Prioritization of candidate protein biomarkers from an In Vitro model system of breast tumor progression toward clinical verification

Journal of Proteome Research

Volumn 9, Issue 3, 2010, Pages 1450-1459

  Lau, Thomas Y K ^a   Power, Karen A ^a   Dijon, Sophie ^b   De Gardelle, Isabelle ^c   McDonnell, Susan ^a   Duffy, Michael J ^c   Pennington, Stephen R ^a   Gallagher, William M ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b UNIV LILLE   (France)

^c ST VINCENT S UNIVERSITY HOSPITAL   (Ireland)

Author keywords

2D DIGE; Biomarker; Breast cancer; Informatics; Mass spectrometry; Model system; Secretion

Indexed keywords

BIOLOGICAL MARKER;

ARTICLE; BLOOD SAMPLING; BREAST TUMOR; CANCER INVASION; CANCER PATIENT; COMPUTER MODEL; CONTROLLED STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VITRO STUDY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; TUMOR GROWTH; TWO DIMENSIONAL GEL ELECTROPHORESIS; VALIDITY;

BLOOD PROTEINS; BREAST NEOPLASMS; CELL LINE, TUMOR; COMPUTER SIMULATION; CULTURE MEDIA, CONDITIONED; DISEASE PROGRESSION; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; KAPLAN-MEIERS ESTIMATE; MASS SPECTROMETRY; MODELS, BIOLOGICAL; NEOPLASM PROTEINS; REPRODUCIBILITY OF RESULTS; TUMOR MARKERS, BIOLOGICAL;

EID: 77949780050     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr900989q     Document Type: Article

References (51)

1. Lau, T. Y K.; O'Connor, D. P.; Brennan, D. J.; Duffy, M. J.; Pennington, S. R.; Gallagher, W. M. Breast cancer proteomics: clinical perspectives. Expert Opin. Biol.Ther. 2007, 7 (2), 209-219
2. Pauiovich, A. G.; Whiteaker, J. R.; Hoofnagle, A. N.; Wang, P. The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline. Proteomics-Clin. Appl. 2008, 2, 1386-1402.
3. Hanash, S. M.; Pitteri, S. J.; Faca, V. M. Mining the plasma proteome for cancer biomarkers. Nature 2008, 452 (7187), 571-579
4. Keshishian, H.; Addona, T.; Burgess, M.; Kuhn, E.; Carr, S. A Quantitative, multiplexed assays for low abundance proteins in plasma by targeted, mass spectrometry and stable isotope dilution. mol. Cell. Proteomics 2007, 6 (2), 2212-2229
5. Anderson, L.; Hunter, C. L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Protemics 2005, 5 (4), 573-588
6. Hu, S.; Loo, I. A.; Wong, D. T. Human body fluid proteome analysis. Protemics 2006, 6 (23), 6326-6353
7. Schenk, S.; Schoenhals, G. J.; de Souza, G.; Mann, M. A. high confidence, manually validated human blood plasma protein reference set. BMC Med. Genomics 2008, 1, 41.
8. Pernemalm, M.; Lewensohn, R.; Lehtiouml, J. Affinity prefractionation for MS-plasma proteomics. Proteomics 2009, 9 (6), 1420-1427.
9. Omenn, G. S.; States, D. J.; Adamski, M.; Blackwell, T. W.; Menon, R.; Hermjakob, H.; Apweiler, R.; Haab, B. B.; Simpson, R. J.; Eddes, J. S.; Kapp, E. A.; Moritz, R. L.; Chan, D. W.; Rai, A. J.; Admon, A.; Aebersold, R.; Eng, J.; Hancock, W. S.; Hefta, S. A.; Meyer, H.; Paik, Y.-K.; Yoo, J.-S.; Ping, P.; Pounds, J.; Adkins, J.; Qian, X.; Wang, R.; Wasinger, V.; Wu, C. Y.; Zhao, X.; Zeng, R.; Archakov, A.; Tsugita, A.; Beer, I.; Pandey, A.; Pisano, M.; Andrews, P.; Tammen, H.; Speicher, D. W.; Hanash, S. M. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005, 5 (13), 3226-3245
10. Jaffe, J. D.; Keshishian, H.; Chang, B.; Addona, T. A.; Gillette, M. A.; Carr, S. A. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification. Mol. Cell. Proteomics 2008, 7(10), 1952-1962
11. Kuzyk, M. A.; Smith, D.; Yang, J.; Cross, T. J.; Jackson, A. M.; Hardie, D. B.; Anderson, N. L.; Borchers, C. H. Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol. Cell. Proteomics 2009, 8 (8), 1860-1877
12. Ho, J.; Kong, J.; Choong, L.; Loh, M.; Toy, W.; Chong, P.; Wong, C.; Shah, N.; Lim, Y. Novel Breast Cancer Metastasis-Associated Proteins. J. Proteome Res. 2009, 8, 583-594
13. Mbeunkui, F.; Metge, B. J.; Shevde, L. A.; Pannell, L. K. Identification of differentially secreted biomarkers using LC-MS/MS in isogenic cell lines representing a progression of breast cancer. J. Proteome Res. 2007, 6 (8), 2993-3002.
14. Hughes, L.; Malone, C.; Chumsri, S.; Burger, A.; McDonnell, S. Characterisation of breast cancer cell lines and establishment of a novel isogenic subclone to study migration, invasion and tumourigenicity. Clin. Exp. Metastasis 2008, 25, 549-557
15. Hughes, L.; O'Brien, S. L.; Gallagher, W. M.; Mcdonnell, S. DNA microarray-based transcriptomic profiling of an isogenic cell culture model of breast tumour cell Invasion. Anticancer Res. 2007, 27 (3A), 1353-1359
16. Chevallet, M.; Diemer, H.; Van Dorssealer, A.; Villiers, C.; Rabilloud, T. Toward a better analysis of secreted proteins: the example of the myeloid cells secretome. Proteomics 2007, 7(11), 1757-1770
17. Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem.1976, 72, 248-254
18. Karp, N. A.; Mccormick, P. S.; Russell, M. R.; Lilley, K. S. Experimental and statistical considerations to avoid false conclu- sions in proteomics studies using differential in-gel electrophoresis. Mol. Cell. Proteomics 2007, 6 (8), 1354-1364
19. Bendtsen, J. D.; Nielsen, H.; von Heijne, G.; Brunak, S. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 2004, 340 (4), 783-795
20. Smedley, D.; Haider, S.; Ballester, B.; Holland, R.; London, D.; Thorisson, G.; Kasprzyk, A BioMart-biological queries made easy. BMC Genomics 2009, 10, 22.
21. Huang, D. W.; Sherman, B. T.; Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4 (1), 44-57.
22. Deutsch, E. W.; Lam, H.; Aebersold, R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep.2008, 9 (5), 429-434
23. van de Vijver, M. J.; He, Y D.; van't Veer, L. J.; Dai, H.; Hart, A. A. M.; Voskuil, D. W.; Schreiber, G. J.; Peterse, J. L.; Roberts, C.; Marton, M. J.; Parrish, M.; Atsma, D.; Witteveen, A.; Glas, A.; Delahaye, L.; van der Velde, T.; Bartelink, H.; Rodenhuis, S.; Rutgers, E. T.; Friend, S. H.; Bernards, R.,. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 2002, 347 (25), 1999-2009.
24. Moody, S. E.; Perez, D.; Pan, T.-c.; Sarkisian, C. J.; Portocarrero, C. P.; Sterner, C. J.; Notorfrancesco, K. L.; Cardiff, R. D.; Chodosh, L. A. The transcriptional repressor Snail promotes mammary tumor recurrence. Cancer Cell 2005, 8 (3), 197-209.
25. Hubner, N. C.; Ren, S.; Mann, M. Peptide separation with immobilized pi strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics 2008, 8 (23-24), 4862-4872
26. Martens, L.; Hermfakob, H.; Jones, P.; Adamski, M.; Taylor, C.; States, D.; Gevaert, K.; Vandekerckhove, J.; Apweiler, R. PRIDE: the proteomics identifications database. Proteomics 2005, 5 (13), 3537-3545
27. Barsnes, H.; Vizcaino, J. A.; Eidhammer, L.; Martens, L. PRIDE Converter: making proteomics data-sharing easy. Nat. Biotechnol. 2009, 27 (7), 598-599
28. Kulasingam, V.; Diamandis, E. P. Proteomics analysis of conditioned media from three breast cancer cell lines: a mine for biomarkers and therapeutic targets. Mol. Cell. Protemics. 2007, 6 (11), 1997-2011.
29. Kulasingam, V.; Diamandis, E. P. Tissue culture-based breast cancer biomarker discovery platform. Int. J. Cancer 2008. 123 (9), 2007-2012
30. Liang, X.; Huuskonen, J.; Hajivandi, M.; Manzanedo, R.; Predki, P.; Amshey, J. R.; Pope, R. M. Identification and quantification of proteins differentially secreted by a pair of normal and malignant breast-cancer cell lines. Proteomics 2009, 9 (1), 182-193
31. Whiteaker, J. R.; Zhang, H.; Zhao, L.; Wang, P.; Kelly-Spratt, K. S.; Ivey, R. G.; Piening, B. D.; Feng, L.-C.; Kasarda, E.; Gurley, K. E.; Eng, J. K.; Chodosh, L. A.; Kemp, C. J.; Mcintosh, M. W.; Paulovlch, A. G. Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J. Proteome Res. 2007, 6 (10), 3962-3975
32. Schulz, D. M.; Böllner, C; Thomas, G.; Atkinson, M.; Esposito, I.; Höfler, H.; Aubele, M. Identification of differentially expressed proteins in triple-negative breast carcinomas using DIGE and mass spectrometry. J. Proteome. Res. 2009, 8 (7), 3430-3438
33. Renz, M.; Betz, B.; Niederacher, D.; Bender, H. G.; Langowski, J. Invasive breast cancer cells exhibit increased mobility of the actinbinding protein CapG. Int. J. Cancer 2008. 122 (7), 1476-1482
34. Sangaletti, S.; Di Carlo, E.; Gariboldi, S.; Miotti, S.; Cappetti, B.; Parenza, M.; Rumio, C.; Brekken, R. A.; Chiodoni, C.; Colombo, M. P. Macrophage-derived SPARC bridges tumor cell-extracellular matrix interactions toward metastasis. Cancer Res. 2008, 68 (21), 9050-9059
35. Halder, S. K. Oncogenic Function of a Novel WD-Domain Protein, STRAP, in Human Carcinogenesis. Cancer Res. 2006, 66 (12), 6156-6166
36. Demonacos, C.; Krstic-Demonacos, M.; Smith, L.; Xu, D.; O'Connor, D. P.; Jansson, M.; Thangue, N. B. L. A new effector pathway links ATM kinase with the DNA damage response. Nat. Cell Biol. 2004, 6 (10), 968-976
37. Baker, A. H.; Edwards, D. R.; Murphy, G. Metalloproteinase inhibitors: biological actions and therapeutic opportunities. J. Cell Sci. 2002, 115 (Pt 19), 3719-3727
38. van de Vijver, M. J.; He, Y D.; van't Veer, L. J.; Dai, H.; Hart, A. A; Voskuil, D. W.; Schreiber, G. J.; Peterse, J. L.; Roberts, C.; Marton, M. J.; Parrish, M.; Atsma, D.; Witteveen, A.; Glas, A.; Delahaye, L; van der Velde, T.; Bartelink, H.; Rodenhuis, S.; Rutgers, E. T.; Friend, S. H.; Bernards, R. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 2002, 347 (25), 1999-2009.
39. Kulasingam, V.; Diamandis, E. Proteomics analysis of conditioned media from three breast cancer cell lines: a mine for biomarkers and therapeutic targets. Mol. Cell. Proteomics 2007, 6 (11), 1997-2011.
40. Nagaraja, G. M.; Othman, M.; Fox, B. P.; Alsaber, R.; Pellegrino, C. M.; Zeng, Y.; Khanna, R.; Tamburini, P.; Swaroop, A.; Kandpal, R. P. Gene expression signatures and biomarkers of noninvasive and invasive breast cancer cells: comprehensive profiles by representational difference analysis, microarrays and proteomics. Oncogene 2006, 25 (16), 2328-2338
41. Jones, C.; Mackay, A.; Grigoriadis, A.; Cossu, A; Reis-Filho, J. S.; Fulford, L.; Dexter, T.; Davies, S.; Bulmer, K.; Ford, E.; Parry, S.; Budroni, M.; Palmieri, G.; Neville, A. M.; O'Hare, M. J.; Lakhani, S. R. Expression profiling of purified normal human luminal and myoepithelial breast cells: identification of novel prognostic markers for breast cancer. Cancer Res. 2004, 64 (9), 3037-3045
42. Mackay, A.; Jones, C.; Dexter, T.; Silva, R. L. A; Bulmer, K.; Jones, A.; Simpson, P.; Harris, R. A.; Jat, P. S.; Neville, A. M.; Reis, L. F. L.; Lakhani, S. R.; O'Hare, M. J. cDNA microarray analysis of genes associated with ERBB2 (HER2/neu) overexpression in human mammary luminal epithelial cells. Oncogene 2003, 22 (17), 2680-2688
43. Orosz, F.; Oláh, J.; Ovádi, J. Triosephosphate isomerase deficiency: New insights into an enigmatic disease. Biochem. Biophys. Acta 2009, 1792, 1168-1174
44. Yang, F.; Xiao, Z.-q.; Zhang, X-z.; Li, C.; Zhang, P.-f Li, M.-y.; Chen, Y.; Zhu, G.-q.; Sun, Y.; Liu, Y.-f.; Chen, Z.-C. Identification of tumor antigens in human lung squamous carcinoma by serological proteome analysis. J. Proteome Res. 2007, 6 (2), 75-78
45. Marhaba, R.; Zöllen, M. CD44 in cancer progression: adhesion, migration and growth regulation. J. Mol. Histol. 2004, 35 (3), 211-231
46. Barrett, T.; Troup, D. B.; Wilhite, S. E.; Ledoux, P.; Rudnev, D.; Evangelista, C.; Kim, I. F.; Soboleva, A.; Tomashevsky, M.; Marshall, K. A.; Phillippy, K. H.; Sherman, P. M.; Muertter, R. N.; Edgar, R. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Adds Res. 2009, 37 (Database issue), D885-90.
47. Lanigan, F.; McKiernan, E.; Brennan, D. J.; Hegarty, S.; Millikan, R. C.; McBryan, J.; Jirstrom, K.; Landberg, G.; Martin, F.; Duffy, M. J.; Gallagher, W. M. Increased claudin-4 expression is associated with poor prognosis and high tumour grade in breast cancer. Int. J. Cancer 2009, 124 (9), 2088-2097
48. Brennan, D. J.; Rexhepaj, E.; O'Brien, S. L.; McSherry, E.; O'Connor, D. P.; Fagan, A.; Culhane, A. C.; Higgins, D. G.; Jirstrom, K.; Millikan, R. C.; Landberg, G.; Duffy, M. J.; Hewitt, S. M.; Gallagher, W. M. Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer. Clin. Cancer Res. 2008, 14 (9), 2681-2689
49. Liu, T.; Qian, W.-J.; Grltsenko, M. A.; Xiao, W.; Moldawer, L. L.; Kaushal, A.; Monroe, M. E.; Varnum, S. M.; Moore, R. J.; Purvine, S. O.; Maier, R. V.; Davis, R. W.; Tompkins, R. G.; Camp, D. G.; Smith, R. D. High dynamic range characterization of the trauma patient plasma proteome. Mol. Cell. Protemics. 2006, 5 (10), 1899-1913
50. DeSouza, L. V.; Taylor, A. M.; Li, W.; Minkoff, M. S.; Romaschin, A. D.; Colgan, T. J.; Siu, K. W. Muitiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantification of endogenous levels of a potential cancer marker in cancerous and normal, endometrial tissues. J. Proteme Res. 2008, 7(8), 3525-3534
51. Anderson, N. L.; Jackson, A.; Smith, D.; Hardie, D.; Borchers, C.; Pearson, T. W. SISCAPA peptide enrichment on magnetic beads using an in-line bead trap device. Mol. Cell. Proteomics 2009, 8 (5), 995-1005.