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The Korean Society for Biotechnology and Bioengineering (한국생물공학회)
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Applications and Developmental Prospect of Protein Microarray Technology

Protein Microarray의 응용 및 발전 전망

  • Oh, Young-Hee (Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST)) ;
  • Han, Min-Kyu (Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST)) ;
  • Kim, Hak-Sung (Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST))
  • Published : 2007.12.31
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Abstract

Analysis of protein interactions/functions in a microarray format has been of great potential in drug discovery, diagnostics, and cell biology, because it is amenable to large-scale and high-throughput biological assays in a rapid and economical way. In recent years, the protein microarray have broaden their utility towards the global analysis of protein interactions on a proteome scale, the functional activity analysis based on protein interactions and post-translational modifications (PTMs), and the discovery of biomarkers through profiling of protein expression between sample and reference pool. As a promising tool for proteomics, the protein microarray technology has advanced outstandingly over the past decade in terms of surface chemistry, acquisition of relevant proteins on a proteomic level, and detection methods. In this article, we briefly describe various techniques for development of protein microarray, and introduce developmental state of protein microarray and its applications.

현재 많은 대학과 기업에서 다양한 방법으로 상용화가 가능한 protein microarray의 개발을 위해 많은 연구를 집중하고 있다. Protein microarray의 제작 및 분석 조건을 최적화하기 위한 연구도 진행되고 있지만 protein microarray로 부터 얻은 분석 결과를 모든 연구자들이 공유하고 통합하기 위한 노력이 절실한 실정이다. 뿐만 아니라, PCR 같은 무한 확장 방법이 존재하지 않는 단백질의 특성을 고려할 때, 좀 더 실용적인 protein microarray를 많이 만들기 위해서는 수많은 단백질들과 결합할 수 있는 특이성이 높고 결합력이 강한 capture molecule들을 개발하는 것이 필수이다. 그러나 이러한 장애에도 불구하고 protein microarray는 아주 적은 시료량으로 high-throughput assay가 가능하다는 장점 때문에 현재의 생명과학의 발전 추세로 볼 때 앞으로 protein microarray가 조만간 실용화될 것이며 이의 시장성은 매우 클 것으로 기대된다. 보다 빠른 실용화를 위해서는 protein microarray의 개발에 필요한 기반 기술의 개발과 동시에 이를 활용하기 위한 contents의 개발도 절실히 요구된다.

Keywords

References

  1. Cutler, P. (2003), Protein arrays: the current state-of-the-art, Proteomics 3, 3-18 https://doi.org/10.1002/pmic.200390007
  2. Madoz-Gurpide, J., Wang H., Misek D. E., Brichory F., and S. M. Hanash (2001), Protein based microarrays: a tool for probing the proteome of cancer cells and tissues, Proteomics 1, 1279-1287 https://doi.org/10.1002/1615-9861(200110)1:10<1279::AID-PROT1279>3.0.CO;2-W
  3. Andersson, O., M. Kozlowski, T. Garachtchenko, C. Nikoloff, N. Lew, D. J. Litman, and G. Chaga (2005), Determination of relative protein abundance by internally normalized ratio algorithm with antibody arrays, J. Proteome Res. 4, 758-767 https://doi.org/10.1021/pr049776f
  4. Schena, M., D. Shalon, R. W. Davis, and P. O. Brown (1995), Quantitative monitoring of gene expression patterns with a complementary DNA microarray, Science 270, 467-470 https://doi.org/10.1126/science.270.5235.467
  5. Angenendt, P. (2005), Progress in protein and antibody microarray technology, Drug Discov. Today 10, 503-511 https://doi.org/10.1016/S1359-6446(05)03392-1
  6. Mitchell, P. (2002), A perspective on protein microarrays, Nat. Biotechnol. 3, 225-229
  7. Tomizaki, K. Y., K. Usui, and H. Mihara (2005), Protein-detecting microarrays: current accomplishments and requirements, Chembiochem. 6, 782-799 https://doi.org/10.1002/cbic.200400232
  8. LaBaer, J. and N. Ramachandran (2005), Protein microarrays as tools for functional proteomics, Curr Opin Chem Biol. 9, 14-19 https://doi.org/10.1016/j.cbpa.2004.12.006
  9. Hong, M. Y., D. Lee, and H. S. Kim (2005), Kinetic and equilibrium binding analysis of protein-ligand interactions at poly(amidoamine) dendrimer monolayers, Anal. Chem. 77, 7326-7334 https://doi.org/10.1021/ac051045r
  10. Ramachandran, N., E. Hainsworth, B. Bhullar, S. Eisenstein, B. Rosen, A. Y. Lau, J. C. Walter, and J. LaBaer (2004), Self-assembling protein microarrays, Science 305, 86-90 https://doi.org/10.1126/science.1097639
  11. Wingren, C., C. Steinhauer, J. Ingvarsson, E. Persson, K. Larsson, and C. A. Borrebaeck (2005), Microarrays based on affinity-tagged single-chain Fv antibodies: sensitive detection of analyte in complex proteomes, Proteomics 5, 1281-1291 https://doi.org/10.1002/pmic.200401009
  12. Bock, C., M. Coleman, B. Collins, J. Davis, G. Foulds, L. Gold, C. Greef, J. Heil, J. S. Heilig, B. Hicke, M. N. Hurst, G. M. Husar, D. Miller, R. Ostroff, H. Petach, D. Schneider, B. Vant-Hull, S. Waugh, A. Weiss, S. K. Wilcox, and D. Zichi (2004), Photoaptamer arrays applied to multiplexed proteomic analysis, Proteomics 4, 609-618 https://doi.org/10.1002/pmic.200300631
  13. Holz. C., O. Hesse, N. Bolotina, U. Stahl, and C. Lang (2002), A micro-scale process for high-throughput expression of cDNAs in the yeast Saccharomyces cerevisiae, Protein Expr. Purif. 25, 372-378 https://doi.org/10.1016/S1046-5928(02)00029-3
  14. Kung, L. A. and M. Snyder (2006), Proteome chips for whole-organism assays, Nat. Rev. Mol. Cell Biol. 7, 617-622 https://doi.org/10.1038/nrm1941
  15. Zhou, H., K. Bouwman, M. Schotanus, C. Verweij, J. A. Marrero, D. Dillon, J. Costa, P. Lizardi, and B. B. Haab (2004), Two-color, rolling-circle amplification on antibody microarrays for sensitive, multiplexed serum-protein measurements, Genome Biol. 5, R28 https://doi.org/10.1186/gb-2004-5-2-p5
  16. Varnum, S. M., R. L. Woodbury, and R. C. Zangar (2004), A protein microarray ELISA for screening biological fluids, Methods Mol. Biol. 264, 161-172
  17. Kyo, M., K. Usui-Aoki, and H. Koga (2005), Label-free detection of proteins in crude cell lysate with antibody arrays by a surface plasmon resonance imaging technique, Anal. Chem. 77, 7115-7121 https://doi.org/10.1021/ac050884a
  18. Espejo, A., J. Cote, A. Bednarek, S. Richard, and M. T. Bedford (2002), A protein-domain microarray identifies novel protein-protein interactions, Biochem. J. 367, 697-702 https://doi.org/10.1042/BJ20020860
  19. Otte, L., U. Wiedemann, B. Schlegel, J. R. Pires, M. Beyermann, P. Schmieder, G. Krause, R. Volkmer-Engert, J. Schneider- Mergener, and H. Oschkinat (2003), WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains, Protein Sci. 12, 491-500 https://doi.org/10.1110/ps.0233203
  20. Stoevesandt, O., M. Elbs, K. Kohler, A. C. Lellouch, R. Fischer, T. Andre, and R. Brock (2005), Peptide microarrays for the detection of molecular interactions in cellular signal transduction, Proteomics 5, 2010-2017 https://doi.org/10.1002/pmic.200401095
  21. Jones, R. B., A. Gordus, J. A. Krall, and G. MacBeath (2006), A quantitative protein interaction network for the ErbB receptors using protein microarrays, Nature 439, 168-174 https://doi.org/10.1038/nature04177
  22. Ho, S. W., G. Jona, C. T. Chen, M. Johnston, and M. Snyder (2006), Linking DNA-binding proteins to their recognition sequences by using protein microarrays, Proc. Natl. Acad. Sci. USA 103, 9940-9945
  23. Kersten, B., A. Possling, F. Blaesing, E. Mirgorodskaya, J. Gobom, and H. Seitz (2004), Protein microarray technology and ultraviolet crosslinking combined with mass spectrometry for the analysis of protein-DNA interactions, Anal. Biochem. 331, 303-13 https://doi.org/10.1016/j.ab.2004.05.008
  24. Zhu, H., M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Snyder (2001), Global analysis of protein activities using proteome chips, Science 293, 2101-2105 https://doi.org/10.1126/science.1062191
  25. Zhu, H., J. F. Klemic, S. Chang, P. Bertone, A. Casamayor, K. G. Klemic, D. Smith, M. Gerstein, M. A. Reed, and M. Snyder (2000), Analysis of yeast protein kinases using protein chips, Nat. Genet. 26, 283-289 https://doi.org/10.1038/81576
  26. Houseman, B. T., J. H. Huh, S. J. Kron, and M. Mrksich (2002), Peptide chips for the quantitative evaluation of protein kinase activity, Nat. Biotechnol. 20, 270-274 https://doi.org/10.1038/nbt0302-270
  27. Hong, Y., B. L. Webb, H. Su, E. J. Mozdy, Y. Fang, Q. Wu, L. Liu, J. Beck, A. M. Ferrie, S. Raghavan, J. Mauro, A. Carre, D. Mueller, F. Lai, B. Rasnow, M. Johnson, H. Min, J. Salon, and J. Lahiri (2005), Functional GPCR microarrays, J. Am. Chem. Soc. 127, 15350-15351 https://doi.org/10.1021/ja055101h
  28. Oh, Y. H., M. Y. Hong, Z. Jin, T. Lee, M. K. Han, S. Park, and H. S. Kim (2007), Chip-based analysis of SUMO (small ubiquitin-like modifier) conjugation to a target protein, Biosens Bioelectron. 22, 1260-1267 https://doi.org/10.1016/j.bios.2006.05.023
  29. Haab, B. B., M. J. Dunham, and P. O. Brown (2001), Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions, Genome Biol. 2, RESEARCH0004
  30. Andersson, O., M. Kozlowski, T. Garachtchenko, C. Nikoloff, N. Lew, D. J. Litman, and G. Chaga (2005), Determination of relative protein abundance by internally normalized ratio algorithm with antibody arrays, J. Proteome Res. 4, 758-67 https://doi.org/10.1021/pr049776f
  31. Han, M. K., M. Y. Hong, D. Lee, D. E. Lee, G. Y. Noh, J. H. Lee, S. H. Kim, and H. S. Kim (2006), Expression Profiling of Proteins in L-Threonine Biosynthetic Pathway of Escherichia coli by using Antibody Microarray, Proteomics 6, 5929-5940 https://doi.org/10.1002/pmic.200600324
  32. Sukhanov, S. and P. Delafontaine (2005), Protein chip-based microarray profiling of oxidized low density lipoprotein-treated cells, Proteomics 5, 1274-1280 https://doi.org/10.1002/pmic.200400985
  33. Sreekumar, A., M. K. Nyati, S. Varambally, T. R. Barrette, D. Ghosh, T. S. Lawrence, and A. M. Chinnaiyan (2001), Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins, Cancer Res. 61, 7585-7593
  34. Miller, J. C., H. Zhou, J. Kwekel, R. Cavallo, J. Burke, E. B. Butler, B. S. Teh, and B. B. Haab (2003), Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers, Proteomics 3, 56-63 https://doi.org/10.1002/pmic.200390009
  35. Steller, S., P. Angenendt, D. J. Cahill, S. Heuberger, H. Lehrach, and J. Kreutzberger (2005), Bacterial protein microarrays for identification of new potential diagnostic markers for Neisseria meningitidis infections, Proteomics 5, 2048-2055 https://doi.org/10.1002/pmic.200401097
  36. Gao, W. M., R. Kuick, R. P. Orchekowski, D. E. Misek, J. Qiu, A. K. Greenberg, W. N. Rom, D. E. Brenner, G. S. Omenn, B. B. Haab, and S. M. Hanash (2005), Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis, BMC Cancer 5, 110 https://doi.org/10.1186/1471-2407-5-110
  37. Zhu, H., S. Hu, G. Jona, X. Zhu, N. Kreiswirth, B. M. Willey, T. Mazzulli, G. Liu, Q. Song, P. Chen, M. Cameron, A. Tyler, J. Wang, J. Wen, W. Chen, S. Compton, and M. Snyder (2006), Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray, Proc. Natl. Acad. Sci. USA 103, 4011-4016
  38. Hiller, R., S. Laffer, C. Harwanegg, M. Huber, W. M. Schmidt, A. Twardosz, B. Barletta, W. M. Becker, K. Blaser, H. Breiteneder, M. Chapman, R. Crameri, M. Duchene, F. Ferreira, H. Fiebig, K. Hoffmann-Sommergruber, T. P. King, T. Kleber-Janke, V. P. Kurup, S. B. Lehrer, J. Lidholm, U. Muller, C. Pini, G. Reese, O. Scheiner, A. Scheynius, H. D. Shen, S. Spitzauer, R. Suck, I. Swoboda, W. Thomas, R. Tinghino, M. Van Hage-Hamsten, T. Virtanen, D. Kraft, M. W. Muller, and R. Valenta (2002), Microarrayed allergen molecules: diagnostic gatekeepers for allergy treatment, FASEB J. 16, 414-416 https://doi.org/10.1096/fj.01-0711fje
  39. Gelperin, D. M., M. A. White, M. L. Wilkinson, Y. Kon, L. A. Kung, K. J. Wise, N. Lopez-Hoyo, L. Jiang, S. Piccirillo, H. Yu, M. Gerstein, M. E. Dumont, E. M. Phizicky, and M. Snyder, E. J. Grayhack (2005), Biochemical and genetic analysis of the yeast proteome with a movable ORF collection, Genes Dev. 19, 2816-2826 https://doi.org/10.1101/gad.1362105
  40. Michaud, G. A., M. Salcius, F. Zhou, R. Bangham, J. Bonin, H. Guo, M. Snyder, P. F. Predki, and B. I. Schweitzer (2003), Analyzing antibody specificity with whole proteome microarrays, Nat. Biotechnol. 21, 1509-1512 https://doi.org/10.1038/nbt910
  41. Abbott, A. (2002), Betting on tomorrow's chips, Nature 415, 112-114 https://doi.org/10.1038/415112a
  42. Zhu, H. and M. Snyder (2003), Protein chip technology, Curr Opin Chem Biol. 7, 55-63 https://doi.org/10.1016/S1367-5931(02)00005-4
  43. Telechem's protocols
  44. Templin, M. F., S. D. Monika Schrenk, C. P. Traub, C. F. Vohringer, and O. J. Thomas (2002), Protein microarray technology, TRENDS in Biotech. 20, 160-166 https://doi.org/10.1016/S0167-7799(01)01910-2