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Protein microarrays and proteomics

Abstract

The system-wide study of proteins presents an exciting challenge in this information-rich age of whole-genome biology. Although traditional investigations have yielded abundant information about individual proteins, they have been less successful at providing us with an integrated understanding of biological systems. The promise of proteomics is that, by studying many components simultaneously, we will learn how proteins interact with each other, as well as with non-proteinaceous molecules, to control complex processes in cells, tissues and even whole organisms. Here, I discuss the role of microarray technology in this burgeoning area.

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Figure 1: The spectrum of protein analysis, ranging from traditional biochemistry to unbiased proteomics.
Figure 2: Current immunoassay strategies used in protein-detecting microarrays.

Bob Crimi

Figure 3: Complications arising from regulated protein–protein interactions.

Bob Crimi

Figure 4: Proof-of-concept experiments showing the detection of protein–protein interactions on a model protein function microarray37.
Figure 5: A 'proteome chip' composed of 6,566 protein samples representing 5,800 unique proteins, which are spotted in duplicate on a single nickel-coated glass microscope slide39.

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References

  1. Kodadek, T. Protein microarrays: prospects and problems. Chem. Biol. 8, 105–115 (2001).

    Article  CAS  Google Scholar 

  2. Heidelberger, M. & Kendall, F.E. A quantitative study of the precipitation reaction between type III pneumococcus polysaccaride and purified homologous antibody. J. Exp. Med. 50, 809–823 (1929).

    Article  CAS  Google Scholar 

  3. Yalow, R.S. & Berson, S.A. Assay of plasma insulin in human subjects by immunological methods. Nature 184, 1648–1649 (1959).

    Article  CAS  Google Scholar 

  4. Engvall, E. & Perlman, P. Enzyme-linked immunosorbent assay (ELISA). Quantitative assay of immunoglobulin G. Immunochemistry 8, 871–874 (1971).

    Article  CAS  Google Scholar 

  5. Ekins, R., Chu, F. & Biggart, E. Multispot, multianalyte, immunoassay. Ann. Biol. Clin. (Paris) 48, 655–666 (1990).

    CAS  Google Scholar 

  6. Silzel, J.W., Cercek, B., Dodson, C., Tsay, T. & Obremski, R.J. Mass-sensing, multianalyte microarray immunoassay with imaging detection. Clin. Chem. 44, 2036–2043 (1998).

    CAS  Google Scholar 

  7. Moody, M.D., Van Arsdell, S.W., Murphy, K.P., Orencole, S.F. & Burns, C. Array-based ELISAs for high-throughput analysis of human cytokines. Biotechniques 31, 186–194 (2001).

    Article  CAS  Google Scholar 

  8. 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. 294, 55–62 (2001).

    Article  CAS  Google Scholar 

  9. Wiese, R., Belosludtsev, Y., Powdrill, T., Thompson, P. & Hogan, M. Simultaneous multianalyte ELISA performed on a microarray platform. Clin. Chem. 47, 1451–1457 (2001).

    CAS  Google Scholar 

  10. Jenison, R., La, H., Haeberli, A., Ostroff, R. & Polisky, B. Silicon-based biosensors for rapid detection of protein or nucleic acid targets. Clin. Chem. 47, 1894–1900 (2001).

    CAS  Google Scholar 

  11. Tam, S.W., Wiese, R., Lee, S., Gilmore, J. & Kumble, K.D. Simultaneous analysis of eight human Th1/Th2 cytokines using microarrays. J. Immunol. Methods 261, 157–165 (2002).

    Article  CAS  Google Scholar 

  12. Schweitzer, B. et al. Multiplexed protein profiling on microarrays by rolling-circle amplification. Nature Biotechnol. 20, 359–365 (2002).

    Article  CAS  Google Scholar 

  13. Lizardi, P. et al. Mutation detection and single-molecule counting using isothermal rolling circle amplification. Nature Genet. 19, 225–232 (1998).

    Article  CAS  Google Scholar 

  14. Haab, B.B., Dunham, M.J. & Brown, P.O. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2, research0004.1–0004.13 (2001).

  15. Sreekumar, A. et al. Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res. 61, 7585–7593 (2001).

    CAS  Google Scholar 

  16. Knezevic, V. et al. Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics 1, 1271–1278 (2001).

    Article  CAS  Google Scholar 

  17. Petricoin, E.F., Zoon, K.C., Kohn, E.C., Barrett, J.C. & Liotta, L.A. Clinical proteomics: translating benchside promise into bedside reality. Nat. Rev. Drug Discov. 1, 683–695 (2002).

    Article  CAS  Google Scholar 

  18. Belov, L., de la Vega, O., dos Remedios, C.G., Mulligan, S.P. & Christopherson, R.I. Immunophenotyping of leukemias using a cluster of differentiation antibody microarray. Cancer Res. 61, 4483–4489 (2001).

    CAS  Google Scholar 

  19. Paweletz, C.P. et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20, 1981–1989 (2001).

    Article  CAS  Google Scholar 

  20. Madoz-Gurpide, J., Wang, H., Misek, D.E., Brichory, F. & Hanash, S.M. Protein based microarrays: a tool for probing the proteome of cancer cells and tissues. Proteomics 1, 1279–1287 (2001).

    Article  CAS  Google Scholar 

  21. Mendoza, L.G. et al. High-throughput microarray-based enzyme-linked immunosorbent assay (ELISA). Biotechniques 27, 778–788 (1999).

    Article  CAS  Google Scholar 

  22. Wiltshire, S. et al. Detection of multiple allergen-specific IgEs on microarrays by immunoassay with rolling circle amplification. Clin. Chem. 46, 1990–1993 (2000).

    CAS  Google Scholar 

  23. Mullenix, M.C., Wiltshire, S., Shao, W., Kitos, G. & Schweitzer, B. Allergen-specific IgE detection on microarrays using rolling circle amplification: correlation with in vitro assays for serum IgE. Clin. Chem. 47, 1926–1929 (2001).

    Google Scholar 

  24. Kim, T.E. et al. Quantitative measurement of serum allergen-specific IgE on protein chip. Exp. Mol. Med. 34, 152–158 (2002).

    Article  CAS  Google Scholar 

  25. Avseenko, N.V., Morozova, T.Y., Ataullakhanov, F.I. & Morozov, V.N. Immunoassay with multicomponent protein microarrays fabricated by electrospray deposition. Anal. Chem. 74, 927–933 (2002).

    Article  CAS  Google Scholar 

  26. Hiller, R. et al. Microarrayed allergen molecules: diagnostic gatekeepers for allergy treatment. FASEB J. 16, 414–416 (2002).

    Article  CAS  Google Scholar 

  27. Joos, T.O. et al. A microarray enzyme-linked immunosorbent assay for autoimmune diagnostics. Electrophoresis 21, 2641–2650 (2000).

    Article  CAS  Google Scholar 

  28. Robinson, W.H. et al. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nature Med. 8, 295–301 (2002).

    Article  CAS  Google Scholar 

  29. Mezzasoma, L. et al. Antigen microarrays for serodiagnosis of infectious diseases. Clin. Chem. 48, 121–130 (2002).

    CAS  Google Scholar 

  30. Fromont-Racine, M., Rain, J.C. & Legrain, P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet. 16, 277–282 (1997).

    Article  CAS  Google Scholar 

  31. Uetz, P. et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627 (2000).

    Article  CAS  Google Scholar 

  32. Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98, 4569–4574 (2001).

    Article  CAS  Google Scholar 

  33. Gavin, A.C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002).

    Article  CAS  Google Scholar 

  34. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183 (2002).

    Article  CAS  Google Scholar 

  35. Ge, H. UPA, a universal protein array system for quantitative detection of protein–protein, protein–DNA, protein–RNA and protein–ligand interactions. Nucleic Acids Res. 28, e3.i–e3.vii (2000).

    Article  Google Scholar 

  36. Arenkov, P. et al. Protein microchips: use for immunoassay and enzymatic reactions. Anal. Biochem. 278, 123–131 (2000).

    Article  CAS  Google Scholar 

  37. MacBeath, G. & Schreiber, S.L. Printing proteins as microarrays for high-throughput function determination. Science 289, 1760–1763 (2000).

    CAS  Google Scholar 

  38. Zhu, H. et al. Analysis of yeast protein kinases using protein chips. Nature Genet. 26, 283–289 (2000).

    Article  CAS  Google Scholar 

  39. Zhu, H. et al. Global analysis of protein activities using proteome chips. Science 293, 2101–2105 (2001).

    Article  CAS  Google Scholar 

  40. Schultz, J., Milpetz, F., Bork, P. & Ponting, C.P. SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl Acad. Sci. USA 95, 5857–5864 (1998).

    Article  CAS  Google Scholar 

  41. Bussow, K. et al. A method for global protein expression and antibody screening on high-density filters of an arrayed cDNA library. Nucleic Acids Res. 26, 5007–5008 (1998).

    Article  CAS  Google Scholar 

  42. Bussow, K., Nordhoff, E., Lubbert, C., Lehrach, H. & Walter, G. A human cDNA library for high-throughput protein expression screening. Genomics 65, 1–8 (2000).

    Article  CAS  Google Scholar 

  43. Lueking, A. et al. Protein microarrays for gene expression and antibody screening. Anal. Biochem. 270, 103–111 (1999).

    Article  CAS  Google Scholar 

  44. Lee, J. & Bedford, M.T. PABP1 identified as an arginine methyltransferase substrate using high-density protein arrays. EMBO Rep. 3, 268–273 (2002).

    Article  CAS  Google Scholar 

  45. Walhout, A.J. et al. GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 328, 575–592 (2000).

    Article  CAS  Google Scholar 

  46. Brizuela, L., Braun, P. & LaBaer, J. FLEXGene repository: from sequenced genomes to gene repositories for high-throughput functional biology and proteomics. Mol. Biochem. Parasitol. 118, 155–165 (2001).

    Article  CAS  Google Scholar 

  47. Albala, J.S. et al. From genes to proteins: high-throughput expression and purification of the human proteome. J. Cell. Biochem. 80, 187–191 (2000).

    Article  CAS  Google Scholar 

  48. Braun, P. et al. Proteome-scale purification of human proteins from bacteria. Proc. Natl Acad. Sci. USA 99, 2654–2659 (2002).

    Article  CAS  Google Scholar 

  49. Chen, R. et al. Simultaneous quantification of six human cytokines in a single sample using microparticle-based flow cytometric technology. Clin. Chem. 45, 1693–1694 (1999).

    CAS  Google Scholar 

  50. Ziauddin, J. & Sabatini, D.M. Microarrays of cells expressing defined cDNAs. Nature 411, 107–110 (2001).

    Article  CAS  Google Scholar 

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MacBeath, G. Protein microarrays and proteomics. Nat Genet 32 (Suppl 4), 526–532 (2002). https://doi.org/10.1038/ng1037

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