How can proteomics reach cancer biomarkers?

Current Proteomics

Volumn 10, Issue 2, 2013, Pages 136-149

  Panis, Carolina ^a   Pizzatti, Luciana ^a   Abdelhay, Eliana ^a  

^a INSTITUTO NACIONAL DE CÂNCER   (Brazil)

Author keywords

Biomarkers; Cancer; Design of studies; Mass spectrometry; Proteomics; Tumor heterogeneity

Indexed keywords

ADENOSINE TRIPHOSPHATASE ASN1; ALPHA 1 ANTITRYPSIN; ALPHA TROPOMYOSIN; CA 15-3 ANTIGEN; CALRETICULIN; CELLULAR RETINOIC ACID BINDING PROTEIN 2; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; GELSOLIN; GLYCOXALASE 1; HEAT SHOCK PROTEIN 70; ISOCITRATE DEHYDROGENASE 2; KERATIN; LAMIN B1; LUMICAN; MACROPHAGE CAPPING PROTEIN; METHYLTHIORIBOSE 1 PHOSPHATE ISOMERASE; MISMATCH REPAIR PROTEIN PMS2; PEPTIDYLPROLYL ISOMERASE; PHOSPHOMANNOMUTASE 2; PROTEIN 14 3 3; PROTEIN ANX3; PROTEIN GP2; PROTEIN GPDA; PROTEIN MFAP4; PROTEIN SEC14L2; TRANSCRIPTION FACTOR SALL4; TUMOR MARKER; TYPE II CYTOSKELETAL 8 PROTEIN; UNCLASSIFIED DRUG; UNINDEXED DRUG;

CANCER PROGNOSIS; CANCER RISK; COMPARATIVE PROTEOMICS; GEL ELECTROPHORESIS; GENETIC ANALYSIS; GENETIC PREDISPOSITION; GENETIC RISK; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; LABEL FREE PROTEOMICS; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN POLYMORPHISM; PROTEIN PROCESSING; PROTEOMICS; QUANTITATIVE PROTEOMICS; REVIEW; RISK ASSESSMENT; SHOTGUN PROTEOMICS; SINGLE NUCLEOTIDE POLYMORPHISM; TANDEM MASS SPECTROMETRY; VALIDATION STUDY;

EID: 84882736607     PISSN: 15701646     EISSN: None     Source Type: Journal    
DOI: 10.2174/1570164611310020006     Document Type: Review

References (107)

1. Li, G.; Xiao, Z.; Liu, J.; Li, C.; Li, F.; Chen, Z. Cancer: a proteomic disease. Sci China Life Sci, 2011, 54(5),403-8.
2. Zeng, Y.; Lu, Y.; Zhu, M.; Oncology. 2nd ed. Beijing: People Health Publishing House, 2003. 11-30.
3. Khleif, S.N.; Doroshow, J.H.; Hait, W.N.; AACR-FDA-NCI Cancer Biomarkers CollaborativeAACR-FDA-NCI Cancer Biomarkers Collaborative consensus report: advancing the use of biomarkers in cancer drug development. Clin Cancer Res, 2010, 1;16(13), 3299-318.
4. Ideker, T.; Thorsson, V.; Ranish J.A.; Christmas, R.; Buhler, J.; Eng, J.K.; Bumgarner, R.; Goodlett, D.R.; Aebersold, R.; Hood, L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science, 2001, 292: 929-934.
5. Tian, Q,; Stepaniants, S.B.; Mao, M.; Weng, L.; Feetham, M.C.; Doyle, M.J.; Yi, E.C.; Dai, H.; Thorsson, V.; Eng, J.; Goodlett, D.; Berger, J.P.; Gunter, B.; Linseley, P,S.; Stoughton, R.B.; Aebersold, R.; Collins, S.J.; Hanlon, W.A.; Hood, L.E. Integrated ge-nomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics, 2004, 3: 960-969.
6. Wilkins, M.R.; Sanchez, J.C.; Gooley, A.A.; Appel, R.D.; Humphery-Smith, I.; Hochstrasser, D.F.; Williams, K.L. Progress with proteome projects: Why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 1996, 13: 19-50.
7. Hwee, Tong. Tan.; Yie, Hou. Lee.; Maxey C.M. Chung. Cancer Proteomics. Mass Spectrometry Reviews, 2012, 31, 583-605.
8. Issaq, H.J.; Fox, S.D.; Chan, K. C; Veenstra T. D.; Global proteomics and metabolomics in cancer biomarker discovery. 2011 34(24):3484-92.
9. Azad, N.S.; Rasool, N.; Annunziata, C.M.; Minasian, L.; Whiteley, G.; Kohn, EC. Proteomics in clinical trials and practice: Present uses and future promise. Mol Cell Proteomics, 2006, 5,1819-1829.
10. MacNeil, J. S., Better Biomarkers for the Diagnostics Labyrinth Genome Technol. 2004, 24-33.
11. Li, J.; Kelm, K.B.; Tezak, Z. Regulatory perspective on translating proteomic biomarkers to clinical diagnostics. Journal of Pro-teomics, 2011, 74, 2682-2690.
12. Pepe, M. S., Etzioni, R., Feng, Z., Potter, J. D., Thompson, M. L., Thornquist, M., Winget, M., Yasui, Y., J. Natl. Cancer Inst. 2001, 93, 1054-1061.
13. Chen, E.I and Yates, J.R. Cancer Proteomics by Quantitative Shotgun Proteomics Mol Oncol. 2007, 1(2): 144-159.
14. Zhang, H.; Hu, H.; Deng, C.; Chun, Y.; Zhou, S.; Huang, F.; Zhou, Q. Integrative System Biology Strategies for Disease Biomarker Discovery. Combinatorial Chemistry & High Throughput Screening, 2012, 15, 286-298.
15. Huang, H.L.; Stasyk, T.; Morandell, S.; Dieplinger, H.; Falkensammer, G.; Griesmacher, A.; Mogg, M.; Schreiber, M.; Feuerstein, I.; Huck, C.W.; Stecher, G.; Bonn, G.K.; Huber, L.A. Biomarker discovery in breast cancer serum using 2-D differential gel electrophoresis/ MALDI-TOF/TOF and data validation by routine clinical assays. Electrophoresis. 2006, 27(8),1641-50.
16. Filiou M.D.; Martins-de-Souza, D; Guest, P.C.; Bahn, S.;Turck, C.W. To label or not to label: Applications of quantitative proteomics in neuroscience research. Proteomics 2012, 12, 7367-73467.
17. Washburn, M.P.; Wolters, D.; Yates JR 3rd.Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 2001, 19(3), 242-7.
18. Qi Wua. B.; Huiming Yuana.; Lihua Zhanga.;Yukui Zhanga. Recent advances on multidimensional liquid chromatography-mass spec-trometry for proteomics: From qualitative to quantitative analy-sis-A review. Analytica Chimica Acta.2012, 731, 1-10.
19. Sandra, K.; Moshir, M.; D'Hondt, F.; Tuytten, R.; Verleysen, K.; Kas, K.; François, I.; Sandra, P. Highiy efficient peptide separations in proteomics: part 2: Bi - and multidimensional liquid-based separation techniques, J. Chromatogr. B, 877, 2009 1019-1039.
20. Qian, W.J.; Jacobs, J.M.; Liu, T.; Camp II D G.;Smith R D. Advances and Challenges in Liquid Chromatography-Mass Spec-trometry-based Proteomics Profiling for Clinical Applications. Mol Cell Proteomics, 2006 5, 1727-1744.
21. Boersema, P.J.; Mohammed, S.; Heck, A.J.R. Hydrophilic interaction liquid chromatography (HILIC) in proteomics. Anal. Bioanal. Chem. 391, 2008, 151-159.
22. van de Meent, M.H.; Eeltink, S.; de Jong, G.J.; Potential of poly(styrene-co divinylbenzene) monolithic columns for the LC-MS analysis of protein digests. Anal Bioanal Chem. 2011, 399(5),1845-52.
23. Pizzatti, L.; Panis, C.; Lemos, G.; Rocha, M.; Cecchini, R.; Souza, G.H.; Abdelhay, E. Label-free MSE proteomic analysis of chronic myeloid leukemia bone marrow plasma: disclosing new insights from therapy resistance. Proteomics. 2012, 12(17),2618-3.1
24. Panis, C.;Pizzatti, L.; Herrera, A.C.; Cecchini, R.; Abdelhay, E. Putative circulating markers of the early and advanced stages of breast cancer identified by high-resolution label-free proteomics. Cancer Lett. 2013, 1;330(1) 57-66.
25. Weinberg, R. A. One renegade cell: How cancer begins. Science Masters Series, 1999, 170 pages.
26. Weinberg, R. A. The Biology of Cancer. Garland Sciences, 2006, 864 pages.
27. Klein, G. and Klein, E. Conversion of solid neoplasms into ascites tumors. Ann N Y Acad Sci, 1956, 63(5): 640-661.
28. Makino, S. Further evidence favoring the concept of the stem cell in ascites tumors of rat. Ann N Y Acad Sci, 1956, 63(5): 818-830.
29. Dexter, D. L.; Kowalski, H. M.; Blazar, B. A.; Fligiel, Z.; Vogel, R. and Heppner, G. H. Heterogeneity of tumor cells from a single mammary tumor. Cancer Res, 1978, 38: 3174-3181.
30. Dexter, D. L.; Spremulli, E. N.; Fligiel, Z.; Barbosa, J. A.; Vogel, R.; VanVoorhees, A. and Calabresi, P. Heterogeneity of cancer cells from a single human colon carcinoma. Am J Med, 1981, 71:949-956.
31. Spremulli, E. N. and Dexter D. L. Human tumor cell heterogeneity and metastasis. J Clin Oncol, 1983, 8:496-509.
32. Dexter, D. L and Leith J. T. Tumor heterogeneity and drug resistance. J Clin Oncol, 1986, 4(2): 244-257.
33. Li, J.; Wang, K.; Jensen, T. D.; Li, S.; Bolund, L. and Wiuf, C. Tumor heterogeneity in neoplasms of breast, colon, and skin. BMC Res Notes, 2010, 3: 321-330.
34. Almendro, V.; Marusyk, A. and Polyak, K. Cellular heterogeneity and molecular evolution in cancer. Ann Rev Pathol Mech Dis, 2013, 8: 277-302.
35. Diaz-Cano, S. J. Tumor heterogeneity: mechanisms and bases for a reliable application of molecular marker design. Int J Mol Sci, 2012, 13: 1951-2011.
36. Rudnick, J. A. and Kuperwasser, C. Stromal biomarkers in breast cancer development and progression. Clin Exp Metastasis, 2012, 29(7): 663-672.
37. Oqino, S.; Fuchs, C. S. and Giovannucci, E. How many molecular subtypes? Implications of the unique tumor principle in personalized medicine. Expert Rev Mol Diagn, 2012, 12(6): 621-628.
38. Hanahan, D. and Weinberg, R. A. Hallmarks of cancer: The next generation. Cell, 2011, 144: 646-674.
39. Guo, Y.; Yang, Y.; Zhou, J.; Czajkowski, D. M.; Liu, B. and Shao, Z. Microdissection of spatially identified single nuclei in a solid tumor for single cell whole genome sequencing. Biotech Rapid Dispatches, 2012, doi: 10.2144/000113860.
40. Tchou, J. and Conejo-Garcia, J. Targeting the tumor stroma as a novel treatment strategy for breast câncer: shifting from the neo-plastic cell-centric to a stroma paradigm. Adv Pharmacol, 2012, 65: 45-61.
41. Fidler, I. J. and Hart, I. R. Biological and experimental consequences of the zonal composition of solid tumors. Cancer Res, 1981, 41: 3266-3267.
42. Fend, F. and Raffeld, M. Laser capture microdissection in pathology. J Clin Pathol, 2000, 53(9): 666-672.
43. Suarez-Qian, C. A.; Goldstein, S. R.; Pohida, T.; Smith, P. D.; Peterson, J. I., Wellner; E.; Ghany, M. and Bonner, R. F. Laser capture microdissection of single cells from complex tissue. Biotech-niques, 1999, 26(2): 328-335.
44. Esposito, G. Complementary techniques: laser-capture microdis-section increasing specificity of gene expression profiling of cancer specimens. Adv Exp Med Biol, 2007, 593: 54-65.
45. Silvestri, A.; Colombatti, A.; Calvert, V. S.; Deng, J.; Mammano, E.; Belluco, C.; De Marchi, F.; Nitti, D.; Liotta, L. A.; Petricoin, E. F. and Pierobon, M. Protein pathway biomarker analysis of human cancer reveals requirement for upfront cellular-enrichment processing. Lab Invest, 2010, 90: 787-796.
46. Hill, J. J.; Tremblay, T. L.; Pen, A.; Li, J.; Robotham, A. C.; Len-ferink, A. E.; Wang, E.; O'Connor-McCourt, M. and Kelly, J. F. Identification of vascular breast tumor markers by laser capture mi-crodissection and label-free LC-MS. J Proteome Res, 2011, 10(5): 2479-2493.
47. Bai, H.; Wang, Z.; Wang, Y.; Zhuo, M.; Zhou, Q.; Duan, J.; Yang, L.; Wu, M.; An, T.; Zhao, J. and Wang J. Detection and clinical significance in intratumoral EGFR mutational heterogeneity in Chinese patients with advanced non-small cell lung cancer. PLoS One, 2013, 8(2): e54170.
48. Webster, J. D.; Simpson, E. R.; Michalowski, A. M.; Hoover, S. B. and Simpson, R. M. Quantifying histological features of cancer biospecimens for biobanking quality assurance using automated morphometric pattern recognition image analysis algorithms. J Biomol Techniques, 2011, 22:108-118.
49. Gerlinger, M.; Rowan, A. J.; Horswell, S.; Larkin, J.; Endesfelder, D.; Gronroos, E.; Martinez, P.; Matthews, N.; Stewart, A.; Tarpey, P.; Varela, I.; Philimore, B.; Begum, S.; McDonald, N. Q.; Butler, A.; Jones, D.; Raine, K.; Latimer, C.; Santos, C. R.; Nohadani, M.; Eklund, A. C.; Spencer-Dene, B.; Clark, G.; Pickering, L., Stamp, G.; Gore, M.; Szallasi, Z.; Downward, J.; Futreal, A. and Swanton, C. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. The New England J Med, 2012, 366(10): 883-893.
50. Chapman, J. A.; Wolman, E.; Wolman, S. R.; Remvikos, Y.; Shackney, S.; Axelrod, D. E.; Baisch, H.; Christensen, I. J.; White, R. A.; Liebovitch, L. S.; Moore, D. H.; Waldman, F. M.; Cornelisse, C. J. and Shankey T. V. Assessing genetic markers of tumour progression in the context of intratumor heterogeneity. Cy-tometry, 1998, 31(1): 67-73.
51. McShane, L. M.; Altman, D. G.; Sauerbrei, W.; Taube, S. E.; Gion, M. and Clark, G. M. REporting recommendations for tumor MARKer prognostic studies (REMARK). British J Cancer, 2005, 93: 387-391.
52. Gosho, M.; Nagashima, K. and Sato, Y. Study designs and statistical analysis for biomarker research. Sensors, 2012, 12: 8966-8986.
53. Kim, S. R. and Paik, S. Genomics of adjuvant therapy for breast cancer. Cancer J, 2011, 17(6): 500-504.
54. Harris, L.; Fritsche, H.; Mennel, R.; Norton, L.; Ravdin, P.; Taube, S.; Somerfield, M. R.; Hayes, D. F. and Bast Jr, R. C. American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer. J Clin Oncol, 2007, 25(33): 5287-5312.
55. Kurien, B. T.; Dorri, Y.; Dillon, S.; Dsouza, A. and Scofield, R. H. An overview of western blotting for determining antibody specificities for immunohistochemistry. Methods Mol Biol, 2011, 717:55-67.
56. Kurien, B. T. and Scofield, R. H. Western blotting. Methods, 2006, 38(4): 283-293.
57. Gallagher, S. R. One-dimensional electrophoresis using nonde-naturing conditions. Curr Protocols Protein Science, 2000, 10.3.1-10.3.11.
58. Bolt, M. W. and Mahoney, P. A. High-efficiency blotting of proteins of diverse sizes following sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Anal Biochem, 1997, 247: 185-192.
59. Signore, M. and Reeder K. A. Antibody validation by western blotting. Methods Mol Biol, 2012, 823: 139-155.
60. Alegria-Schaffer, A.; Lodge, A. and Vattem, K. Performing and optimizing western blots with an emphasis on chemiluminescent detection. Methods Enzymol, 2009, 463: 573-599.
61. Kondo, T. Tissue proteomics for cancer biomarker development: laser microdissection and 2D-DIGE. BMB Rep, 2008, 41(9): 626-634.
62. Hammond, M. E. H.; Hayes, D. F.; Dowsett, M.; Allred, D. C; Hagerty, K. L.; Badve, S,; Fitzgibbons, P. L.; Francis, G.; Goldstein, N. S.; Hayes, M.; Hicks, D. G.; Lester, S.; Love, R.; Mangu, P. B.; McShane, L.; Miller, K.; Osborne, C. K.; Paik, S.; Perlmut-ter, J.; Rhodes, A.; Sasano, H.; Schwartz, J. N.; Sweep, F. C. G.; Taube, S.; Torlakovic, E. E.; Valenstein, P.; Viale, G.; Visscher, D.; Wheeler, T.; Williams, R. B.; Wittliff, J. L. and Wolff A. C. American Society of Clinical Oncology/College of American Pa-thologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer. Arch Pathol Lab Med, 2010,134: 907-922.
63. Maclntyre, N. Unmasking antigens for immunohistochemistry. Br J Med Sci, 2001, 58(3): 190-196.
64. Syrbu, S. I. and Cohen, M. B. An enhanced antigen-retrieval protocol for immunohistochemical staining of formalin-fixed, paraffin-embedded tissues. Methods Mol Biol, 2011, 717: 101-110.
65. Leong, T. Y. and Leong, A. S. How does antigen retrieval work? Adv Anat Pathol, 2007, 14(2): 129-131.
66. AlKuraya, K.; Simon, R. and Sauter, G. Tissue microarrays for high-throughput molecular pathology. Ann Saudi Med, 2004, 24(3): 169-174.
67. Hewitt, S. M. Tissue microarrays as a tool in the discovery and validation of predictive biomarkers. Methods Mol Biol, 2012, 823: 201-214.
68. Axelrod, D. E.; Miller, N. and Chapman, J. A. W. Avoiding pitfalls in the statistical analysis of heterogeneous tumors. Biomed Informatics Insights, 2009,2: 11-18.
69. Camp, R. L.; Neumeister, V. and Rimm D. L. A decade of tissue microarrays: progress in the discovery and validation of cancer biomarkers. J Clin Oncol, 2008, 26(34): 5630-5637.
70. Boja, E.; Rivers R.; Kinsinger, C; Mesri, M.; Hiltke,T.; Rahbar, A.; Rodriguez, H. Restructuring proteomics through verification. Biomark Med. 2010, 4(6), 799-803.
71. Bozovic, A.; Kulasingam, V.Quantitative mass spectrometry-based assay development and validation: From small molecules to proteins. Clin Biochem. 2012 Oct 3. pii:S0009-9120(12)00554-1.
72. Lemoine, J.; Fortin, T.; Salvador, A.; Jaffuel, A.; Charrier, JP.; Cho-quet-Kastylevsky, G. The current status of clinical proteomics and the use of MRM and MRM3 for biomarker validation.Expert Rev. Mol. Diagn. 2012,12(4), 333-342.
73. Zhong D, Chen X, Gu J, Li X, Guo J. Applications of liquid chro-matography-tandem mass spectrometry in drug and biomedical analyses. Clin. Chim. Ada, 2001, 313(1-2), 147-150.
74. Carrascal M, Schneider K, Calaf RE et al. Quantitative electrospray LC-MS and LC-MS/MS in biomedicine. J. Pharm. Biomed. Anal. 1998, 17(6-7) 1129-1138.
75. Dinicola, S.; D'Anselmi, F.; Pasqualato, A.; Proietti, S.; Lisi, E.; Alessandra Cucina, A.; Bizzarri, M. A Systems Biology Approach to Cancer:Fractals, Attractors, and Nonlinear Dynamics. OMICS A Journal of Integrative Biology, 2011, 15, 3, 93-104.
76. Davalieva, K.; Kiprijanovska, S.; Broussard, C; Petrusevska, G. and Efremov, G. D. Proteomic analysis of infiltrating ductal carcinoma tissues by coupled 2-D DIGE/MS/MS analysis. Molec Biol, 2012, 46(3): 469-480.
77. Lopez-Árias, E.; Aguilar-Lemarroy, A.; Jave-Suarez L. F.; Morgan-Villela, G.; Mariscal-Ramirez, I.; Martínez-Velazquez, M.; Alvarez, A. H.; Gutiérrez-Ortega, A. and Hernández-Guitiérrez, R. Alpha 1-antitrypsin: a novel tumor-associated antigen identified in patients with early-stage breast cancer. Electrophoresis, 2012, 33(14): 2130-2137.
78. Muraoka, S.; Kume, H.; Watanabe, S.; Adachi, J.; Kuwano, M.; Sato, M.; Kawasaki, N.; Kodera, Y.; Ishitobi, M.; Inaji, H.; Miyamoto, Y.; Kato, K. and Tomonaga, T. Strategy for SRM-based verification of biomarker candidates discovered by iTRAQ method in limited breast cancer tissue samples. J Proteome Res, 2012, 11(8): 4201-4210.
79. Fonseca-Sánchez, M. A.; Rodríguez Cuevas, S.; Mendoza-Hernández, G.; Bautista-Piña, V.; Arechaga Ocampo, E.; Hidalgo Miranda, A.; Quintanar Jurado, V.; Marchat L. A.; Alvarez-Sánchez, E.; Pérez-Plasencia, C. and López-Camarillo, C. Breast cancer proteomics reveals a positive correlation between glyox-alase 1 expression and high tumor grade. Int J Oncol, 2012, 41(2): 670-680.
80. Descotes, F.; Jézéquel, P.; Spyratos, F.; Campion, L.; Grenot, C.; Lerebours, F.; Campone, M.; Guérin-Charbonnel, C.; Lanoe, D.; Adams, M.; André, J.; Carlioz, A.; Martin, P. M.; Chassevent, A.; Jourdan, M. L.; Guette, C.; Zanella-Cleon, I. and Ricolleau, G. Identification of potential prognostic biomarkers for node-negative breast tumors by proteomic analysis: a multicentric 2004 national PHRC study. Int J Oncol, 2012, 41(1): 92-104.
81. Fan, N. J.; Gao, C. F.; Zhao, G.; Wang, X. L. and Liu, Q. Y. Serum peptidome patterns of breast cancer based on magnetic bead separation and mass spectrometry analysis. Diagn Pathol, 2012, 7:45.
82. Hodginson, V. C.; ElFadl, D.; Agarwal, V.; Garimella, V.; Russel, C.; Long, E. D.; Fox, J. N.; McManus, P. L.; Mahapatra, T. K.; Kneeshaw, P. J.; Drew, P. J.; Lind, M. J. and Cawkwell, L. Pro-teomic identification of predictive biomarkers of resistance to neoadjuvant chemotherapy in luminal breast cancer: a possible role for 14-3-3 theta/tau and tBID? J Proteomics, 2012, 75(4): 1276-1283.
83. Geiger, T.; Madden, S. F.; Gallagher W. M.; Cox, J. and Mann, M. Proteomic portrait of human breast cancer progression identifies novel prognostic markers. Cancer Res, 2012, 72(9): 2428-2439.
84. Lee, H. H.; Lim, C. A.; Cheong, Y. T.; Singh M and Gam, L H. Comparison of protein expression profiles of different stages of lymph nodes metastasis in breast cancer. Int J Biol Sci, 2012, 8:353-363.
85. Cawthorn, T. R.; Moreno, J. C.; Dharsee, M.; Tran-Thanh, D.; Ackloo, S.; Zhu, P. H.; Sardana, G.; Chen, J.; Kupchak, P.; Jacks, L. M.; Miller, N. A.; Youngson, B. J.; Iakovlev, V.; Guidos, C. J.; Vallis, K. A.; Evans, K. E.; McCready, D.; Leong, W. L. and Done, S. J. Proteomic analyses reveal high expression of decorin and en-doplasmin (HSP90B1) are associated with breast cancer metastasis and decreased survival. PLoS One, 2012, 7(2): e30992.
86. Gormley, M.; Tchafa, A.; Meng, R.; Zhong, Z. and Quong, A. A. Proteomic profiling of infiltrating ductal carcinoma reveals increased cellular interactions with tissue microenvironment. J Pro-teome Res, 2012, 11: 2236-2246.
87. Dumont, B.; Castronovo, V.; Peulen, O.; Blétard, N.; Clézardin, P.; Delvenne, P.; De Pauw, E. A.; Turtoi, A. and Bellahcéne, A. Differential proteomic analysis of a human breast tumor and its matched bone metastasis identifies cell membrane and extracellular proteins associated with bone metastasis. J Proteome Res, 2011, 11:2247-2260.
88. Li, J.; Xie, Z.; Shi, L.; Zhao, Z.; Hou, J.; Chen, X.; Cui, Z.; Xue, P.; Cai, T.; Wu, P.; Guo, S. and Yang F. Purification, identification and profiling of serum amyloid A proteins from sera of advanced stage cancer patients. J Chromatogr B Analyt Technol Biomed Life Sci, 2012, 889-890: 3-9.
89. Tian, Y.; Esteva, F. J.; Song, J. and Zhang H. Altered expression of sialylated glycoproteins in breast cancer using hydrazide chemistry and mass spectrometry. Molec Cell Proteomics, 2012, 11: 1-10.
90. Custodio, A.; López-Farré, A. J.; Zamorano-León, J. J.; Mateos-Cáceres, P. J.; Macaya, C.; Caldés, T.; de la Hoya, M.; Oliveira, E.; Puente, J.; Díaz-Rubio, E. and Pérez-Segura, P. Changes in the expression of plasma proteins associated with thrombosis in BRCA1 mutation carriers. J Cancer Res Clin Oncol, 2012 138(5): 867-875.
91. Zhang, K.; Yuan, K.; Wu, H.; Li, Q.; Wang, Y.; Chen, S.; Zhang, L.; Gu, H. and Fu, R. Identification of potential markers related to neoadjuvant chemotherapy sensitivity of breast cancer by SELDI-TOF MS. Appl Biochem Biotechnol, 2012, 166(3): 753-763.
92. Hodginson, V. C.; Agarwal, V.; ElFadl, D.; Fox, J. N.; McManus, P. L.; Mahapatra, T. K.; Kneeshaw, P. J.; Drew, P. J.; Lind, M. J. and Cawkwell, L. Pilot and feasibility study: comparative proteo-mic analysis by 2-DE MADLI TOF/TOF MS reveals 14-3-3 proteins as putative biomarkers of response to neoadjuvant chemotherapy in ER-positive breast cancer. J Proteomics, 2012, 75(9): 2745-2752.
93. Yang, W. S.; Moon, H. G.; Kim, H. S.; Choi, E. J.; Yu, M. H.; Noh, D. Y. and Lee, C. Proteomic approach reveals FKBP4 and S100A9 as potential prediction markers of therapeutic response to neoadjuvant chemotherapy in patients with breast cancer. J Pro-teome Res, 2011, 11: 1078-1088.
94. Suh, E. J.; Kabir, M. H.; Kang, U. B.; Lee, J. W.; Yu, J.; Noh, D. Y. and Lee, C. Comparative profiling of plasma proteome from breast cancer patients revelas thrombospondin-1 and BRWD3 as serological biomarkers. Exp Mol Medicine, 2012, 44(1): 36-44.
95. Thakur, D.; Rejtar, T.; Wang, W.; Bones, J.; Cha, S.; Clodfelder-Miller, B.; Richardson, E.; Binns, S.; Dahiya, S.; Sgroi, D. and Karger, B. L. Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dode-cyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and porous layer open tubular (PLOT) LC-MS/MS. J Chromatogr A, 2011, 1218(45): 8168-8174.
96. Khamis, Z. I.; Sahab, Z. J.; Byers, S. W. and Sang, Q. X. A. Novel stromal biomarkers in human breast cancer tissues provide evidence for the more malignant phenotype of estrogen receptor-negative tumors. J Biomed Biotechnol, 2011, 1-7.
97. Wang, L.; Su, D.; Yan, H. J.; Xu, J. H.; Zheng, Z. G.; Hu, Y. J.; Pan, X. D.; Ding, X. W.; Chen, C.; Chen, B.; Mao, W. M. and Meng, X. L. Primary study of lymph node metastasis-related serum biomarkers in breast cancer. Anat Record, 2011, 294: 1818-1824.
98. Gast, M. C.; Zapatka, M.; van Tinteren, H.; Bontenbal, M.; Span, P. N.; Tjan-Heijnen, V. C.; Knol, J. C.; Jimenez, C. R.; Schellens, J. H. and Beijnen, J. H. Postoperative serum proteomic profiles may predict recurrence-free survival in high-risk primary breast cancer. J Cancer Res Clin Oncol, 2011, 137(12): 1773-1783.
99. Jézéquel, P.; Campion, L.; Spyratos, F.; Loussouarn, D.; Campone, M.; Guérin-Charbonnel, C.; Joalland, M. P.; André, J.; Descotes, F.; Grenot, C.; Roy, P.; Carlioz, A.; Martin, P. M.; Chassevent, A.; Jourdan, M. L. and Ricolleau, G. Validation of tumor-associated macrophage ferritin light chain as a prognostic biomarker in node-negative breast cancer tumors: A multicentric 2004 national PHRC study. Int J Cancer, 2012, 131(2): 426-437.
100. Opstal-van Winden, A. W.; Krop, E. J.; Karedal, M. H.; Gast, M. C.; Lindh, C. H.; Jeppsson, M. C.; Jonsson, B. A.; Grobbee, D. E.; Peeters, P. H.; Beijnen, J. H.; van Gils, C. H. and Vermeulen, R. C. Searching for early breast cancer biomarkers by serum protein profiling of pre-diagnostic serum; a nested case-control study. BMC Cancer, 2011, 11: 381.
101. Bohm, D.; Keller, K.; Wehrwein, N.; Lebrecht, A.; Schmidt, M.; Kolbl, H. and Grus, F. H. Serum proteome profiling of primary breast cancer indicates a specific biomarker profile. Oncology Reports, 2011, 26: 1051-1056.
102. Hyung, S. W.; Lee, M. Y.; Yu, J. H.; Shin, B.; Jung, H. J.; Park, J.M.; Han, W.; Lee, K. M.; Moon, H. G.; Aebersold, R.; Hwang, D.; Lee, S. W.; Yu, M. H. and Noh, D. Y. A serum protein profile predictive of the resistance to neoadjuvant chemotherapy in advanced breast cancers. Moll Cell Proteomics, 2011, 10(10): M111.011023.
103. Li, C. I. Discovery and validation of breast cancer early detection biomarkers in preclinical samples. Horm Cancer, 2011, 2(2): 125-131.
104. rd; Wulfkuhle, J.; Liotta, L. A.; Lem, S.; Baker, J. C. Jr; Ford, A. C.; Wilke, L. G.; Zalles, C.; Kuderer, N. M.; Hoffman, A. W.; Shivraj, M.; Mehta, P.; Williams, J.; Tolbert, N.; Lee, L. W.; Pilie, P. J.; Yu, D. and Seewaldt, V. L. Pilot and feasibility study: prospective proteomic profiling of mammary epithelial cells from high-risk women provides evidence of activation of pro-survival pathways. Breast Cancer Res Treat, 2012, 132(2): 487-498.
105. Riley, C. P.; Zhang, X.; Nakshatri, H.; Schneider, B.; Regnier, F. E.; Adamec, J. and Buck, C. A large, consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples. J Transl Med, 2011, 9: 80.
106. Rower, C.; Koy, C.; Hecker, M.; Reimer, T.; Gerber, B.; Thiesen, H. J. and Glocker, M. O. Mass spectrometric characterization of protein structure details refines the proteome signature for invasive ductal breast carcinoma. J Am Soc Mass Spectrom, 2011, 22(3): 440-456.
107. Atahan, K.; Kupeli, H.; Gur, S.; Yiqitbasi, T.; Baskin, Y.; Yigit, S.; Deniz, M.; Cokmez, A. and Tarcan, E. The value of serum bio-markers (Bc1, Bc2, Bc3) in the diagnosis of early breast cancer. Int J Med Sci, 2011, 8(2): 148-155.