Clinical proteomics of breast cancer

Current Genomics

Volumn 11, Issue 7, 2010, Pages 528-536

  Baskin, Y ^a   Yigitbasi T ^b  

^a DOKUZ EYLUL UNIVERSITY   (Turkey)

^b ATATURK TRAINING AND RESEARCH HOSPITAL   (Turkey)

Author keywords

Breast cancer; Early diagnosis; Mass spectrometry; Matrix assisted laser desorption ionisation; Micro array techniques; Prognostic markers; Proteomic techniques; Surface enhanced laser desorption ionisation

Indexed keywords

DOXORUBICIN; IMATINIB; PACLITAXEL; TAMOXIFEN; TUMOR MARKER;

ADJUVANT THERAPY; ARTICLE; BREAST CANCER; ELECTROSPRAY; FOLLOW UP; GEL ELECTROPHORESIS; HUMAN; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PROGNOSIS; PROTEOMICS; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TISSUE MICROARRAY; TREATMENT RESPONSE;

EID: 78650033628     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920210793175930     Document Type: Article

References (109)

1. Jemal, A.; Siegel, R.; Ward, E.; Hao, Y.; Xu, J.; Thun, M.J. Cancer Statistics. Cancer J. Clin., 2009, 59, 225-249.
2. Hamzaoglu, O.; Özcan, U. Turkey Health Statistics. 1rd ed. Turkish Medical Association publication. Ankara, 2006.
3. ® - NCI's Comprehensive Cancer Database National Cancer Institute. http://www.cancer.gov/cancer_information/pdq. Updated: 01/04/2010.
4. National Cancer Institute, DCCPS, Surveillance Research Program, Cancer Statistics Branch. www.seer.cancer.gov. 2010.
5. Petterson, S.D.; Aebersold, R.H. Proteomics: First decade and beyond. Nat. Genet. Suppl., 2003, 33, 311-332.
6. Baskin Y. Changes in concepts of the technological progress: personalized medicine. Turk. Bull. Hyg. Exp. Biol., 2007, 64, 41-48.
7. Baskin, Y. Extracellular matrix proteins: nidogen and fibronectin. Effects of molecular structures on biological function. PhD Thesis, Dokuz Eylul University, Institute of Medical Sciences, Izmir, Turkey, 2005.
8. Celis, J.E.; Gromov, P. Proteomics in tranlational cancer research: Toward an integrated approach. Cancer Cell, 2003, 3, 9-15.
9. Bertucci, F.; Birnbaum, D.; Goncalves, A. Proteomics in breast cancer. Mol. Cell. Proteomics, 2006, 10, 1772-1786.
10. Qian, W.J.; Jacobs, J.M.; Liu, T.; Camp, D.G. 2nd.; Smith, R.D. Advances and challenges in liquid chromatography-mass spectrometry- based proteomics profiling for clinical applications. Mol. Cell Proteomics, 2006, 10, 1727-1744.
11. O'Farrell, P.H. High-resolution two-dimensional electrophoresis of proteins. J. Biol. Chem., 1975, 250, 4007-4021.
12. Bravo, R.; Bellatin, J.; Celis, J.E. 35S-methionine labelled polypeptides from HELA cells. Coordinates and percentage of some major polypeptides. Cell. Biol. Int. Rep., 1981, 5, 93-96.
13. Görg, A.; Obermaier, C.; Boguth, G.; Harder, A.; Scheibe, B.; Wildgruber, R.; Weiss, W. The current state of 2DE with Immobilized pH gradients. Electrophoresis, 2000, 21, 1037-1053.
14. Somiari, R.I.; Somiari, S.; Russell, S.; Shriver, C. D. Proteomics of breast carcinoma. J. Chromatogr. B Anal. Technol. Biomed. Life Sci., 2005, 815, 215-225.
15. Wall, D.B.; Kachman, M.T.; Gong, S.; Hinderer, R.; Parus, S.; Misek, D.E.; Hanash, S.M.; Lubman, D.M. Isoelectric focusing nonporous RP HPLC: a two-dimensional liquid-phase separation method for mapping of cellular proteins with identification using MALDITOF mass spectrometry. Anal. Chem., 2000, 72, 1099-1111.
16. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope- coded affinity tags. Nat. Biotechnol., 1999, 17, 994-999.
17. Pawlik, T.; Hawke, D.; Liu, Y.; Krishnamurthy, S.; Fritsche, H.; Hunt, K.; Kuerer, H. Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein. BMC Cancer, 2006, 6, 68.
18. Jessani, N.; Niessen, S.; Wei, B. Q.; Nicolau, M.; Humphrey, M.; Ji, Y.; Han, W.; Noh, D. Y.; Yates, J. R.; III, Jeffrey, S. S.; Cravatt, B. F. A streamlined platform for high-content functional proteomics of primary human specimens. Nat. Method, 2005, 2, 691-697.
19. Celis, J.E.; Gromov, P. Proteomics in tranlational cancer research: Toward an integrated approach. Cancer Cell, 2003, 3, 9-15.
20. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature, 2003, 422, 198-207.
21. Hong, H.; Dragan, Y.; Epstein, J.; Teitel, C.; Chen, B.; Xie, Q.; Fang, H.; Shi, L.; Perkins, R.; Tong, W. Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS). BMC Bioinformatics, 2005, 6(Suppl 2), S5.
22. Li, J.; Zhang, Z.; Rosenzweig, J.; Wang, Y. Y.; Chan, D. W. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin. Chem., 2002, 48, 1296-1304.
23. Kononen, J.; Bubendorf, L.; Kallioniemi, A.; Barlund, M.; Schraml, P.; Leighton, S.; Torhorst, J.; Mihatsch, M. J.; Sauter, G.; Kallioniemi, O. P. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat. Med., 1998, 4, 844-847.
24. Hedenfalk, I.; Duggan, D.; Chen, Y.; Radmacher, M.; Bittner, M.; Simon, R.; Meltzer, P.; Gusterson, B.; Esteller, M.; Kallioniemi, O. P.; Wilfond, B.; Borg, A.; Trent, J. Gene-expression profiles in hereditary breast cancer. N. Engl. J. Med., 2001, 344, 539-548.
25. Schlehe, B.; Schmutzler, R. Hereditary breast cancer. Chirurg, 2008, 79, 1047-1054.
26. Palacios, J.; Honrado, E.; Osorio, A.; Cazorla, A.; Sarrio, D.; Barroso, A.; Rodriguez, S.; Cigudosa, J. C.; Diez, O.; Alonso, C.; Lerma, E.; Dopazo, J.; Rivas, C.; Benitez, J. Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers. Breast Cancer Res. Treat., 2005, 90, 5-14.
27. Mangia, A.; Chiriatti, A.; Tommasi, S.; Menolascina, F.; Petroni, S.; Zito, F.A.; Simone, G.; Schittulli, F.; Paradiso, A. BRCA1expression and molecular alterations in familial breast cancer. Histol. Histopathol., 2009, 24, 69-76.
28. Turashvili, G.; Bouchal, J.; Ehrmann, J.; Fridman, E.; Skarda, J.; Kolar, Z. Novel immunohistochemical markers for the differentiation of lobular and ductal invasive breast carcinomas. Biomed. Pap. Med. Fac. Univ. Palacky Olomouc. Czech. Repub., 2007, 151, 59-64.
29. Jacquemier, J.; Padovani, L.; Rabayrol, L.; Lakhani, S. R.; Penault-Llorca, F.; Denoux, Y.; Fiche, M.; Figueiro, P.; Maisongrosse, V.; Ledoussal, V.; Martinez Penuela, J.; Udvarhely, N.; El Makdissi, G.; Ginestier, C.; Geneix, J.; Charafe-Jauffret, E.; Xerri, L.; Eisinger, F.; Birnbaum, D.; and Sobol, H. Typical medullary breast carcinomas have a basal/ myoepithelial phenotype. J. Pathol., 2005, 207, 260-268.
30. Bertucci, F.; Finetti, P.; Cervera, N.; Charafe-Jauffret, E.; Mamessier, E.; Adelaide, J.; Debono, S.; Houvenaeghel, G.; Maraninchi, D.; Viens, P.; Charpin, C.; Jacquemier, J.; Birnbaum, D. Gene expression profiling shows medullary breast cancer is a subgroup of basal breast cancers. Cancer Res., 2006, 66, 4636-4644.
31. Moreira, J. M.; Ohlsson, G.; Rank, F. E.; Celis, J. E. Downregulation of the tumor suppressor protein 14-3-3 is a sporadic event in cancer of the breast. Mol. Cell. Proteomics, 2005, 4, 555-569.
32. Simon, R.; Nocito, A.; Hubscher, T.; Bucher, C.; Torhorst, J.; Schraml, P.; Bubendorf, L.; Mihatsch, M. M.; Moch, H.; Wilber, K.; Schotzau, A.; Kononen, J.; Sauter, G. Patterns of her-2/neu amplification and overexpression in primary and metastatic breast cancer. J. Natl. Cancer Inst., 2001, 93, 1141-1146.
33. Taranger-Charpin, C.; Andrac-Meyer, L.; Dales, J.P.; Carpentier-Meunier, S.; Andonian, C.; Lavaut, M.N.; Allasia, C.; Bonnier, P. High-throughput quantification of tissue microarrays, identification of candidate target proteins in inflammatory breast cancer. Bull. Acad. Natl. Med., 2007, 191, 361-74.
34. Van den Eynden, G.G.; Van der Auwera, I.; Van Laere, S.; Colpaert, C. G.; van Dam, P.; Merajver, S.; Kleer, C. G.; Harris, A. L.; Van Marck, E. A.; Dirix, L.Y.; Vermeulen, P.B.Validation of a tissue microarray to study differential protein expression in inflammatory and non-inflammatory breast cancer. Breast Cancer Res. Treat., 2004, 85, 13-22.
35. Charafe-Jauffret, E.; Tarpin, C.; Bardou, V. J.; Bertucci, F.; Ginestier, C.; Braud, A. C.; Puig, B.; Geneix, J.; Hassoun, J.; Birnbaum, D.; Jacquemier, J.; Viens, P. Immunophenotypic analysis of inflammatory breast cancers, identification of an 'inflammatory signature'. J. Pathol., 2004, 202, 265-273.
36. Ben Hamida, A.; Labidi, I.S.; Mrad, K.; Charafe-Jauffret, E.; Ben Arab, S.; Esterni, B.; Xerri, L.; Viens, P.; Bertucci, F.; Birnbaum, D.; Jacquemier, J. Markers of subtypes in inflammatory breast cancer studied by immunohistochemistry: prominent expression of Pcadherin. BMC Cancer, 2008, 29, 28.
37. Sorlie, T.; Perou, C. M.; Tibshirani, R.; Aas, T.; Geisler, S.; Johnsen, H.; Hastie, T.; Eisen, M. B.; van de Rijn, M.; Jeffrey, S. S.; Thorsen, T.; Quist, H.; Matese, J. C.; Brown, P. O.; Botstein, D.; Eystein Lonning, P.; Borresen-Dale, A. L. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad. Sci. USA, 2001, 98, 10869-10874.
38. Sorlie, T.; Tibshirani, R.; Parker, J.; Hastie, T.; Marron, J. S.; Nobel, A.; Deng, S.; Johnsen, H.; Pesich, R.; Geisler, S.; Demeter, J.; Perou, C. M.; Lonning, P. E.; Brown, P. O.; Borresen-Dale, A. L.; Botstein, D. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc. Natl. Acad. Sci. USA, 2003, 100, 8418-8423.
39. Sotiriou, C.; Neo, S. Y.; McShane, L. M.; Korn, E. L.; Long, P. M.; Jazaeri, A.; Martiat, P.; Fox, S. B.; Harris, A. L.; Liu, E. T. Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Proc. Natl. Acad. Sci. USA, 2003, 100, 10393-10398.
40. Korsching, E.; Packeisen, J.; Agelopoulos, K.; Eisenacher, M.; Voss, R.; Isola, J.; van Diest, P. J.; Brandt, B.; Boecker, W.; Buerger, H. Cytogenetic alterations and cytokeratin expression patterns in breast cancer: integrating a new model of breast differentiation into cytogenetic pathways of breast carcinogenesis. Lab. Investig., 2002, 82, 1525-1533.
41. Callagy, G.; Cattaneo, E.; Daigo, Y.; Happerfield, L.; Bobrow, L. G.; Pharoah, P. D.; Caldas, C. Molecular classification of breast carcinomas using tissue microarrays. Diagn. Mol. Pathol., 2003, 12, 27-34.
42. Zhang, D. H.; Salto-Tellez, M.; Chiu, L. L.; Shen, L.; Koay, E. S. Tissue microarray study for classification of breast tumors. Life Sci., 2003, 73, 3189-3199.
43. Jacquemier, J.; Ginestier, C.; Rougemont, J.; Bardou, V. J.; Charafe-Jauffret, E.; Geneix, J.; Adelaide, J.; Koki, A.; Houvenaeghel, G.; Hassoun, J.; Maraninchi, D.; Viens, P.; Birnbaum, D.; Bertucci, F. Protein expression profiling identifies subclasses of breast cancer and predicts prognosis. Cancer Res., 2005, 65, 767-779.
44. Abd El-Rehim, D. M.; Ball, G.; Pinder, S. E.; Rakha, E.; Paish, C.; Robertson, J. F.; Macmillan, D.; Blamey, R. W.; Ellis, I. O. Highthroughput protein expression analysis using tissue microarray technology of a large well-characterised series identifies biologically distinct classes of breast cancer confirming recent cDNA expression analyses. Int. J. Cancer, 2005, 116, 340-350.
45. Makretsov, N. A.; Huntsman, D. G.; Nielsen, T. O.; Yorida, E.; Peacock, M.; Cheang, M. C.; Dunn, S. E.; Hayes, M.; Van De Rijn, M.; Bajdik, C.; Gilks, C. B. Hierarchical clustering analysis of tissue microarray immunostaining data identifies prognostically significant groups of breast carcinoma. Clin. Cancer Res., 2004, 10, 6143-6151.
46. Mulligan, A.M.; Pinnaduwage, D.; Bull, S.B.; O'Malley, F.P.; Andrulis, I.L. Prognostic effect of basal-like breast cancers is time dependent, evidence from tissue microarray studies on a lymph node-negative cohort. Clin. Cancer Res., 2008, 14, 4168-4174.
47. Bhargava, R.; Beriwal, S.; McManus, K.; Dabbs, D.J. CK5 is more sensitive than CK5/6 in identifying the basal-like phenotype of breast carcinoma. Am. J. Clin. Pathol., 2008, 130, 724-730.
48. Nielsen, T. O.; Hsu, F. D.; Jensen, K.; Cheang, M.; Karaca, G.; Hu, Z.; Hernandez-Boussard, T.; Livasy, C.; Cowan, D.; Dressler, L.; Akslen, L. A.; Ragaz, J.; Gown, A. M.; Gilks, C. B.; van de Rijn, M.; Perou, C. M. Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma. Clin. Cancer Res., 2004, 10, 5367-5374.
49. Rakha, E. A.; Putti, T. C.; Abd El-Rehim, D. M.; Paish, C.; Green, A. R.; Powe, D. G.; Lee, A. H.; Robertson, J. F.; Ellis, I. O. Morphological and immunophenotypic analysis of breast carcinomas with basal and myoepithelial differentiation. J. Pathol., 2006, 208, 495-506.
50. Harigopal, M.; Heymann, J.; Ghosh, S.; Anagnostou, V.; Camp, R.L.; Rimm, D.L. Estrogen receptor co-activator (AIB1) protein expression by automated quantitative analysis (AQUA) in a breast cancer tissue microarray and association with patient outcome. Breast Cancer Res. Treat., 2009, 115, 77-85.
51. Rakha, E.A.; Boyce, R.W.; Abd El-Rehim, D.; Kurien, T.; Green, A.R.; Paish, E.C.; Robertson, J.F.; Ellis, I.O. Expression of mucins (MUC1, MUC2, MUC3, MUC4, MUC5AC and MUC6) and their prognostic significance in human breast cancer. Mod. Pathol., 2005, 18, 1295-304.
52. Ristimaki, A.; Sivula, A.; Lundin, J.; Lundin, M.; Salminen, T.; Haglund, C.; Joensuu, H.; Isola, J. Prognostic significance of elevated cyclooxygenase-2 expression in breast cancer. Cancer Res., 2002, 62, 632-635.
53. Poremba, C.; Heine, B.; Diallo, R.; Heinecke, A.; Wai, D.; Schaefer, K. L.; Braun, Y.; Schuck, A.; Lanvers, C.; Bankfalvi, A.; Kneif, S.; Torhorst, J.; Zuber, M.; Kochli, O. R.; Mross, F.; Dieterich, H.; Sauter, G.; Stein, H.; Fogt, F.; Boecker, W. Telomerase as a prognostic marker in breast cancer: high-throughput tissue microarray analysis of hTERT and hTR. J. Pathol., 2002, 198, 181-189.
54. Spizzo, G.; Went, P.; Dirnhofer, S.; Obrist, P.; Simon, R.; Spichtin, H.; Maurer, R.; Metzger, U.; von Castelberg, B.; Bart, R.; Stopatschinskaya, S.; Kochli, O. R.; Haas, P.; Mross, F.; Zuber, M.; Dietrich, H.; Bischoff, S.; Mirlacher, M.; Sauter, G.; Gastl, G. High Ep-CAM expression is associated with poor prognosis in nodepositive breast cancer. Breast Cancer Res. Treat., 2004, 86, 207-213.
55. Brandt, B.; Kemming, D.; Packeisen, J.; Simon, R.; Helms, M.; Feldmann, U.; Matuschek, A.; Kersting, C.; Hinrichs, B.; Bidart, J. M.; Bellet, D.; Bartkowiak, K.; Dankbar, N.; Dittmar, T.; Sauter, G.; Boecker, W.; Buerger, H. Expression of early placenta insulinlike growth factor in breast cancer cells provides an autocrine loop that predominantly enhances invasiveness and motility. Endocr. Relat. Cancer, 2005, 12, 823-837.
56. Ginestier, C.; Bardou, V. J.; Popovici, C.; Charafe-Jauffret, E.; Bertucci, F.; Geneix, J.; Adélaïde, J.; Chaffanet, M.; Hassoun, J.; Viens, P.; Jacquemier, J.; Birnbaum, D. Loss of FHIT protein expression is a marker of adverse evolution in good prognosis localized breast cancer. Int. J. Cancer, 2003, 107, 854-862.
57. Nevalainen, M. T.; Xie, J.; Torhorst, J.; Bubendorf, L.; Haas, P.; Kononen, J.; Sauter, G.; Rui, H. Signal transducer and activator of transcription-5 activation and breast cancer prognosis. J. Clin. Oncol., 2004, 22, 2053-2206.
58. Callagy, G. M.; Pharoah, P. D.; Pinder, S. E.; Hsu, F. D.; Nielsen, T. O.; Ragaz, J.; Ellis, I. O.; Huntsman, D.; Caldas, C. Bcl-2 is a prognostic marker in breast cancer independently of the Nottingham Prognostic Index. Clin. Cancer Res., 2006, 12, 2468-2475.
59. Mehra, R.; Varambally, S.; Ding, L.; Shen, R.; Sabel, M. S.; Ghosh, D.; Chinnaiyan, A. M.; Kleer, C.G. Identification of GATA3 as a breast cancer prognostic marker by global gene expression metaanalysis. Cancer Res., 2005, 65, 11259-11264.
60. Moyano, J. V.; Evans, J. R.; Chen, F.; Lu, M.; Werner, M. E.; Yehiely, F.; Diaz, L. K.; Turbin, D.; Karaca, G.; Wiley, E.; Nielsen, T. O.; Perou, C. M.; Cryns, V. L. B-crystallin is a novel oncoprotein that predicts poor clinical outcome in breast cancer. J. Clin. Investig., 2006, 116, 261-270.
61. van de Rijn, M.; Perou, C. M.; Tibshirani, R.; Haas, P.; Kallioniemi, O.; Kononen, J.; Torhorst, J.; Sauter, G.; Zuber, M.; Kochli, O. R.; Mross, F.; Dieterich, H.; Seitz, R.; Ross, D.; Botstein, D.; Brown, P. Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. Am. J. Pathol., 2002, 161, 1991-1996.
62. Stein, T.; Price, K. N.; Morris, J. S.; Heath, V. J.; Ferrier, R. K.; Bell, A. K.; Pringle, M. A.; Villadsen, R.; Petersen, O. W.; Sauter, G.; Bryson, G.; Mallon, E. A.; Gusterson, B. A. Annexin A8 is upregulated during mouse mammary gland involution and predicts poor survival in breast cancer. Clin. Cancer Res., 2005, 11, 6872-6879.
63. Bertucci, F.; Borie, N.; Ginestier, C.; Groulet, A.; Charafe-Jauffret, E.; Adelaide, J.; Geneix, J.; Bachelart, L.; Finetti, P.; Koki, A.; Hermitte, F.; Hassoun, J.; Debono, S.; Viens, P.; Fert, V.; Jacquemier, J.; Birnbaum, D. Identification and validation of an ERBB2 gene expression signature in breast cancers. Oncogene, 2004, 23, 2564-2575.
64. Jacquemier, J.; Ginestier, C.; Rougemont, J.; Bardou, V. J.; Charafe-Jauffret, E.; Geneix, J.; Adelaide, J.; Koki, A.; Houvenaeghel, G.; Hassoun, J.; Maraninchi, D.; Viens, P.; Birnbaum, D.; Bertucci, F. Protein expression profiling identifies subclasses of breast cancer and predicts prognosis. Cancer Res., 2005, 65, 767-779.
65. Linke, S. P.; Bremer, T. M.; Herold, C. D.; Sauter, G.; Diamond, C. A multimarker model to predict outcome in tamoxifen treated breast cancer patients. Clin. Cancer Res., 2006, 12, 1175-1183.
66. Simon, R.; Panussis, S.; Maurer, R.; Spichtin, H.; Glatz, K.; Tapia, C.; Mirlacher, M.; Rufle, A.; Torhorst, J.; Sauter, G. KIT (CD117)-positive breast cancers are infrequent and lack KIT gene mutations. Clin. Cancer Res., 2004, 10, 178-183.
67. Linke, S. P.; Bremer, T. M.; Herold, C. D.; Sauter, G.; Diamond, C. A multimarker model to predict outcome in tamoxifen-treated breast cancer patients. Clin. Cancer Res., 2006, 12, 1175-1183.
68. Rouzier, R.; Perou, C. M.; Symmans, W. F.; Ibrahim, N.; Cristofanilli, M.; Anderson, K.; Hess, K. R.; Stec, J.; Ayers, M.; Wagner, P.; Morandi, P.; Fan, C.; Rabiul, I.; Ross, J. S.; Hortobagyi, G. N.; Pusztai, L. Breast cancer molecular subtypes respond differently to preoperative chemotherapy. Clin. Cancer Res., 2005, 11, 5678-5685.
69. Callesen, A.K.; Vach, W.; Jørgensen, P.E.; Cold, S.; Mogensen, O.; Kruse, T.A.; Jensen, O.N.; Madsen, J.S. Reproducibility of mass spectrometry based protein profiles for diagnosis of breast cancer across clinical studies: a systematic review. J. Proteome Res., 2008, 7, 1395-1402.
70. Umar, A.; Dalebou, J.C.; Timmermans, A.M.; Foekens, J.A.; Luider, T.M. Method optimisation for peptide profiling of microdissected breast car-cinoma tissue by matrix-assisted laser desorption/ionisation-time of flight and matrix-assisted laser desorption/ ionisation-time of flight/time of flight-mass spectrometry. Proteomics, 2005, 5, 2680-2688.
71. Sanders, M.E.; Dias, E.C.; Xu, B.J.; Mobley, J.A.; Billheimer, D.; Roder, H.; Grigorieva, J.; Dowsett, M.; Arteaga, C.L.; Caprioli, R.M. Differentiating pro-teomic biomarkers in breast cancer by laserlaser capture microdissection and MALDI MS. J. Proteome Res., 2008, 7, 1500-1507.
72. Good, D.M.; Thongboonkerd, V.; Novak, J.; Bascands, J.L.; Schanstra, J.P.; Coon, J.J.; Dominiczak, A.; Mischak, H. Body fluid proteomics for biomarker discovery: lessons from the past hold the key to success in the future. J. Proteome Res., 2007, 6, 4549-4555.
73. Hanash, SçM.; Pitteri, S.J.; Faca, V.M. Mining the plasma proteome for cancer biomarkers. Nature, 2008, 452, 571-579.
74. Becker, S.; Cazares, L.H.; Watson, P.; Lynch, H.; Semmes, O.J.; Drake, R.R.; Laronga, C. Surfaced-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) differentiation of serum protein profiles of BRCA-1 and sporadic breast cancer. Ann. Surg. Oncol., 2004, 11, 907-914.
75. Laronga, C.; Becker, S.; Watson, P.; Gregory, B.; Cazares, L.; Lynch, H.; Perry, R.R.; Wright, G.L Jr.; Drake, R.R.; Semmes, O.J. SELDI-TOF serum profiling for prognostic and diagnostic classification of breast cancers. Dis. Markers, 2003, 19, 229-238.
76. Vlahou, A.; Laronga, C.; Wilson, L.; Gregory, B.; Fournier, K.; McGaughey, D.; Perry, R.R.; Wright, G.L. Jr.; Semmes, OJ. A novel approach toward development of a rapid blood test for breast cancer. Clin. Breast Cancer, 2003, 4, 203-209.
77. Belluco, C.; Petricoin, E.F.; Mammano, E.; Facchiano, F.; Ross-Rucker, S.; Nitti, D.; Di, Maggio. C.; Liu, C.; Lise, M.; Liotta, L.A.; Whiteley, G. Serum proteomic analysis identifies a highly sensitive and specific discriminatory pattern in stage 1 breast cancer. Ann. Surg. Oncol., 2007, 14, 2470-2476.
78. Li, J.; Zhang, Z.; Rosenzweig, J.; Wang, Y.Y.; Chan, D.W. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin. Chem., 2002, 48, 1296-1304.
79. Li, J.; Orlandi, R.; White, C.N.; Rosenzweig, J.; Zhao, J.; Seregni, E.; Morelli, D.; Yu, Y.; Meng, X.Y.; Zhang, Z.; Davidson, N.E.; Fung, E.T.; Chan, D.W. Independent validation of candidate breast cancer serum biomarkers identified by mass spectrometry. Clin. Chem., 2005, 51, 2229-2235.
80. Li, J.; Zhang, Z.; Rosenzweig, J.; Wang, Y.Y.; Chan, D.W. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin. Chem., 2002, 48, 1296-1304.
81. Li, J.; Orlandi, R.; White, C.N.; Rosenzweig, J.; Zhao, J.; Seregni, E.; Morelli, D.; Yu, Y.; Meng, X.Y.; Zhang, Z.; Davidson, N.E.; Fung, E.T.; Chan, D.W. Independent validation of candidate breast cancer serum biomarkers identified by mass spectrometry. Clin. Chem., 2005, 51, 2229-2235.
82. Mathelin, C.; Cromer, A.; Wendling, C.; Tomasetto, C.; Rio, M.C. Serum biomarkers for detection of breast cancers: a prospective study. Breast Cancer Res. Treat., 2006, 96, 83-90.
83. van Winden, A.W.; Gast, M.C.; Beijnen, J.H.; Rutgers, E.J.; Grobbee, D.E.; Peeters, P.H.; van Gils, C.H. Validation of previously identified serum biomarkers for breast cancer with SELDI-TOF MS: a case control study. B.M.C. Med. Genomics, 2009, 19, 4.
84. Gonçalves, A.; Esterni, B.; Bertucci, F.; Sauvan, R.; Chabannon, C.; Cubizolles, M.; Bardou, V.J.; Houvenaegel, G.; Jacquemier, J.; Granjeaud, S.; Meng, X.Y.; Fung, E.T.; Birnbaum, D.; Maraninchi, D.; Viens, P.; Borg, J.P. Postoperative serum proteomic profiles may predict metastatic relapse in highrisk primary breast cancer patients receiving adjuvant chemotherapy. Oncogene, 2006, 25, 981-989.
85. Song, J.; Patel, M.; Rosenzweig, C.N.; Chan-Li, Y.; Sokoll, L.J.; Fung, E.T.; Choi-Miura, N.H.; Goggins, M.; Chan, D.W.; Zhang, Z. Quantification of fragments of human serum inter-alpha-trypsin inhibitor heavy chain 4 by a surface-enhanced laser desorption/ionization-based immunoassay. Clin. Chem., 2006, 52, 1045-1053.
86. Villanueva, J.; Shaffer, D.R.; Philip, J.; Chaparro, C.A.; Erdjument-Bromage, H.; Olshen, A.B.; Fleisher, M.; Lilja, H.; Brogi, E.; Boyd, J.; Sanchez-Carbayo, M.; Holland, E.C.; Cordon-Cardo, C.; Scher, H.I.; Tempst, P. Differential exoprotease activities confer tumor-specific serum peptidome patterns. Clin. Invest., 2006, 116, 271-284.
87. Fung, E.T.; Yip, T.T.; Lomas, L.; Wang, Z.; Yip, C.; Meng, X.Y.; Lin, S.; Zhang, F.; Zhang, Z.; Chan, D.W.; Weinberger, S.R. Classification of cancer types by measuring variants of host response proteins using SELDI serum assays. Int. J. Cancer, 2005, 115, 783-789.
88. Shi, Q.; Haris, L.N.; Lu, X.; Li, X.; Hwang, J.; Gentleman, R.; Iglehart, J.D.; Miron, A.; Shi, Q.; Haris, L.N.; Lu, X.; Li, X.; Hwang, J.; Gentleman, R.; Iglehart, J.D.; Miron, A. Declining plasma fibrinogen alpha fragment identifies HER2-positive breast cancer patients and reverts to normal levels after surgery. J. Proteome Res., 2006, 5, 2947-2955.
89. Sauter, E.R.; Zhu, W.; Fan, X.J.; Wassell, R.P.; Chervoneva, I.; Du Bois, G.C.; Sauter, E.R.; Zhu, W.; Fan, XJ.; Wassell, R.P.; Chervoneva, I.; Du, Bois. G.C. Proteomic analysis of nipple aspirate fluid to detect biologic markers of breast cancer. Br. J. Cancer, 2002, 86, 1440-1443.
90. Sauter, E.R.; Shan, S.; Hewett, J.E.; Speckman, P.; Du Bois, G.C. Proteomic analysis of nipple aspirate fluid using SELDI-TOF-MS. Int. J. Cancer, 2005, 114, 791-796.
91. Paweletz, C.P.; Trock, B.; Pennanen, M.; Tsangaris, T.; Magnant, C.; Liotta, L.A.; Petricoin, E.F. 3rd. Proteomic patterns of nipple aspirate fluids obtained by SELDI-TOF: potential for new biomarkers to aid in the diagnosis of breast cancer. Dis. Markers, 2001, 17, 301-307.
92. Streckfus, C.F.; Bigler, L.R.; Zwick, M. The use of surfaceenhanced laser desorption/ionization time-of-flight mass spectrometry to detect putative breast cancer markers in saliva: a feasibility study. J. Oral Pathol. Med., 2006, 35, 292-300.
93. Gonçalves, A.; Esterni, B.; Bertucci, F.; Sauvan, R.; Chabannon, C.; Cubizolles, M.; Bardou, V.J.; Houvenaegel, G.; Jacquemier, J.; Granjeaud, S.; Meng, X.Y.; Fung, E.T.; Birnbaum, D.; Maraninchi, D.; Viens, P.; Borg, J.P. Postoperative serum proteomic profiles may predict metastatic relapse in highrisk primary breast cancer patients receiving adjuvant chemotherapy. Oncogene, 2006, 25, 981-989.
94. Ricolleau, G.; Charbonnel, C.; Lodé, L.; Loussouarn, D.; Joalland, MP.; Bogumil, R.; Jourdain, S.; Minvielle, S.; Campone, M.; Déporte-Fety, R.; Campion, L.; Jézéquel, P. Surfaceenhanced laser desorption/ionization time of flight mass spectrometry protein profiling identifies ubiquitin and ferritin light chain as prognostic biomarkers in node-negative breast cancer tumors. Proteomics, 2006, 6, 1963-1975.
95. Gonçalves, A.; Charafe-Jauffret, E.; Bertucci, F.; Audebert, S.; Toiron, Y.; Esterni, B.; Monville, F.; Tarpin, C.; Jacquemier, J.; Houvenaeghel, G.; Chabannon, C.; Extra, J.M.; Viens, P.; Borg, J.P.; Birnbaum, D. Protein profiling of human breast tumor cells identifies novel biomarkers associated with molecular subtypes. Mol. Cell Proteomics, 2008, 7, 1420-1433.
96. Sanders, M.E.; Dias, E.C.; Xu, B.J.; Mobley, J.A; Billheimer, D.; Roder, H.; Grigorieva, J.; Dowsett, M.; Arteaga, C.L.; Caprioli, R.M. Differentiating proteomic biomarkers in breast cancer by laser capture microdissection and MALDI MS. J. Proteome Res., 2008, 7, 1500-1507.
97. Leong, S.; Christopherson, R.I.; Baxter, R.C. Profiling of apoptotic changes in human breast cancer cells using SELDITOF mass spectrometry. Cell Physiol. Biochem., 2007, 20, 579-590.
98. Dekker, L.J.; Boogerd, W.; Stockhammer, G.; Dalebout, J.C.; Siccama, I.; Zheng, P.; Bonfrer, J.M.; Verschuuren, J.J.; Jenster, G.; Verbeek, M.M.; Luider, T.M.; Smitt, P.A. MALDITOF mass spectrometry analysis of cerebrospinal fluid tryptic peptide profilesto diagnose leptomeningeal metastases in patients with breast cancer. Mol. Cell Proteomics, 2005, 4, 1341-1349.
99. Römpp, A.; Dekker, L.; Taban, I.; Jenster, G.; Boogerd, W.; Bonfrer, H.; Spengler, B.; Heeren, R.; Smitt, P.S.; Luider, T.M. Identification of leptomeningeal metastasis-related proteins in cerebrospinal fluid of patients with breast cancer by a combination of MALDI-TOF, MALDI-FTICR and nanoLC-FTICR MS. Proteomics, 2007, 7, 474-481.
100. Brozkova, K.; Budinska, E.; Bouchal, P.; Hernychova, L.; Knoflickova, D.; Valik, D.; Vyzula, R.; Vojtesek, B.; Nenutil, R. Surfaceenhancedlaser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression. Breast Cancer Res., 2008, 10, 48.
101. Troester, M. A.; Hoadley, K. A.; Sorlie, T.; Herbert, B. S.; Borresen-Dale, A. L.; Lonning, P. E.; Shay, J. W.; Kaufmann, W. K.; Perou, C. M. Cell-type-specific responses to chemotherapeutics in breast cancer. Cancer Res., 2004, 64, 4218-4226.
102. Bertucci, F.; Finetti, P.; Rougemont, J.; Charafe-Jauffret, E.; Cervera, N.; Tarpin, C.; Nguyen, C.; Xerri, L.; Houlgatte, R.; Jacquemier, J.; Viens, P.; Birnbaum, D. Gene expression profiling identifies molecular subtypes of inflammatory breast cancer. Cancer Res., 2005, 65, 2170-2178.
103. Dowling, P.; Maurya, P.; Meleady, P.; Glynn, S.A.; Dowd, A.J.; Henry, M.; Clynes, M. Purification and identification of a 7.6-kDa protein in media conditioned by superinvasive cancer cells. Anticancer Res., 2007, 27, 1309-1317.
104. Leong, S.; Christopherson, R.I.; Baxter, R.C. Profiling of apoptotic changes in human breast cancer cells using SELDI TOF mass spectrometry. Cell Physiol. Biochem., 2007, 20, 579-590.
105. Heike, Y.; Hosokawa, M.; Osumi, S.; Fujii, D.; Aogi, K.; Takigawa, N.; Ida, M.; Tajiri, H.; Eguchi, K.; Shiwa, M.; Wakatabe, R.; Arikuni, H.; Takaue, Y.; Takashima, S. Identification of serum proteins related to adverse effects induced by docetaxel infusion from protein expression profiles of serum using SELDI ProteinChip system. Anticancer Res., 2005, 25, 1197-1203.
106. Pusztai, L.; Gregory, B.W.; Baggerly, K.A.; Peng, B.; Koomen, J.; Kuerer, H.M.; Esteva, F.J.; Symmans, W.F.; Wagner, P.; Hortobagyi, G.N.; Laronga, C.; Semmes, O.J.; Wright, G.L Jr; Drake RR., Vlahou, A. Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma. Anticancer Res., 2005, 25, 1197-1203.
107. Haris, L.; Fritsche, H.; Mannel, R.; Norton, L.; Ravdin, P.; Taube, S.; Somerfield, M.R.; Hayes, D.F.; Bast, R.C. Jr. ASCO 2007 update of recommendations for the use of tumor markers in breast cancer. J. Clin. Oncol., 2007, 25, 1-26.
108. Baskin, Y. The Proteomic Methods in Describing the Breast Cancer Markers Lecture. IInd Multidisciplinary Cancer Research Symposium, with International Participations. February 24-27, 2009, Bursa, Turkey.
109. Baskin, Y. The Proteomic Methods as A New Approach in Describing the Cancer Markers Clinical Biochemistry Specialists Association 5th National Congress, Poster Presentation, 11-15 January 2009, Bursa, Turkey.