Discovering cancer biomarkers from clinical samples by protein microarrays

Proteomics - Clinical Applications

Volumn 9, Issue 1-2, 2015, Pages 98-110

  Hu, Bin ^a   Niu, Xin ^a   Cheng, Li ^b,c   Yang, Li Na ^b,c   Li, Qing ^a   Wang, Yang ^a   Tao, Sheng Ce ^b,c   Zhou, Shu Min ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b Shanghai Jiao Tong University   (China)

^c School of Medicine   (China)

Author keywords

Cancer biomarker; Cancer metastasis; Clinical samples; Protein microarray

Indexed keywords

GLYCAN; LECTIN; PLASMA PROTEIN; TUMOR MARKER; PROTEOME; TUMOR PROTEIN;

ANTIBODY DETECTION; BLOOD ANALYSIS; BODY FLUID; BREAST CANCER; CANCER GROWTH; CANCER RESEARCH; CANCER STAGING; CANCER TISSUE; CELL LYSATE; DRUG RESEARCH; HUMAN; IMMUNOBLOTTING; METASTASIS; MICROTECHNOLOGY; NONHUMAN; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN MICROARRAY; REVIEW; SIGNAL TRANSDUCTION; TISSUE MICROARRAY; METABOLISM; NEOPLASMS; PROCEDURES;

BODY FLUIDS; HUMANS; NEOPLASM PROTEINS; NEOPLASMS; PROTEIN ARRAY ANALYSIS; PROTEOME; TUMOR MARKERS, BIOLOGICAL;

EID: 84922795379     PISSN: 18628346     EISSN: 18628354     Source Type: Journal    
DOI: 10.1002/prca.201400094     Document Type: Review

References (99)

1. Mishra, A., Verma, M., Cancer biomarkers: are we ready for the prime time? Cancers 2010, 2, 190-208.
2. Musolino, A., Bella, M. A., Bortesi, B., Michiara, M. et al., BRCA mutations, molecular markers, and clinical variables in early-onset breast cancer: a population-based study. Breast 2007, 16, 280-292.
3. Lamparella, N., Barochia, A., Almokadem, S., Impact of genetic markers on treatment of non-small cell lung cancer. Adv. Exp. Med. Biol. 2013, 779, 145-164.
4. Cedrone, A., Covino, M., Caturelli, E., Pompili, M. et al., Utility of alpha-fetoprotein (AFP) in the screening of patients with virus-related chronic liver disease: does different viral etiology influence AFP levels in HCC? A study in 350 western patients. Hepatogastroenterology 2000, 47, 1654-1658.
5. Murdoch, W. J., Van Kirk, E. A., Smedts, A. M., Complement-inhibiting effect of ovarian cancer antigen CA-125. Cancer Lett. 2006, 236, 54-57.
6. Dunn, P. M., McKinstry, M., CA19-9 and pancreatic cancer. Ann. Intern. Med. 1989, 9, 704-709.
7. Filella, X., Molina, R., Pique, J. M., Grau, J. J. et al., CEA as a prognostic factor in colorectal cancer. Anticancer Res. 1994, 14, 705-708.
8. Bantis, A., Grammaticos, P., Prostatic specific antigen and bone scan in the diagnosis and follow-up of prostate cancer. Can diagnostic significance of PSA be increased? Hell. J. Nucl. Med. 2012, 15, 241-246.
9. Perez-Rivas, L. G., Jerez, J. M., Fernandez-De Sousa, C. E., de Luque, V. et al., Serum protein levels following surgery in breast cancer patients: a protein microarray approach. Int. J. Oncol. 2012, 41, 2200-2206.
10. Zhou, J., Belov, L., Solomon, M. J., Chan, C. et al., Colorectal cancer cell surface protein profiling using an antibody microarray and fluorescence multiplexing. J. Vis. Exp. 2011, doi: 10.3791/3322
11. MacBeath, G., Protein microarrays and proteomics. Nat. Genet. 2002, 32(Suppl), 526-532.
12. Kolch, W., Mischak, H., Pitt, A. R., The molecular make-up of a tumour: proteomics in cancer research. Clin. Sci. 2005, 108, 369-383.
13. Hudson, B. I., Carter, A. M., Harja, E., Kalea, A. Z. et al., Identification, classification, and expression of RAGE gene splice variants. FASEB J. 2008, 22, 1572-1580.
14. Gulmann, C., Sheehan, K. M., Conroy, R. M., Wulfkuhle, J. D. et al., Quantitative cell signalling analysis reveals down-regulation of MAPK pathway activation in colorectal cancer. J. Pathol. 2009, 218, 514-519.
15. Kuno, A., Kato, Y., Matsuda, A., Kaneko, M. K. et al., Focused differential glycan analysis with the platform antibody-assisted lectin profiling for glycan-related biomarker verification. Mol. Cell. Proteomics 2009, 8, 99-108.
16. Zhou, S. M., Cheng, L., Guo, S. J., Zhu, H., Tao, S. C., Lectin microarray: a powerful tool for glycan related biomarker discovery. Comb. Chem. High Throughput Screen. 2011, 8, 711-719.
17. Roberts, E., Charboneau, L., Espina, V., Liotta, L. et al., Application of laser capture microdissection and protein microarray technologies in the molecular analysis of airway injury following pollution particle exposure. J. Toxicol. Environ. Health A 2004, 67, 851-861.
18. Zhu, H., Bilgin, M., Bangham, R., Hall, D. et al., Global analysis of protein activities using proteome chips. Science 2001, 293, 2101-2105.
19. MacBeath, G., Schreiber, S. L., Printing proteins as microarrays for high-throughput function determination. Science 2000, 289, 1760-1763.
20. Delehanty, J. B., Ligler, F. S., Method for printing functional protein microarrays. Biotechniques 2003, 34, 380-385.
21. Festa, F., Rollins, S. M., Vattem, K., Hathaway, M. et al., Robust microarray production of freshly expressed proteins in a human milieu. Proteomics Clin. Appl. 2013, 7, 372-377.
22. Beare, P. A., Chen, C., Bouman, T., Pablo, J. et al., Candidate antigens for Q fever serodiagnosis revealed by immunoscreening of a Coxiella burnetii protein microarray. Clin. Vaccine Immunol. 2008, 15, 1771-1779.
23. Liu, B. C., Zhang, L., Lv, L. L., Wang, Y. L. et al., Application of antibody array technology in the analysis of urinary cytokine profiles in patients with chronic kidney disease. Am. J. Nephrol. 2006, 26, 483-490.
24. Reineke, U., Ivascu, C., Schlief, M., Landgraf, C. et al., Identification of distinct antibody epitopes and mimotopes from a peptide array of 5520 randomly generated sequences. J. Immunol. Methods 2002, 267, 37-51.
25. Wang, Y. C., Nakagawa, M., Garitaonandia, I., Slavin, I. et al., Specific lectin biomarkers for isolation of human pluripotent stem cells identified through array-based glycomic analysis. Cell Res. 2011, 21, 1551-1563.
26. Ellmark, P., Ingvarsson, J., Carlsson, A., Lundin, B. S. et al., Identification of protein expression signatures associated with Helicobacter pylori infection and gastric adenocarcinoma using recombinant antibody microarrays. Mol. Cell. Proteomics 2006, 5, 1638-1646.
27. Fry, S. A., Afrough, B., Lomax-Browne, H. J., Timms, J. F. et al., Lectin microarray profiling of metastatic breast cancers. Glycobiology 2011, 21, 1060-1070.
28. Mor, G., Visintin, I., Lai, Y., Zhao, H. et al., Serum protein markers for early detection of ovarian cancer. Proc. Natl. Acad. Sci. USA 2005, 102, 7677-7682.
29. Lueking, A., Possling, A., Huber, O., Beveridge, A. et al., A nonredundant human protein chip for antibody screening and serum profiling. Mol. Cell. Proteomics 2003, 2, 1342-1349.
30. Liu, C. X., Wu, F. L., Jiang, H. W., He, X. et al., Global identification of CobB interactors by an Escherichia coli proteome microarray. Acta Biochim. Biophys. Sin. 2014, 7, 548-555.
31. Chen, C. S., Korobkova, E., Chen, H., Zhu, J. et al., A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. Nat. Methods 2008, 5, 69-74.
32. Gelperin, D. M., White, M. A., Wilkinson, M. L., Kon, Y. et al., Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev. 2005, 19, 2816-2826.
33. Jeong, J. S., Jiang, L., Albino, E., Marrero, J. et al., Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Mol. Cell. Proteomics 2012, 11, O111 016253.
34. Hu, C. J., Song, G., Huang, W., Liu, G. Z. et al., Identification of new autoantigens for primary biliary cirrhosis using human proteome microarrays. Mol. Cell. Proteomics 2012, 11, 669-680.
35. Kumble, K. D., Protein microarrays: new tools for pharmaceutical development. Anal. Bioanal. Chem. 2003, 377, 812-819.
36. Zhu, X. D., Niedernhofer, L., Kuster, B., Mann, M. et al., ERCC1/XPF removes the 3' overhang from uncapped telomeres and represses formation of telomeric DNA-containing double minute chromosomes. Mol. Cell 2003, 12, 1489-1498.
37. Newman, R. H., Hu, J., Rho, H. S., Xie, Z. et al., Construction of human activity-based phosphorylation networks. Mol. Syst. Biol. 2013, 9, 655.
38. Lu, J. Y., Lin, Y. Y., Boeke, J. D., Zhu, H., Using functional proteome microarrays to study protein lysine acetylation. Methods Mol. Biol. 2013, 981, 151-165.
39. Lin, Y. Y., Lu, J. Y., Zhang, J., Walter, W. et al., Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell 2009, 136, 1073-1084.
40. Jeong, J. S., Rho, H. S., Zhu, H., A functional protein microarray approach to characterizing posttranslational modifications on lysine residues. Methods Mol. Biol. 2011, 723, 213-223.
41. Paweletz, C. P., Charboneau, L., Bichsel, V. E., Simone, N. L. et al., Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 2001, 20, 1981-1989.
42. Liotta, L. A., Espina, V., Mehta, A. I., Calvert, V. et al., Protein microarrays: meeting analytical challenges for clinical applications. Cancer Cell 2003, 3, 317-325.
43. Rapkiewicz, A., Espina, V., Zujewski, J. A., Lebowitz, P. F. et al., The needle in the haystack: application of breast fine-needle aspirate samples to quantitative protein microarray technology. Cancer 2007, 111, 173-184.
44. Hu, S., Loo, J. A., Wong, D. T., Human body fluid proteome analysis. Proteomics 2006, 6, 6326-6353.
45. Liotta, L. A., Kohn, E. C., The microenvironment of the tumour-host interface. Nature 2001, 411, 375-379.
46. Hudson, M. E., Pozdnyakova, I., Haines, K., Mor, G., Snyder, M., Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays. Proc. Natl. Acad. Sci. USA 2007, 104, 17494-17499.
47. Babel, I., Barderas, R., Díaz-Uriarte, R., Martínez-Torrecuadrada, J. L. et al., Identification of tumor-associated autoantigens for the diagnosis of colorectal cancer in serum using high density protein microarrays. Mol Cell Proteomics 2009, 10, 2382-2395.
48. Zhong, L., Hidalgo, G. E., Stromberg, A. J., Khattar, N. H. et al., Using protein microarray as a diagnostic assay for non-small cell lung cancer. Am. J. Respir. Crit. Care Med. 2005, 172, 1308-1314.
49. Lin, H. S., Talwar, H. S., Tarca, A. L., Ionan, A. et al., Autoantibody approach for serum-based detection of head and neck cancer. Cancer Epidemiol. Biomarkers Prev. 2007, 16, 2396-2405.
50. Anderson, K. S., Sibani, S., Wallstrom, G., Qiu, J. et al., Protein microarray signature of autoantibody biomarkers for the early detection of breast cancer. J. Proteome Res. 2011, 10, 85-96.
51. Woodbury, R. L., Varnum, S. M., Zangar, R. C., Elevated HGF levels in sera from breast cancer patients detected using a protein microarray ELISA. J. Proteome Res. 2002, 1, 233-237.
52. Orchekowski, R., Hamelinck, D., Li, L., Gliwa, E. et al., Antibody microarray profiling reveals individual and combined serum proteins associated with pancreatic cancer. Cancer Res. 2005, 65, 11193-11202.
53. Wingren, C., Sandstrom, A., Segersvard, R., Carlsson, A. et al., Identification of serum biomarker signatures associated with pancreatic cancer. Cancer Res. 2012, 72, 2481-2490.
54. Gao, W. M., Kuick, R., Orchekowski, R. P., Misek, D. E. et al., Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis. BMC Cancer 2005, 5, 110.
55. Miller, J. C., Zhou, H., Kwekel, J., Cavallo, R. et al., Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics 2003, 3, 56-63.
56. Sanchez-Carbayo, M., Socci, N. D., Lozano, J. J., Haab, B. B., Cordon-Cardo, C., Profiling bladder cancer using targeted antibody arrays. Am. J. Pathol. 2006, 168, 93-103.
57. Huang, R. P., Huang, R., Fan, Y., Lin, Y., Simultaneous detection of multiple cytokines from conditioned media and patient's sera by an antibody-based protein array system. Anal. Biochem. 2001, 294, 55-62.
58. Celis, J. E., Gromov, P., Cabezon, T., Moreira, J. M. 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, 327-344.
59. Celis, J. E., Moreira, J. M., Cabezon, T., Gromov, P. 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, 492-522.
60. Hudelist, G., Pacher-Zavisin, M., Singer, C. F., Holper, T. et al., Use of high-throughput protein array for profiling of differentially expressed proteins in normal and malignant breast tissue. Breast Cancer Res. Treat. 2004, 86, 281-291.
61. Smith, L., Watson, M. B., O'Kane, S. L., Drew, P. J. et al., The analysis of doxorubicin resistance in human breast cancer cells using antibody microarrays. Mol. Cancer Ther. 2006, 5, 2115-2120.
62. Bartling, B., Hofmann, H. S., Boettger, T., Hansen, G. et al., Comparative application of antibody and gene array for expression profiling in human squamous cell lung carcinoma. Lung Cancer 2005, 49, 145-154.
63. Tannapfel, A., Anhalt, K., Hausermann, P., Sommerer, F. et al., Identification of novel proteins associated with hepatocellular carcinomas using protein microarrays. J. Pathol. 2003, 201, 238-249.
64. Knezevic, V., Leethanakul, C., Bichsel, V. E., Worth, J. M. et al., Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics 2001, 1, 1271-1278.
65. Ghobrial, I. M., McCormick, D. J., Kaufmann, S. H., Leontovich, A. A. et al., Proteomic analysis of mantle-cell lymphoma by protein microarray. Blood 2005, 105, 3722-3730.
66. Belov, L., Huang, P., Chrisp, J. S., Mulligan, S. P., Christopherson, R. I., Screening microarrays of novel monoclonal antibodies for binding to T-, B- and myeloid leukaemia cells. J. Immunol. Methods 2005, 305, 10-19.
67. Belov, L., Mulligan, S. P., Barber, N., Woolfson, A. et al., Analysis of human leukaemias and lymphomas using extensive immunophenotypes from an antibody microarray. Br. J. Haematol. 2006, 135, 184-197.
68. Ellmark, P., Belov, L., Huang, P., Lee, C. S. et al., Multiplex detection of surface molecules on colorectal cancers. Proteomics 2006, 6, 1791-1802.
69. Kaufman, K. L., Belov, L., Huang, P., Mactier, S. et al., An extended antibody microarray for surface profiling metastatic melanoma. J. Immunol. Methods 2010, 358, 23-34.
70. Huang, W. L., Li, Y. G., Lv, Y. C., Guan, X. H. et al., Use of lectin microarray to differentiate gastric cancer from gastric ulcer. World J. Gastroenterol. 2014, 20, 5474-5482.
71. Roy, B., Chattopadhyay, G., Mishra, D., Das, T. et al., On-chip lectin microarray for glycoprofiling of different gastritis types and gastric cancer. Biomicrofluidics 2014, 8, 034107.
72. Fokas, E., Engenhart-Cabillic, R., Daniilidis, K., Rose, F., An, H. X., Metastasis: the seed and soil theory gains identity. Cancer Metastasis Rev. 2007, 26, 705-715.
73. Sahai, E., Mechanisms of cancer cell invasion. Curr. Opin. Genet. Dev. 2005, 15, 87-96.
74. Pantel, K., Brakenhoff, R. H., Brandt, B., Detection, clinical relevance and specific biological properties of disseminating tumour cells. Nat. Rev. Cancer 2008, 8, 329-340.
75. Zieglschmid, V., Hollmann, C., Bocher, O., Detection of disseminated tumor cells in peripheral blood. Crit. Rev. Clin. Lab. Sci. 2005, 42, 155-196.
76. Paterlini-Brechot, P., Benali, N. L., Circulating tumor cells (CTC) detection: clinical impact and future directions. Cancer Lett. 2007, 253, 180-204.
77. Ludwig, J. A., Weinstein, J. N., Biomarkers in cancer staging, prognosis and treatment selection. Nat. Rev. Cancer 2005, 5, 845-856.
78. Vazquez-Martin, A., Colomer, R., Menendez, J. A., Protein array technology to detect HER2 (erbB-2)-induced 'cytokine signature' in breast cancer. Eur. J. Cancer 2007, 43, 1117-1124.
79. Chen, C., Duckworth, C. A., Fu, B., Pritchard, D. M. et al., Circulating galectins -2, -4 and -8 in cancer patients make important contributions to the increased circulation of several cytokines and chemokines that promote angiogenesis and metastasis. Br. J. Cancer 2014, 110, 741-752.
80. Chen, C., Duckworth, C. A., Zhao, Q., Pritchard, D. M. et al., Increased circulation of galectin-3 in cancer induces secretion of metastasis-promoting cytokines from blood vascular endothelium. Clin. Cancer Res. 2013, 19, 1693-1704.
81. Carlsson, A., Wingren, C., Ingvarsson, J., Ellmark, P. et al., Serum proteome profiling of metastatic breast cancer using recombinant antibody microarrays. Eur. J. Cancer 2008, 44, 472-480.
82. Hong, S. H., Misek, D. E., Wang, H., Puravs, E. et al., An autoantibody-mediated immune response to calreticulin isoforms in pancreatic cancer. Cancer Res. 2004, 64, 5504-5510.
83. Cho-Chung, Y. S., Autoantibody biomarkers in the detection of cancer. Biochim. Biophys. Acta 2006, 1762, 587-591.
84. Wulfkuhle, J. D., Aquino, J. A., Calvert, V. S., Fishman, D. A. et al., Signal pathway profiling of ovarian cancer from human tissue specimens using reverse-phase protein microarrays. Proteomics 2003, 3, 2085-2090.
85. Grubb, R. L., Deng, J., Pinto, P. A., Mohler, J. L. et al., Pathway biomarker profiling of localized and metastatic human prostate cancer reveal metastatic and prognostic signatures. J. Proteome Res. 2009, 8, 3044-3054.
86. Wulfkuhle, J. D., Speer, R., Pierobon, M., Laird, J. et al., Multiplexed cell signaling analysis of human breast cancer applications for personalized therapy. J. Proteome Res. 2008, 7, 1508-1517.
87. Chiechi, A., Novello, C., Magagnoli, G., Petricoin, E. F., 3rd et al., Elevated TNFR1 and serotonin in bone metastasis are correlated with poor survival following bone metastasis diagnosis for both carcinoma and sarcoma primary tumors. Clin. Cancer Res. 2013, 19, 2473-2485.
88. Li, S., Mo, C., Peng, Q., Kang, X. et al., Cell surface glycan alterations in epithelial mesenchymal transition process of Huh7 hepatocellular carcinoma cell. PLoS One 2013, 8, e71273.
89. Dallas, M. R., Chen, S. H., Streppel, M. M., Sharma, S. et al., Sialofucosylated podocalyxin is a functional E- and L-selectin ligand expressed by metastatic pancreatic cancer cells. Am. J. Physiol. Cell Physiol. 2012, 303, C616-C624.
90. Fry, S., Afrough, B., Leathem, A., Dwek, M., Lectin array-based strategies for identifying metastasis-associated changes in glycosylation. Methods Mol. Biol. 2012, 878, 267-272.
91. Tao, S. C., Li, Y., Zhou, J., Qian, J. et al., Lectin microarrays identify cell-specific and functionally significant cell surface glycan markers. Glycobiology 2008, 18, 761-769.
92. Rambaruth, N. D., Dwek, M. V., Cell surface glycan-lectin interactions in tumor metastasis. Acta Histochem. 2011, 113, 591-600.
93. Greenbaum, D., Baruch, A., Hayrapetian, L., Darula, Z. et al., Chemical approaches for functionally probing the proteome. Mol. Cell. Proteomics 2002, 1, 60-68.
94. Wilson, D. S., Nock, S., Recent developments in protein microarray technology. Angew. Chem. Int. Ed. Engl. 2003, 42, 494-500.
95. Jessani, N., Liu, Y., Humphrey, M., Cravatt, B. F., Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. Proc. Natl. Acad. Sci. USA 2002, 99, 10335-10340.
96. Huels, C., Muellner, S., Meyer, H. E., Cahill, D. J., The impact of protein biochips and microarrays on the drug development process. Drug Discov. Today 2002, 7, S119-S124.
97. He, J., Liu, Y., Xie, X., Zhu, T. et al., Identification of cell surface glycoprotein markers for glioblastoma-derived stem-like cells using a lectin microarray and LC-MS/MS approach. J. Proteome Res. 2010, 9, 2565-2572.
98. Tan, Z., Lu, W., Li, X., Yang, G. et al., Altered N-glycan expression profile in epithelial-to-mesenchymal transition of NMuMG Cells revealed by an integrated strategy using mass spectrometry and glycogene and lectin microarray analysis. J. Proteome Res. 2014, 13, 2783-2795.
99. Woodard, C. L., Goodwin, C. R., Wan, J., Xia, S. et al., Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. PLoS One 2013, 8, e72671.