Proteomic analysis of tissue samples in translational breast cancer research

Expert Review of Proteomics

Volumn 11, Issue 3, 2014, Pages 285-302

  Gromov, Pavel ^a,b   Moreira, José M A ^b,c   Gromova, Irina ^a,b  

^a DANISH CANCER SOCIETY RESEARCH CENTER   (Denmark)

^b Institute of Cancer Biolog   (Denmark)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

breast cancer; gel based proteomics; immunohistochemistry; peptide centric proteomics; protein arrays; tumor heterogeneity

Indexed keywords

BIOLOGICAL MARKER; CYCLOPHILIN A; CYTOCHROME B5; EPIDERMAL GROWTH FACTOR RECEPTOR 2; TAMOXIFEN; TRANSGELIN; PROTEOME; TUMOR MARKER;

APOCRINE CARCINOMA; BREAST; BREAST CANCER; BREAST CARCINOMA; CANCER CELL POPULATION HETEROGENEITY; CANCER GROWTH; CANCER RESEARCH; CANCER RISK; CANCER TISSUE; CLINICAL PRACTICE; COLON ADENOMA; CROSS LINKING; EXPERIMENTAL DESIGN; FUNCTIONAL STATUS; GENETIC HETEROGENEITY; HUMAN; IMMUNOHISTOCHEMISTRY; IMMUNOHISTOLOGY; INTERSTITIAL FLUID; INTRADUCTAL CARCINOMA; INVASIVE CARCINOMA; LASER CAPTURE MICRODISSECTION; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR WEIGHT; NIPPLE ASPIRATION; PHENOTYPE; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROGRESSION FREE SURVIVAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN MICROARRAY; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEIN STABILITY; PROTEOMICS; REVIEW; STRENGTH; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TANDEM MASS SPECTROMETRY; TISSUE MICROARRAY; TREATMENT RESPONSE; TRIPLE NEGATIVE BREAST CANCER; TUMOR MICROENVIRONMENT; TWO DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS; WEAKNESS; WESTERN BLOTTING; BREAST TUMOR; CHEMISTRY; FEMALE; PATHOLOGY; TRANSLATIONAL RESEARCH;

BREAST NEOPLASMS; FEMALE; HUMANS; PROTEIN ARRAY ANALYSIS; PROTEOME; TRANSLATIONAL MEDICAL RESEARCH; TUMOR MARKERS, BIOLOGICAL;

EID: 84900991924     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.2014.899469     Document Type: Review

References (147)

1. Jemal A, Bray F, Center MM, et al. Global cancer statistics. CA Cancer J Clin 2011; 61(2):69-90
2. Reis-Filho JS, Pusztai L. Gene expression profiling in breast cancer: classification, prognostication, and prediction. Lancet 2011;378(9805):1812-23
3. Dawson SJ, Rueda OM, Aparicio S, et al. A new genome-driven integrated classification of breast cancer and its implications. EMBO J 2013;32(5):617-28
4. Baron JA. Screening for cancer with molecular markers: progress comes with potential problems. Nat Rev Cancer 2012; 12(5):368-71
5. Cole KD, He HJ, Wang L. Breast cancer biomarker measurements and standards. Proteomics Clin Appl 2013;7(1-2):17-29
6. Diamandis EP. Cancer biomarkers: can we turn recent failures into success? J Natl Cancer Inst 2010;102(19):1462-7
7. Buchen L. Cancer: missing the mark. Nature 2011;471(7339):428-32
8. Hanash SM. Why have protein biomarkers not reached the clinic? Genome Med 2011; 3(10):66
9. Chang L, Buxter RC. Breast cancer biomarkers: proteomic discovery and translation to clinically relevant samples. Expert Rev Proteomics 2012;9(6):599-614
10. Diamandis EP. The failure of protein cancer biomarkers to reach the clinic: why, and what can be done to address the problem? BMC Med 2012;10:87
11. Kamel D, Brady B, Tabchy A, et al. Proteomic classification of breast cancer. Curr Drug Targets 2012;13(12):1495-509
12. Lam SW, Jimenez CR, Boven E. Breast cancer classification by proteomic technologies: current state of knowledge. Cancer Treat Rev 2014;40(1):129-38
13. Veenstra TD. Proteomics research in breast cancer: balancing discovery and hypothesis-driven studies. Expert Rev Proteomics 2011;8(2):139-41
14. Veenstra TD. Where are all the biomarkers? Expert Rev Proteomics 2011;8(6):681-3
15. Jesneck JL, Mukherjee S, Yurkovetsky Z, et al. Do serum biomarkers really measure breast cancer? BMC Cancer 2009;9:164
16. Taguchi A, Hanash SM. Unleashing the power of proteomics to develop blood-based cancer markers. Clin Chem 2013;59(1): 119-26
17. Bedard PL, Hansen AR, Ratain MJ, et al. Tumour heterogeneity in the clinic. Nature 2013;501(7467):355-64
18. Meacham CE, Morrison SJ. Tumour heterogeneity and cancer cell plasticity. Nature 2013;501(7467):328-37
19. Junttila MR, de Sauvage FJ. Influence of tumour micro-environment heterogeneity on therapeutic response. Nature 2013; 501(7467):346-54
20. Burrell RA, McGranahan N, Bartek J, et al. The causes and consequences of genetic heterogeneity in cancer evolution. Nature 2013;501(7467):338-45
21. Curtis C, Shah SP, Chin S-F, et al. The genomic and transcriptomic architecture of 2, 000 breast tumours reveals novel subgroups. Nature 2012;486(7403):346-52
22. Ng CK, Pemberton HN, Reis-Filho JS. Breast cancer intratumor genetic heterogeneity: causes and implications. Expert Rev Anticancer Ther 2012;12(8): 1021-32
23. Wallstrom G, Anderson KS, LaBaer J. Biomarker discovery for heterogeneous diseases. Cancer Epidemiol Biomarkers Prev 2013;22(5):747-55
24. Valent P, Bonnet D, Wohrer S, et al. Heterogeneity of neoplastic stem cells: theoretical, functional, and clinical implications. Cancer Res 2013;73(3): 1037-45
25. Harrell J C, Dye WW, Harvell DM, et al. Contaminating cells alter gene signatures in whole organ versus laser capture microdissected tumors: a comparison of experimental breast cancers and their lymph node metastases. Clin Exp Metastasis 2008; 25(1):81-8
26. Espina V, Mueller C. Reduction of preanalytical variability in specimen procurement for molecular profiling. Methods Mol Biol 2012;823:49-57
27. Ralton LD, Murray GI. The use of formalin fixed wax embedded tissue for proteomic analysis. J Clin Pathol 2011; 64(4):297-302
28. Giusti L, Lucacchini A. Proteomics studies of formalin-fixed paraffin-embedded tissues. Expert Rev Proteomics 2013;10(2):165-77
29. Sprung RW Jr, Brock JW, Tanksley JP. Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol Cell Proteomics 2009;8(8):1988-98
30. Fuller AP, Palmer-Toy D, Erlander MG, et al. Laser capture microdissection and advanced molecular analysis of human breast cancer. J Mammary Gland Biol Neoplasia 2003;8(3):335-45
31. Espina V, Wulfkuhle J, Liotta LA. Application of laser microdissection and reverse-phase protein microarrays to the molecular profiling of cancer signal pathway networks in the tissue microenvironment. Clin Lab Med 2009;29:1-13
32. Liu NQ, Braakman RB, Stingl C, et al. Proteomics pipeline for biomarker discovery of laser capture microdissected breast cancer tissue. J Mammary Gland Biol Neoplasia 2012;17(2):155-64
33. Gromov P, Celis JE, Gromova I, et al. A single lysis solution for the analysis of tissue samples by different proteomic technologies. Mol Oncol 2008;2(4):368-79
34. Polyak K, Haviv I, Campbell IG. Co-evolution of tumor cells and their microenvironment. Trends Genet 2009; 25(1):30-8
35. Ma XJ, Dahiya S, Richardson E, et al. Gene expression profiling of the tumor microenvironment during breast cancer progression. Breast Cancer Res 2009;11(1): R7
36. Korkaya H, Liu S, Wicha MS. Breast cancer stem cells, cytokine networks, and the tumor microenvironment. J Clin Invest 2011;121:3804-9
37. Boral D, Nie D. Cancer stem cells and niche mircoenvironments. Front Biosci (Elite Ed) 2012;4:2502-14
38. Gromov P, Gromova I, Olsen CJ, et al. Tumor interstitial fluid-a treasure trove of cancer biomarkers. Biochim Biophys Acta 2013;1834(11):2259-70
39. Haslene-Hox H, Tenstad O, Wiig H. Interstitial fluid-a reflection of the tumor cell microenvironment and secretome. Biochim Biophys Acta 2013;1834(11): 2347-59
40. Hu S, Loo JA, Wong DT. Human body fluid proteome analysis. Proteomics 2006; 6(23):6326-53
41. Celis JE, Gromov P, Cabezón T, et al. Proteomic characterization of the interstitial fluid perfusing the breast tumor microenvironment: a novel resource for biomarker and therapeutic target discovery. Mol Cell Proteomics 2004;3(4):327-44
42. Celis JE, Moreira JM, Cabezón T, et al. Identification of extracellular and intracellular signaling components of the mammary adipose tissue and its interstitial fluid in high risk breast cancer patients: toward dissecting the molecular circuitry of epithelial-adipocyte stromal cell interactions. Mol Cell Proteomics 2005;4(4):492-522
43. Gromov P, Gromova I, Bunkenborg J, et al. Up-regulated proteins in the fluid bathing the tumour cell microenvironment as potential serological markers for early detection of cancer of the breast. Mol Oncol 2010;4(1):65-89
44. Dua RS, Isacke CM, Gui GP. The intraductal approach to breast cancer biomarker discovery. J Clin Oncol 2006; 24(7):1209-16
45. Sauter ER, Ehya H, Babb J, et al. Biological markers of risk in nipple aspirate fluid are associated with residual cancer and tumour size. Br J Cancer 1999;81(7):1222-7
46. Mannello F, Ligi D. Resolving breast cancer heterogeneity by searching reliable protein cancer biomarkers in the breast fluid secretome. BMC Cancer 2013;13:344
47. Celis JE, Gromov P. 2D protein electrophoresis: can it be perfected? Curr Opin Biotechnol 1999;10(1):16-21
48. May C, Brosseron F, Pfeiffer K, et al. Proteome analysis with classical 2D-PAGE. Methods Mol Biol 2012;893:37-46
49. May C, Brosseron F, Chartowski P, et al. Differential proteome analysis using 2D-DIGE. Methods Mol Biol 2012;893: 75-82
50. Rogowska-Wrzesinska A, Le Bihan MC, Thaysen-Andersen M, et al. 2D gels still have a niche in proteomics. J Proteomics 2013;88:4-13
51. Marouga R, David S, Hawkins E. The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem 2005; 382(3):669-78
52. Kondo T, Hirohashi S. Application of 2D-DIGE in cancer proteomics toward personalized medicine. Methods Mol Biol 2009;577:135-54
53. Kondo T. Tissue proteomics for cancer biomarker development: laser microdissection and 2D-DIGE. BMB Rep 2008;41(9):626-34
54. Wulfkuhle JD, Sgroi DC, Krutzsch H, et al. Proteomics of human breast ductal carcinoma in situ. Cancer Res 2002;62(22): 6740-9
55. Somiari RI, Sullivan A, Russell S, et al. High-throughput proteomic analysis of human infiltrating ductal carcinoma of the breast. Proteomics 2003;3(10):1863-73
56. Deng SS, Xing TY, Zhou HY, et al. Comparative proteome analysis of breast cancer and adjacent normal breast tissues in human. Genomics Proteomics Bioinformatics 2006;4(3):165-72
57. Weitzel LR, Byers T, Allen J, et al. Discovery and verification of protein differences between Er positive/Her2/neu negative breast tumor tissue and matched adjacent normal breast tissue. Breast Cancer Res Treat 2010;124(2):297-305
58. Fonseca-Sánchez MA, Rodŕiguez Cuevas S, Mendoza-Hernández G, et al. Breast cancer proteomics reveals a positive correlation between glyoxalase 1 expression and high tumor grade. Int J Oncol 2012;41(2): 670-80
59. Lee HH, Lim CA, Cheong YT, et al. Comparisons of protein expression profiles of different stages of lymh nodes metastasis in breast cancer. Int J Bio Sci 2012;8(3): 353-62
60. Zhang D, Tai LK, Wong LL, et al. Proteomic study reveals that proteins involved in metabolic and detoxification pathways are highly expressed in HER-2/neu-positive breast cancer. Mol Cell Proteomics 2005;4(11):1686-96
61. Zhang D, Tai LK, Wong LL, et al. Proteomics of breast cancer: enhanced expression of cytokeratin19 in human epidermal growth factor receptor type 2 positive breast tumors. Proteomics 2005;5(7):1797-805
62. Zhang D, Tai LK, Wong LL, et al. Proteomic characterization of differentially expressed proteins in breast cancer: expression of hnRNP H1, RKIP and GRP78 is strongly associated with HER-2/neu status. Proteomics Clin Appl 2008;2(1): 99-107
63. Schulz DM, Böllner C, Thomas G, et al. Identification of differentially expressed proteins in triple-negative breast carcinomas using DIGE and mass spectrometry. J Proteome Res 2009;8(7):3430-8
64. Durán MC, Vega F, Moreno-Bueno G, et al. Characterisation of tumoral markers correlated with ErbB2 (HER2/Neu) overexpression and metastasis in breast cancer. Proteomics Clin Appl 2008;2(9): 1313-26
65. Neubauer H, Clare SE, Kurek R, et al. Breast cancer proteomics by laser capture microdissection, sample pooling, 54-cm IPG IEF, and differential iodine radioisotope detection. Electrophoresis 2006;27(9): 1840-52
66. Neubauer H, Clare SE, Wozny W, et al. Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1. Breast Cancer Res 2008;10(5):R85
67. Semaan SM, Wang X, Marshall AG, et al. Identification of Potential Glycoprotein Biomarkers in Estrogen Receptor Positive (ER+) and Negative (ER-) Human Breast Cancer Tissues by LC-LTQ/FT-ICR Mass Spectrometry. J Cancer 2012;3:269-84
68. Kabbage M, Trimeche M, Bergaoui S, et al. Calreticulin expression in infiltrating ductal breast carcinomas: relationships with disease progression and humoral immune responses. Tumour Biol 2013;34(2):1177-88
69. Chahed K, Kabbage M, Hamrita B, et al. Detection of protein alterations in male breast cancer using two dimensional gel electrophoresis and mass spectrometry: the involvement of several pathways in tumorigenesis. Clin Chim Acta 2008; 388(1-2):106-14
70. Gromov P, Gromova I, Friis E, et al. Proteomic profiling of mammary carcinomas identifies C7orf24, a gamma-glutamyl cyclotransferase, as a potential cancer biomarker. J Proteome Res 2010;9(8):3941-53
71. Li J, Gromov P, Gromova I, et al. Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis. Proteomics 2008;8(23-24): 5038-52
72. Cabezón T, Gromova I, Gromov P, et al. Proteomic profiling of triple-negative breast carcinomas in combination with a three-tier orthogonal technology approach identifies Mage-A4 as potential therapeutic target in estrogen receptor negative breast cancer. Mol Cell Proteomics 2013;12(2):381-94
73. Celis JE, Gromov P, Cabezón T, et al. 15-prostaglandin dehydrogenase expression alone or in combination with ACSM1 defines a subgroup of the apocrine molecular subtype of breast carcinoma. Mol Cell Proteomics 2008;7(10):1795-809
74. Celis JE, Cabezón T, Moreira JM, et al. Molecular characterization of apocrine carcinoma of the breast: validation of an apocrine protein signature in a well-defined cohort. Mol Oncol 2009;3(3):220-37
75. Celis JE, Gromova I, Cabezón T, et al. Identification of a subset of breast carcinomas characterized by expression of cytokeratin 15: relationship between CK15+ progenitor/amplified cells and pre-malignant lesions and invasive disease. Mol Oncol 2007;1(3):321-49
76. Celis JE, Moreira JM, Gromova I, et al. Characterization of breast precancerous lesions and myoepithelial hyperplasia in sclerosing adenosis with apocrine metaplasia. Mol Oncol 2007;1(1):97-119
77. Celis JE, Gromova I, Gromov P, et al. Molecular pathology of breast apocrine carcinomas: a protein expression signature specific for benign apocrine metaplasia. FEBS Lett 2006;580(12):2935-44
78. Celis JE, Gromov P, Moreira JM, et al. Apocrine cysts of the breast: biomarkers, origin, enlargement, and relation with cancer phenotype. Mol Cell Proteomics 2006;5(3):462-83
79. Moreira JM, Cabezon T, Gromova I, et al. Tissue proteomics of the human mammary gland: towards an abridged definition of the molecular phenotypes underlying epithelial normalcy. Mol Oncol 2010;4(6):539-61
80. Vaudel M, Sickmann A, Martens L. Current methods for global proteome identification. Expert Rev Proteomics 2012; 9(5):519-32
81. Zhang Y, Fonslow BR, Shan B, et al. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013;113(4): 2343-94
82. Zang L, Palmer Toy D, Hancock WS, et al. Proteomic analysis of ductal carcinoma of the breast using laser capture microdissection, LC-MS, and 16O/18O isotopic labeling. J Proteome Res 2004;3(3): 604-12
83. Burkhart JM, Vaudel M, Zahedi RP, et al. iTRAQ protein quantification: a quality-controlled workflow. Proteomics 2011;11(6): 1125-34
84. Bouchal P, Roumeliotis T, Hrstka R, et al. Biomarker discovery in low-grade breast cancer using isobaric stable isotope tags and two-dimensional liquid chromatography tandem mass spectrometry (iTRAQ-2DLC-MS/MS) based quantitative proteomic analysis. J Proteome Res 2009;8(1):362-73
85. Muraoka S, Kume H, Watanabe S, et al. Strategy for SRM-based verification of biomarker candidates discovered by iTRAQ method in limited breast cancer tissue samples. J Proteome Res 2012; 11(8): 4201-10
86. Xie F, Liu T, Qian WJ, et al. Liquid chromatography-mass spectrometry-based quantitative proteomics. J Biol Chem 2011; 286(29):25443-9
87. Cha S, Imielinski MB, Rejtar T, et al. In situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection: annotation by protein set enrichment analysis and gene ontology. Mol Cell Proteomics 2010;9(11):2529-44
88. Rezaul K, Thumar JK, Lundgren DH, et al. Differential protein expression profiles in estrogen receptor-positive and-negative breast cancer tissues using label-free quantitative proteomics. Genes Cancer 2010;1(3):251-71
89. Traub F, Jost M, Hess R, et al. Peptidomic analysis of breast cancer reveals a putative surrogate marker for estrogen receptor-negative carcinomas. Lab Invest 2006;86(3):246-53
90. He J, Whelan SA, Lu M, et al. Proteomic-based biosignatures in breast cancer classification and prediction of therapeutic response. Int J Proteomics 2011;2011:896476
91. Greenwood C, Metodieva G, Al-Janabi K, et al. Stat1 and CD74 overexpression is co-dependent and linked to increased invasion and lymph node metastasis in triple-negative breast cancer. J Proteomics 2012;75(10):3031-40
92. Dumont B, Castronovo V, Peulen O, et al. 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 2012;11(4): 2247-60
93. Semaan SM, Wang X, Stewart PA, et al. Differential phosphopeptide expression in a benign breast tissue, and triple-negative primary and metastatic breast cancer tissues from the same African-American woman by LC-LTQ/FT-ICR mass spectrometry. Biochem Biophys Res Commun 2011; 412(1):127-31
94. Umar A, Kang H, Timmermans AM, et al. Identification of a putative protein profile associated with tamoxifen therapy resistance in breast cancer. Mol Cell Proteomics 2009; 8(6):1278-94
95. Olsson N, Carlsson P, James P, et al. Grading breast cancer tissues using molecular portraits. Mol Cell Proteomics 2013; 12(12):3612-23
96. Raso C, Cosentino C, Gaspari M, et al. Characterization of breast cancer interstitial fluids by TmT labeling, LTQ-orbitrap velos mass spectrometry, and pathway analysis. J Proteome Res 2012;11(6):3199-210
97. Li J, Lu Y, Akbani R, et al. TCPA: a resource for cancer functional proteomics data. Nat Methods 2013;10(11):1046-7
98. Haab BB. Applications of antibody array platforms. Curr Opin Biotechnol 2006; 17(4):415-21
99. Huang R, Jiang W, Yang J, et al. A biotin label-based antibody array for high-content profiling of protein expression. Cancer Genomics Proteomics 2010;7(3):129-41
100. Zong Y, Zhang S, Chen HT, et al. Forward-phase and reverse-phase protein microarray. Methods Mol Biol 2007;381: 363-74
101. Rapkiewicz A, Espina V, Zujewski JA, et al. The needle in the haystack: application of breast fine-needle aspirate samples to quantitative protein microarray technology. Cancer 2007;111(3):173-84
102. Pierobon M, Belluco C, Liotta LA, et al. Reverse phase protein microarrays for clinical applications. Methods Mol Biol 2011;785:3-12
103. Malinowsky K, Raychaudhuri M, Buchner T, et al. Common protein biomarkers assessed by reverse phase protein arrays show considerable intratumoral heterogeneity in breast cancer tissues. PLoS ONE 2012;7(7):e40285
104. Tabchy A, Hennessy BT, Gonzalez-Angulo AM, et al. Quantitative proteomic analysis in breast cancer. Drugs Today 2011;47(2):169-82
105. Gonzalez-Angulo AM, Hennessy BT, Meric-Bernstam F, et al. Functional proteomics can define prognosis and predict pathologic complete response in patients with breast cancer. Clin Proteomics 2011; 8(1):11
106. Assadi M, Lamerz J, Jarutat T, et al. Multiple protein analysis of formalin-fixed and paraffin-embedded tissue samples with reverse phase protein arrays. Mol Cell Proteomics 2013;12(9):2615-22
107. Wulfkuhle JD, Speer R, Pierobon M, et al. Multiplexed cell signaling analysis of human breast cancer applications for personalized therapy. J Proteome Res 2008;7:1508-17
108. Pilie PG, Ibarra-Drendall C, Troch MM, et al. Protein microarray analysis of mammary epithelial cells from obese and non obese women at high risk for breast cancer: feasibility data. Cancer Epidemiol Biomarkers Prev 2011;20(3):476-82
109. Ibarra-Drendall C, Troch MM, Barry WT, et al. 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;132:487-98
110. Hodgkinson VC, ELFadl D, Agarwal V, et al. Proteomic 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):1276-83
111. Gonzalez-Angulo AM, Liu S, Chen H, et al. Functional proteomics characterization of residual breast cancer after neoadjuvant systemic chemotherapy. Ann Oncol 2013; 24(4):909-16
112. Sohn J, Do KA, Liu S, et al. Functional proteomics characterization of residual triple negative breast cancer after standard neoadjuvant chemotherapy. Ann Oncol 2013;24(10):2522-6
113. Gujral TS, Karp RL, Finski A, et al. Profiling phospho-signaling networks in breast cancer using reverse-phase protein arrays. Oncogene 2013;32(29):3470-6
114. Wulfkuhle JD, Berg D, Wolff C, et al. Molecular analysis of HER2 signaling in human breast cancer by functional protein pathway activation mapping. Clin Cancer Res 2012;18(23):6426-35
115. Tessitore A, Zazzeroni F, Alesse E. Reverse-phase protein microarray highlights HER2 signaling activation in immunohistochemistry/FISH/HER2-negative breast cancers. Expert Rev Proteomics 2013;10(3):223-6
116. Zhang H, Pelech S. Using protein microarrays to study phosphorylation-mediated signal transduction. Semin Cell Dev Biol 2012; 23(8):872-82
117. Angenendt P, Glokler J, Sobek J, et al. Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications. J Chromatogr 2003;1009:97-104
118. Espina V, Mueller C, Liotta LA. Phosphoprotein stability in clinical tissue and its relevance for reverse phase protein microarray technology. Methods Mol Biol 2011;785:23-43
119. Chiechi A, Mueller C, Boehm KM, et al. Improved data normalization methods for reverse phase protein microarray analysis of complex biological samples. Biotechniques 2012;0(0):1-7
120. He J, Shen D, Chung DU, et al. Tumor proteomic profiling predicts the susceptibility of breast cancer to chemotherapy. Int J Oncol 2009;35(4): 683-92
121. Ricolleau G, Charbonnel C, Lodé L, et al. Surface-enhanced 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(6):1963-75
122. Diamandis EP. Serum proteomic profiling by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for cancer diagnosis: next steps. Cancer Res 2006; 66(11):5540-1
123. Ng EW, Wong MY, Poon TC. Advances in MALDI Mass Spectrometry in Clinical Diagnostic Applications. Top Curr Chem 2014;336:139-75
124. Caprioli RM, Farmer TB, Gile J. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal Chem 1997; 69(23):4751-60
125. Chaurand P, Stoeckli M, Caprioli RM. Direct profiling of proteins in biological tissue sections by MALDI mass spectrometry. Anal Chem 1999;71(23): 5263-70
126. Chaurand P, Schwartz SA, Reyzer ML, et al. Imaging mass spectrometry: principles and potentials. Toxicol Pathol 2005;33(1): 92-101
127. Angel PM, Caprioli RM. Matrix-assisted laser desorption ionization imaging mass spectrometry: in situ molecular mapping. Biochemistry 2013;52(22):3818-28
128. Cillero-Pastor B, Heeren RM. Matrix-assited laser desorption ionization mass spectrometry imaging for peptide and protein analysis: a critical review of on tissue digestion. J Proteome Res 2014;13(2): 325-35
129. Neubert P, Walch A. Current frontiers in clinical research application of MALDI imaging mass spectrometry. Expert Rev Proteomics 2013;10(3):259-73
130. McDonnell LA, Corthals GL, Willems SM, et al. Peptide and protein imaging mass spectrometry in cancer research. J Proteomics 2010;73(10):1921-44
131. Lemaire R, Desmons A, Tabet J C, et al. Direct analysis and MALDI imaging of formalin-fixed, paraffin embedded tissue sections. J Proteome Res 2007;6:1295-305
132. Wisztorski M, Franck J, Salzet M, et al. MALDI direct analysis and imaging of frozen versus FFPE tissues: what strategy for which sample? Methods Mol Biol 2010;656:303-22
133. Casadonte R, Caprioli RM. Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometry. Nat Protoc 2011;6(11): 1695-709
134. Fowler CB, O'Leary TJ, Mason JT. Toward improving the proteomic analysis of formalin-fixed, paraffin-embedded tissue. Expert Rev Proteomics 2013;10(4):389-400
135. Xu BJ, Caprioli RM, Sanders ME, et al. Direct analysis of laser capture microdissected cells by MALDI mass spectrometry. J Am Soc Mass Spectrom 2002;13(11):1292-7
136. Sanders ME, Dias EC, Xu BJ, et al. Differentiating proteomic biomarkers in breast cancer by laser capture microdissection and MALDI MS. J Proteome Res 2008;7(4):1500-7
137. Balluff B, Elsner M, Kowarsch A, et al. Classification of HER2/neu status in gastric cancer using a breast-cancer derived proteome classifier. J Proteome Res 2010; 9(12):6317-22
138. Bauer JA, Chakravarthy AB, Rosenbluth JM, et al. Identification of markers of taxane sensitivity using proteomic and genomic analyses of breast tumors from patients receiving neoadjuvant paclitaxel and radiation. Clin Cancer Res 2010;16(2): 681-90
139. Ide Y, Waki M, Hayasaka T, et al. Human breast cancer tissues contain abundant phosphatidylcholine(36:1) with high stearoyl-CoA desaturase-1 expression. PLoS One 2013;8(4):e61204
140. Kawashima M, Iwamoto N, Kawaguchi-Sakita N, et al. High-resolution imaging mass spectrometry reveals detailed spatial distribution of phosphatidylinositols in human breast cancer. Cancer Sci 2013; 104(10):1372-9
141. Thomson TA, Zhou C, Chu C, et al. Tissue microarray for routine analysis of breast biomarkers in the clinical laboratory. Am J Clin Pathol 2009;132(6):899-905
142. Metzger GJ, Dankbar SC, Henriksen J, et al. Development of multigene expression signature maps at the protein level from digitized immunohistochemistry slides. PLoS One 2012;7(3):e33520
143. Ebhardt HA. Selected reaction monitoring mass spectrometry: a methodology overview. Methods Mol Biol 2014;1072:209-22
144. Kuzyk MA, Parker CE, Domanski D, et al. Development of MRM-based assays for the absolute quantitation of plasma proteins. Methods Mol Biol 2013;1023:53-82
145. Percy AJ, Chambers AG, Yang J, et al. Method and platform standardization in MRM-based quantitative plasma proteomics. J Proteomics 2013;95:66-76
146. Haslene-Hox H, Oveland E, Woie K, et al. Increased WD-repeat containing protein 1 in interstitial fluid from ovarian carcinomas shown by comparative proteomic analysis of malignant and healthy gynecological tissue. Biochim Biophys Acta 2013;1834(11):2347-59
147. Narumi R, Murakami T, Kuga T, et al. A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples. J Proteome Res 2012; 11(11):5311-2532