Microarray Approaches to Autoantibody Profiling

Clinical Proteomics: From Diagnosis to Therapy

Volumn , Issue , 2008, Pages 511-532

  Astle, John M ^a   Kodadek, Thomas ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

Antigen mimic microarrays; Autoantibody profiling; Native antigen microarrays

Indexed keywords

EID: 84889345428     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527622153.ch28     Document Type: Chapter

References (73)

1. Smyth, M. J., Godfrey, D. I. and Trapani, J. A. (2001) A fresh look at tumor immunosurveillance and immunotherapy. Nature Immunology, 2 (4), 293-299.
2. Penn, I. (2000) Post-transplant malignancy: the role of immunosuppression. Drug Safety, 23 (2), 101-113.
3. Finn, O. J. (2005) Immune response as a biomarker for cancer detection and a lot more. The New England Journal of Medicine, 353 (12), 1288-1290.
4. Abu-Shakra, M., Buskila, D., Ehrenfeld, M., Conrad, K. and Shoenfeld, Y. (2001) Cancer and autoimmunity: autoimmune and rheumatic features in patients with malignancies. Annals of the Rheumatic Diseases, 60 (5), 433-441.
5. Koziol, J. A., Zhang, J. Y., Casiano, C. A., Peng, X. X., Shi, F. D., Feng, A. C., Chan, E. K. and Tan, E. M. (2003) Recursive partitioning as an approach to selection of immune markers for tumor diagnosis. Clinical Cancer Research, 9 (14), 5120-5126.
6. Wang, X., Yu, J., Sreekumar, A., Varambally, S., Shen, R., Giacherio, D., Mehra, R., Montie, J. E., Pienta, K. J., Sanda, M. G., Kantoff, P. W., Rubin, M. A., Wei, J. T., Ghosh, D. and Chinnaiyan, A. M. (2005) Autoantibody signatures in prostate cancer. The New England Journal of Medicine, 353 (12), 1224-1235.
7. Tan, E. M. (2001) Autoantibodies as reporters identifying aberrant cellular mechanisms in tumorigenesis. The Journal of Clinical Investigation, 108 (10), 1411-1415.
8. Ekins, R. P. (1989) Multi-analyte immunoassay. Journal of Pharmaceutical and Biomedical Analysis, 7 (2), 155-168.
9. Fodor, S. P., Read, J. L., Pirrung, M. C., Stryer, L., Lu, A. T. and Solas, D. (1991) Light-directed, spatially addressable parallel chemical synthesis. Science, 251 (4995), 767-773.
10. Schena, M., Shalon, D., Davis, R. W. and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270 (5235), 467-470.
11. Espina, V., Mehta, A. I., Winters, M. E., Calvert, V., Wulfkuhle, J., Petricoin, E. F., III and Liotta, L. A. (2003) Protein microarrays: molecular profiling technologies for clinical specimens. Proteomics, 3 (11), 2091-2100.
12. Sobek, J., Bartscherer, K., Jacob, A., Hoheisel, J. D. and Angenendt, P. (2006) Microarray technology as a universal tool for high-throughput analysis of biological systems. Combinatorial Chemistry and High Throughput Screening, 9 (5), 365-380.
13. Kang, M., Trofin, L., Mota, M. O. and Martin, C. R. (2005) Protein capture in silica nanotube membrane 3-D microwell arrays. Analytical Chemistry, 77 (19), 6243-6249.
14. Ziauddin, J. and Sabatini, D. M. (2001) Microarrays of cells expressing defined cDNAs. Nature, 411 (6833), 107-110.
15. Palmer, E. and Freeman, T. (2005) Cell-based microarrays: current progress, future prospects. Pharmacogenomics, 6 (5), 527-534.
16. Bailey, S. N. et al. (2006) Microarrays of lentiviruses for gene function screens in immortalized and primary cells. Natural Methods, 3 (2), 117-122.
17. Ramachandran, N., Hainsworth, E., Bhullar, B., Eisenstein, S., Rosen, B., Lau, A. Y., Walter, J. C. and LaBaer, J. (2004) Self-assembling protein microarrays. Science, 305 (5680), 86-90.
18. Robinson, W. H. (2006) Antigen arrays for antibody profiling. Current Opinion in Chemical Biology, 10 (1), 67-72.
19. Robinson, W. H. et al. (2003) Protein microarrays guide tolerizing DNA vaccine treatment of autoimmune encephalomyelitis. Nature Biotechnology, 21 (9), 1033-1039.
20. Quackenbush, J. (2006) Microarray analysis and tumor classification. The New England Journal of Medicine, 354 (23), 2463-2472.
21. Robinson, W. H., DiGennaro, C., Hueber, W., Haab, B. B., Kamachi, M., Dean, E. J., Fournel, S., Fong, D., Genovese, M. C., de Vegvar, H. E., Skriner, K., Hirschberg, D. L., Morris, R. I., Muller, S., Pruijn, G. J., van Venrooij, W. J., Smolen, J. S., Brown, P. O., Steinman, L. and Utz, P. J. (2002) Autoantigen microarrays for multiplex characterization of autoantibody responses. Nature Medicine, 8 (3), 295-301.
22. Soussi, T. (2000) p53 antibodies in the sera of patients with various types of cancer: a review. Cancer Research, 60 (7), 1777-1788.
23. Sidhu, S. S., Lowman, H. B., Cunningham, B. C. and Wells, J. A. (2000) Phage display for selection of novel binding peptides. Methods in Enzymology, 328, 333-363.
24. Chatterjee, M., Mohapatra, S., Ionan, A., Bawa, G., Ali-Fehmi, R., Wang, X., Nowak, J., Ye, B., Nahhas, F. A., Lu, K., Witkin, S. S., Fishman, D., Munkarah, A., Morris, R., Levin, N. K., Shirley, N. N., Tromp, G., Abrams, J., Draghici, S. and Tainsky, M. A. (2006) Diagnostic markers of ovarian cancer by high-throughput antigen cloning and detection on arrays. Cancer Research, 66 (2), 1181-1190.
25. Fernandez-Madrid, F., Tang, N., Alansari, H., Granda, J. L., Tait, L., Amirikia, K. C., Moroianu, M., Wang, X. and Karvonen, R. L. (2004) Autoantibodies to annexin XI-A and other autoantigens in the diagnosis of breast cancer. Cancer Research, 64 (15), 5089-5096.
26. Zhong, L., Hidalgo, G. E., Stromberg, A. J., Khattar, N. H., Jett, J. R. and Hirschowitz, E. A. (2005) Using protein microarray as a diagnostic assay for non-small cell lung cancer. American Journal of Respiratory and Critical Care Medicine, 172 (10), 1308-1314.
27. Raman, R., Raguram, S., Venkataraman, G., Paulson, J. C. and Sasisekharan, R. (2005) Glycomics: an integrated systems approach to structure-function relationships of glycans. Natural Methods, 2 (11), 817-824.
28. Paulson, J. C., Blixt, O., and Collins, B. E. (2006) Sweet spots in functional glycomics. Nature Chemistry and Biology, 2 (5), 238-248.
29. Wang, D., Liu, S., Trummer, B. J., Deng, C. and Wang, A. (2002) Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells. Nature Biotechnology, 20 (3), 275-281.
30. Blixt, O., Head, S., Mondala, T., Scanlan, C., Huflejt, M. E., Alvarez, R., Bryan, M. C., Fazio, F., Calarese, D., Stevens, J., Razi, N., Stevens, D. J., Skehel, J. J., van Die, I., Burton, D. R., Wilson, I. A., Cummings, R., Bovin, N., Wong, C. H. and Paulson, J. C. (2004) Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. Proceedings of the National Academy of Sciences of the United States of America, 101 (49), 17033-17038.
31. Schwarz, M., Spector, L., Gargir, A., Shtevi, A., Gortler, M., Altstock, R. T., Dukler, A. A. and Dotan, N. (2003) A new kind of carbohydrate array, its use for profiling antiglycan antibodies, and the discovery of a novel human cellulose-binding antibody. Glycobiology, 13 (11), 749-754.
32. Dotan, I., Fishman, S., Dgani, Y., Schwartz, M., Karban, A., Lemer, A., Weishauss, O., Spector, L., Shtevi, A., Altstock, R. T., Dotan, N. and Halpem, Z. (2006) Antibodies against laminaribioside and chitobioside are novel serologic markers in Crohn's disease. Gastroenterology, 131 (2), 366-378.
33. Lawrie, C. H., Marafioti, T., Hatton, C. S., Dirnhofer, S., Roncador, G., Went, P., Tzankov, A., Pileri, S. A., Pulford, K. and Banham, A. H. (2006) Cancerassociated carbohydrate identification in Hodgkin's lymphoma by carbohydrate array profiling. International Journal of Cancer, 118 (12), 3161-3166.
34. Kakugawa, Y., Wada, T., Yamaguchi, K., Yamanami, H., Ouchi, K., Sato, I. and Miyagi, T. (2002) Up-regulation of plasma membrane-associated ganglioside sialidase (Neu3) in human colon cancer and its involvement in apoptosis suppression. Proceedings of the National Academy of Sciences of the United States of America, 99 (16), 10718-10723.
35. Hakomori, S. (2002) Glycosylation defining cancer malignancy: new wine in an old bottle. Proceedings of the National Academy of Sciences of the United States of America, 99 (16), 10231-10233.
36. Hakomori, S. (2001) Tumor-associated carbohydrate antigens defining tumor malignancy: basis for development of anti-cancer vaccines. Advances in Experimental Medicine and Biology, 491, 369-402.
37. Stevens, J., Blixt, O., Tumpey, T. M., Taubenberger, J. K., Paulson, J. C. and Wilson, I. A. (2006) Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus. Science, 312 (5772), 404-410.
38. Kanter, J. L., Narayana, S., Ho, P. P., Catz, I., Warren, K. G., Sobel, R. A., Steinman, L. and Robinson, W. H. (2006) Lipid microarrays identify key mediators of autoimmune brain inflammation. Nature Medicine, 12 (1), 138-143.
39. Balboni, I., Chan, S. M., Kattah, M., Tenenbaum, J. D., Butte, A. J. and Utz, P. J. (2006) Multiplexed protein array platforms for analysis of autoimmune diseases. Annu Rev Immunol, 24, 391-418.
40. Nam, M. J., Madoz-Gurpide, J., Wang, H., Lescure, P., Schmalbach, C. E., Zhao, R., Misek, D. E., Kuick, R., Brenner, D. E. and Hanash, S. M. (2003) Molecular profiling of the immune response in colon cancer using protein microarrays: occurrence of autoantibodies to ubiquitin C-terminal hydrolase L3. Proteomics, 3 (11), 2108-2115.
41. Janzi, M., Odling, J., Pan-Hammarstrom, Q., Sundberg, M., Lundeberg, J., Uhlen, M., Hammarstrom, L. and Nilsson, P. (2005) Serum microarrays for large scale screening of protein levels. Molecular and Cellular Proteomics, 4 (12), 1942-1947.
42. Emmert-Buck, M. R., Bonner, R. F., Smith, P. D., Chuaqui, R. F., Zhuang, Z., Goldstein, S. R., Weiss, R. A. and Liotta, L. A. (1996) Laser capture microdissection. Science, 274 (5289), 998-1001.
43. Paweletz, C. P., Charboneau, L., Bichsel, V. E., Simone, N. L., Chen, T., Gillespie, J. W., Emmert-Buck, M. R., Roth, M. J., Petricoin, E. F. III and Liotta, L. A. (2001) Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene, 20 (16), 1981-1989.
44. Chan, S. M., Ermann, J., Su, L., Fathman, C. G. and Utz, P. J. (2004) Protein microarrays for multiplex analysis of signal transduction pathways. Nature Medicine, 10 (12), 1390-1396.
45. Haab, B. B. (2006) Applications of antibody array platforms. Current Opinion in Biotechnology, 17 (4), 415-421.
46. Sanchez-Carbayo, M. (2006) Antibody arrays: technical considerations and clinical applications in cancer. Clinical Chemistry, 52 (9), 1651-1659.
47. Hudelist, G., Pacher-Zavisin, M., Singer, C. F., Holper, T., Kubista, E., Schreiber, M., Manavi, M., Bilban, M. and Czerwenka, K. (2004) Use of highthroughput protein array for profiling of differentially expressed proteins in normal and malignant breast tissue. Breast Cancer Research and Treatment, 86 (3), 281-291.
48. Belov, L., de la Vega, O., dos Remedios, C. G., Mulligan, S. P. and Christopherson, R. I. (2001) Immunophenotyping of leukemias using a cluster of differentiation antibody microarray. Cancer Research, 61 (11), 4483-4489.
49. Mor, G., Visintin, I., Lai, Y., Zhao, H., Schwartz, P., Rutherford, T., Yue, L., Bray-Ward, P. and Ward, D. C. (2005) Serum protein markers for early detection of ovarian cancer. Proceedings of the National Academy of Sciences of the United States of America, 102 (21), 7677-7682.
50. Miller, J. C., Zhou, H., Kwekel, J., Cavallo, R., Burke, J., Butler, E. B., The, B. S. and Haab, B. B. (2003) Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics, 3 (1), 56-63.
51. Gao, W. M., Kuick, R., Orchekowski, R. P., Misek, D. W., Qui, J., Greenberg, A. K., Rom, W. N., Brenner, D. E., Omenn, G. S., Haab, B. B. and Hanash, S. M. (2005) Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis. BMC Cancer, 5, 110.
52. Srivastava, M., Eidelman, O., Jozwik, C., Paweletz, C., Huang, W., Zeitlin, P. L. and Pollard, H. B. (2006) Serum proteomic signature for cystic fibrosis using an antibody microarray platform. Molecular Genetics and Metabolism, 87 (4), 303-310.
53. Ellmark, P., Belov, L., Huang, P., Lee, C. S., Solomon, M. J., Morgan, D. K. and Christopherson, R. I. (2006) Multiplex detection of surface molecules on colorectal cancers. Proteomics, 6 (6), 1791-1802.
54. Christopherson, R. I., Stoner, K., Barber, N., Belov, L., Woolfson, A., Scott, M., Bendall, L. and Mulligan, S. P. (2006) Classification of AML using a monoclonal antibody microarray. Methods in Molecular Medicine, 125, 241-251.
55. Ellmark, P., Ingvarsson, J., Carlsson, A., Lundin, B. S., Wingren, C. and Borrebaeck, C. A. (2006) Identification of protein expression signatures associated with H. pylori infection and gastric adenocarcinoma using recombinant antibody microarrays. Molecular and Cellular Proteomics, 5 (9), 1638-1646.
56. Belov, L., Mulligan, S. P., Barber, N., Woolfson, A., Scott, M., Stoner, K., Chrisp, J. S., Sewell, W. A., Bradstock, K. F., Bendall, L., Pascovici, D. S., Thomas, M., Erber, W., Huang, P., Sartor, M., Young, G. A., Wiley, J. S., Juneja, S., Wierda, W. G., Green, A. R., Keating, M. J. and Christopherson, R. I. (2006) Analysis of human leukaemias and lymphomas using extensive immunophenotypes from an antibody microarray. British Journal of Haematology, 135 (2), 184-197.
57. Woolfson, A., Stebbing, J., Tom, B. D., Stoner, K. J., Gilks, W. R., Kreil, D. P., Mulligan, S. P., Belov, L., Chrisp, J. S., Errington, W., Wildfire, A., Erber, W. N., Bower, M., Gazzard, B., Christopherson, R. I. and Scott, M. A. (2005) Conservation of unique cellsurface CD antigen mosaics in HIV-1-infected individuals. Blood, 106 (3), 1003-1007.
58. Qin, S., Qui, W., Ehrlich, J. R., Ferdinand, A. S., Richie, J. P., O'leary, M. P., Lee, M. L. and Liu, B. C. (2006) Development of a ''reverse capture'' autoantibody microarray for studies of antigen-autoantibody profiling. Proteomics, 6 (10), 3199-3209.
59. Hosse, R. J., Rothe, A., and Power, B. E. (2006) A new generation of protein display scaffolds for molecular recognition. Protein Science, 15 (1), 14-27.
60. Rothe, A., Hosse, R. J., and Power, B. E. (2006) In vitro display technologies reveal novel biopharmaceutics. FASEB Journal, 20 (10), 1599-1610.
61. Silverman, J. et al. (2005) Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains. Nature Biotechnology, 23 (12), 1556-1561.
62. Kodadek, T., Reddy, M. M., Olivos, H. J., Bachhawat-Sikder, K. and Alluri, P. G. (2004) Synthetic molecules as antibody replacements. Accounts of Chemical Research, 37 (9), 711-718.
63. Reddy, M. M., Bachhawat-Sikder, K. and Kodadek, T. (2004) Transformation of low-affinity lead compounds into high-affinity protein capture agents. Chemistry and Biology, 11 (8), 1127-1137.
64. Bunka, D. H. and Stockley, P. G. (2006) Aptamers come of age-at last. Nature Reviews Microbiology, 4 (8), 588-596.
65. Collett, J. R., Cho, E. J. and Ellington, A. D. (2005) Production and processing of aptamer microarrays. Methods, 37 (1), 4-15.
66. Quintana, F. J., Hagedom, P. H., Elizur, G., Merbl, Y., Domany, E. and Cohen, I. R. (2004) Functional immunomics: microarray analysis of IgG autoantibody repertoires predicts the future response of mice to induced diabetes. Proceedings of the National Academy of Sciences of the United States of America, 101 (Suppl. 2), 14615-14621.
67. Mintz, P. J., Kim, J., Do, K. A., Wang, X., Zinner, R. G., Cristofanilli, M., Arap, M. A., Hong, W. K., Troncoso, P., Logothetis, C. J., Pasqualini, R. and Arap, W. (2003) Fingerprinting the circulating repertoire of antibodies from cancer patients. Nature Biotechnology, 21 (1), 57-63.
68. Vidal, C. I., Mintz, P. J., Lu, K., Ellis, L. M., Manenti, L., Giavazzi, R., Gershenson, D. M., Broaddus, R., Liu, J., Arap, W. and Pasquialini, R. (2004) An HSP90-mimic peptide revealed by fingerprinting the pool of antibodies from ovarian cancer patients. Oncogene, 23 (55), 8859-8867.
69. Simon, R. J., Kania, R. S., Zuckermann, R. N., Huebner, V. D., Jewell, D. A., Banville, S., Ng, S., Wang, L., Rosenberg, S., Marlowe, C. K., Spellmeyer, D. C., Tan, R., Frankel, A. D., Santi, D. V., Cohen, F. E. and Bartlett, P. A. (1992) Peptoids: a modular approach to drug discovery. Proceedings of the National Academy of Sciences of the United States of America, 89 (20), 9367-9371.
70. Moe, G. R. and Granoff, D. M. (2001) Molecular mimetics of Neisseria meningitidis serogroup B polysaccharide. International Reviews of Immunology, 20 (2), 201-220.
71. Reddy, M. M. and Kodadek, T. (2005) Protein ''fingerprinting'' in complex mixtures with peptoid microarrays. Proceedings of the National Academy of Sciences of the United States of America, 102 (36), 12672-12677.
72. Pusztai, L. and Hess, K. R. (2004) Clinical trial design for microarray predictive marker discovery and assessment. Annals of Oncology, 15 (12), 1731-1737.
73. Billings, P. R. (2006) Three barriers to innovative diagnostics. Nature Biotechnology, 24 (8), 917-918.