cancer biomarkers. J Proteomics 2010, 73:2291-2305.
19. Jia D., Yan M., Wang X., Hao X., Liang L., Liu L., et al. Development of a highly metastatic model that reveals a crucial role of fibronectin in lung cancer cell migration and invasion. BMC Cancer 2010, 10:364-384.
20. Lin H.C., Zhang F.L., Geng Q., Yu T., Cui Y.Q., Liu X.H., et al. Quantitative proteomic analysis identifies CPNE3 as a novel metastasis-promoting gene in NSCLC. J Proteome Res 2013, 12:3423-3433.
21. Wang X.M., Li J., Yan M.X., Liu L., Jia D.S., Geng Q., et al. Integrative analyses identify osteopontin, LAMB3 and ITGB1 as critical pro-metastatic genes for lung cancer. PLoS One 2013, 8:e55714.
22. Karagiannis G.S., Pavlou M.P., Diamandis E.P. Cancer secretomics reveal pathophysiological pathways in cancer molecular oncology. Mol Oncol 2010, 4:496-510.
23. Ngounou Wetie A.G., Sokolowska I., Woods A.G., Wormwood K.L., Dao S., Patel S., et al. Automated mass spectrometry-based functional assay for the routine analysis of the secretome. J Lab Autom 2013, 18:19-29.
24. Faca V.M., Hanash S.M. In-depth proteomics to define the cell surface and secretome of ovarian cancer cells and processes of protein shedding. Cancer Res 2009, 69:728-730.
25. Martosella J., Zolotarjova N. Multi-component immunoaffinity subtraction and reversed-phase chromatography of human serum. Methods Mol Biol 2008, 425:27-39.
26. Liu B., Qiu F.H., Voss C., Xu Y., Zhao M.Z., Wu Y.X., et al. Evaluation of three high abundance protein depletion kits for umbilical cord serum proteomics. Proteome Sci 2011, 9:24-41.
27. Gan C.S., Chong P.K., Pham T.K., Wright P.C. Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ). J Proteome Res 2007, 6:821-827.
28. Shilov I.V., Seymour S.L., Patel A.A., Loboda A., Tang W.H., Keating S.P., et al. The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol Cell Proteomics 2007, 6:1638-1655.
29. Petersen T.N., Brunak S., von Heijne G., Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011, 8:785-786.
30. Bennuru S., Semnani R., Meng Z., Ribeiro J.M., Veenstra T.D., Nutman T.B. Brugia malayi excreted/secreted proteins at the host/parasite interface: stage- and gender-specific proteomic profiling. PLoS Negl Trop Dis 2009, 3:e410.
31. Chen Y., Yu P., Luo J., Jiang Y. Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT. Mamm Genome 2003, 14:859-865.
32. Simpson R.J., Kalra H., Mathivanan S. ExoCarta as a resource for exosomal research. J Extracell Vesicles 2012, 1-13.
33. Lukaszewicz-Zajac M., Mroczko B., Gryko M., Kedra B., Szmitkowski M. Comparison between clinical significance of serum proinflammatory proteins (IL-6 and CRP) and classic tumor markers (CEA and CA 19-9) in gastric cancer. Clin Exp Med 2011, 11:89-96.
34. Baek J.M., Jin Q., Ensor J., Boulbes D.R., Esteva F.J. Serum CD44 levels and overall survival in patients with HER2-positive breast cancer. Breast Cancer Res Treat 2011, 130:1029-1036.
35. Hyung S.W., Lee M.Y., Yu J.H., Shin B., Jung H.J., Park J.M., et al. A serum protein profile predictive of the resistance to neoadjuvant chemotherapy in advanced breast cancers. Mol Cell Proteomics 2011, 10. [M111 011023].
36. Dowling P., Clarke C., Hennessy K., Torralbo-Lopez B., Ballot J., Crown J., et al. Analysis of acute-phase proteins, AHSG, C3, CLI, HP and SAA, reveals distinctive expression patterns associated with breast, colorectal and lung cancer. Int J Cancer 2012, 131:911-923.
37. Suleiman L., Negrier C., Boukerche H. Protein S: a multifunctional anticoagulant vitamin K-dependent protein at the crossroads of coagulation, inflammation, angiogenesis, and cancer. Crit Rev Oncol Hematol 2013, 88:637-654.
38. Karhemo P.R., Ravela S., Laakso M., Ritamo I., Tatti O., Makinen S., et al. An optimized isolation of biotinylated cell surface proteins reveals novel players in cancer metastasis. J Proteomics 2012, 77:87-100.
39. Hagikura M., Murakumo Y., Hasegawa M., Jijiwa M., Hagiwara S., Mii S., et al. Correlation of pathological grade and tumor stage of urothelial carcinomas with CD109 expression. Pathol Int 2010, 60:735-743.
40. Ohshima Y., Yajima I., Kumasaka M.Y., Yanagishita T., Watanabe D., Takahashi M., et al. CD109 expression levels in malignant melanoma. J Dermatol Sci 2010, 57:140-142.
41. Hockla A., Radisky D.C., Radisky E.S. Mesotrypsin promotes malignant growth of breast cancer cells through shedding of CD109. Breast Cancer Res Treat 2010, 124:27-38.
42. Du C., Liang J.R., Chen D.D., Xu B., Zhuo W.H., Gao Y.H., et al. iTRAQ-based proteomic analysis of the metabolism mechanism associated with silicon response in the marine diatom Thalassiosira pseudonana. J Proteome Res 2014, [Epub ahead of print].
43. Liu Y., Huttenhain R., Surinova S., Gillet L.C., Mouritsen J., Brunner R., et al. Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics 2013, 13:1247-1256.
44. Johnson D., Boyes B., Fields T., Kopkin R., Orlando R. Optimization of data-dependent acquisition parameters for coupling high-speed separations with LC-MS/MS for protein identifications. J Biomol Tech 2013, 24:62-72.
45. Aggarwal K., Choe L.H., Lee K.H. Shotgun proteomics using the iTRAQ isobaric tags. Brief Funct Genomic Proteomic 2006, 5:112-120.
46. Aharinejad S., Salama M., Paulus P., Zins K., Berger A., Singer C.F. Elevated CSF1 serum concentration predicts poor overall survival in women with early breast cancer. Endocr Relat Cancer 2013, 20:777-783.
47. Al-Alwan L.A., Chang Y., Mogas A., Halayko A.J., Baglole C.J., Martin J.G., et al. Differential roles of CXCL2 and CXCL3 and their receptors in regulating normal and asthmatic airway smooth muscle cell migration. J Immunol 2013, 191:2731-2741.
48. Na K.Y., Bacchini P., Bertoni F., Kim Y.W., Park Y.K. Syndecan-4 and fibronectin in osteosarcoma. Pathology 2012, 44:325-330.
49. Kosanam H., Prassas I., Chrystoja C.C., Soleas I., Chan A., Dimitromanolakis A., et al. Laminin, gamma 2 (LAMC2): a promising new putative pancreatic cancer biomarker identified by proteomic analysis of pancreatic adenocarcinoma tissues. Mol Cell Proteomics 2013, 12:2820-2832.
50. Richter G.H., Fasan A., Hauer K., Grunewald T.G., Berns C., Rossler S., et al. G-Protein coupled receptor 64 promotes invasiveness and metastasis in Ewing sarcomas through PGF and MMP1. J Pathol 2013, 230:70-81.
51. Wang H.Y., Li Y.Y., Shao Q., Hou J.H., Wang F., Cai M.B., et al. Secreted protein acidic and rich in cysteine (SPARC) is associated with nasopharyngeal carcinoma metastasis and poor prognosis. J Transl Med 2012, 10:27.
52. Chen J., Shi D., Liu X., Fang S., Zhang J., Zhao Y. Targeting SPARC by lentivirus-mediated RNA interference inhibits cervical cancer cell growth and metastasis. BMC Cancer 2012, 12:464-483.
53. Tassi E., McDonnell K., Gibby K.A., Tilan J.U., Kim S.E., Kodack D.P., et al. Impact of fibroblast growth factor-binding protein-1 expression on angiogenesis and wound healing. Am J Pathol 2011, 179:2220-2232.
54. Saraon P., Musrap N., Cretu D., Karagiannis G.S., Batruch I., Smith C., et al. Proteomic profiling of androgen-independent prostate cancer cell lines reveals a role for protein S during the development of high grade and castration-resistant prostate cancer. J Biol Chem 2012, 287:34019-34031.
55. Emori M., Tsukahara T., Murase M., Kano M., Murata K., Takahashi A., et al. High expression of CD109 antigen regulates the phenotype of cancer stem-like cells/cancer-initiating cells in the novel epithelioid sarcoma cell line ESX and is related to poor prognosis of soft tissue sarcoma. PLoS One 2013, 8:e84187.
56. Caccia D., Zanetti Domingues L., Micciche F., De Bortoli M., Carniti C., Mondellini P., et al. Secretome compartment is a valuable source of biomarkers for cancer-relevant pathways. J Proteome Res 2011, 10:4196-4207.
57. Sakakura H., Murakumo Y., Mii S., Hagiwara S., Kato T., Asai M., et al. Detection of a soluble form of CD109 in serum of CD109 transgenic and tumor xenografted mice. PLoS One 2014, 9:e83385.
58. Paltridge J.L., Belle L., Khew-Goodall Y. The secretome in cancer progression. Biochim Biophys Acta 1834, 2013:2233-2241.
59. Saraf S., Saraf S., Kaur C.D., Gupta A., Jangdey M. Matrix metalloproteinase enzymes and their naturally derived inhibitors: novel targets in photocarcinoma therapy. Ageing Res Rev 2013, 13C:65-74.