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Disease proteomics toward bedside reality

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Abstract

The human genome has been sequenced, and investigation of its products has become possible in a sequencebased framework. More than 200000 protein species are expressed in the body from ≈30000 human genes. The term proteome, coined as a linguistic equivalent to the concept of genome, is used to describe the complete set of proteins that is expressed, and modified following expression, by the entire genome in a cell at any one time. Protein types and amounts expressed in a body vary greatly depending upon whether it is healthy or ill. Therefore, proteomics is attracting an increasing interest in its application to better understanding of disease processes, to development of new biomarkers for diagnosis and early detection of disease, and to accelerate drug development. There are numerous opportunities for medicine, although it is quite challenging to meet the needs for high sensitivity and high throughput required for disease-related investigations.

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References

  1. Nature. Proteomics, transcriptomics: what’s in a name? Nature (Lond) 1999; 402: 715.

    Google Scholar 

  2. Blackstock W, Nishimura T, Fujita Y. Proteome analysis in pharmaceutical industries. Protein Nucleic Acid Enzyme 1998; 43: 2214–21.

    CAS  Google Scholar 

  3. Patterson SD. Proteomics: the industrialization of protein chemistry. Curr Opin Biotechnol 2000; 11: 413–8.

    Article  PubMed  CAS  Google Scholar 

  4. Blackstock WP, Weir MP. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol 1999; 17: 121–7.

    Article  PubMed  CAS  Google Scholar 

  5. Petricoin EF, Zoon KC, Kohn EC, Barrett JC, Liotta LA. Clinical proteomics: translating benchside promise into bedside reality. Nat Rev Drug Discov 2002; l: 683–95.

    Article  Google Scholar 

  6. O’Farrel PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975; 250: 4007–21.

    Google Scholar 

  7. Hanash S. 2-D or not 2-D-is there a future for 2-D gels in proteomics? Insights from York proteomic meeting. Proteomics 2001; l: 635–7.

    Google Scholar 

  8. http://prospector.ucsf.edu.

  9. http://www.matrix-science.com.

  10. Tanaka K, Ido Y, Akita S, Yoshida Y, Yoshida T. Detection of high mass molecules by laser desorption time-of-flight mass spectrometry. Proc Japan-China Joint Symp Mass Spectrom 1987; 2: 185–8.

    Google Scholar 

  11. Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 1988; 60: 2299–301.

    Article  PubMed  CAS  Google Scholar 

  12. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. Electrospray ionization for mass spectrometry of large biomolecules. Science 1989; 246: 64–71.

    Article  PubMed  CAS  Google Scholar 

  13. Hanash S, Madoz-Gurpide J, Misek DE. Identification of novel targets for cancer therapy using expression proteomics. Leukemia 2002;16: 478–85.

    Article  PubMed  CAS  Google Scholar 

  14. Van Eyk JE. Proteomics: unraveling the complexity of heart disease and striving to change cardiology. Curr Opin Mol Ther 2001; 3: 546–53.

    PubMed  Google Scholar 

  15. Li XP, Pleissner KP, Regitz-Zagrosek V, Salnikow J, Jungblut P. A two-dimensional electrophoresis database of rat heart proteins. Electrophoresis 1999; 20: 891–7.

    Article  PubMed  CAS  Google Scholar 

  16. Evans G, Wheeler CH, Corbett JM, Dunn MJ. Construction of HSC-2D PAGE: a two-dimensional gel electrophoresis database of heart proteins. Electrophoresis 1997; 18: 471–9.

    Article  PubMed  CAS  Google Scholar 

  17. van der Velden J, Klein LJ, Zaremba R, Boontje NM, Huybregts MAJM, Stooker W, et al. Effects of calcium, inorganic phosphate, and pH on isometric force in single skinned cardiomyocytes from donor and failing human hearts. Circulation 2001; 104: 1140–6.

    Article  Google Scholar 

  18. Arrell DK, Neverova I, Fraser H, Marbán E, van Eyk JE. Proteomic analysis of pharmacologically preconditioned cardiomyocytes reveals novel phosphorylation of myosin light chain 1. Circ Res 2001; 89: 480–7.

    Article  PubMed  CAS  Google Scholar 

  19. Ping P, Zhang J, Pierce Jr WM, Bolli R. Functional proteomic analysis of protein kinase Ce signaling complexes in the normal heart and during cardioprotection. Circ Res 2001; 88: 59–62.

    Article  PubMed  CAS  Google Scholar 

  20. Heinke MY, Wheeler CH, Chang D, Einstein R, Drake-Holland A, Dunn MJ, et al. Protein changes observed in pacing-induced heart failure using two-dimensional electrophoresis. Electrophoresis 1998; 19: 2021–30.

    Article  PubMed  CAS  Google Scholar 

  21. Westbrook JA, Yan JX, Wait R, Welson SY, Dunn MJ. Zoomingin on the proteome: very narrow-range immobilised pH gradients reveal more protein species and isoforms. Electrophoresis 2001; 22: 2865–71.

    Article  PubMed  CAS  Google Scholar 

  22. Patton WF. Detection technologies in proteome analysis. J Chromatogr B 2002; 771: 3–31.

    Article  CAS  Google Scholar 

  23. Zhou G, Li H, DeCamp D, Chen S, Shu H, Gong Y, et al. 2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers. Mol Cell Proteomics 2001; l: 117–24.

    Google Scholar 

  24. Scike M, Kondo T, Fujii K, Yamada T, Gemma A, Kudo S, et al. Proteomic signature of human cancer cells. Proteomics 2004; 4: 2776–88.

    Article  Google Scholar 

  25. Zuo X, Speicher DW. Comprehensive analysis of complex proteomes using microscale solution isoelectrofocusing prior to narrow pH range two-dimensional electrophoresis. Proteomics 2002; 2: 58–68.

    Article  PubMed  CAS  Google Scholar 

  26. Anderson NL, Polanski M, Pieper R, Gatlin T, Tirumalai RS, Conrads TP, et al. The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol Cell Proteomics 2004; 3. 4: 311–26.

    Article  PubMed  CAS  Google Scholar 

  27. Stoeckli M, Chaurand P, Hallahan DE, Caprioli RM. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat Med 2001; 7: 493–6.

    Article  PubMed  CAS  Google Scholar 

  28. Oda Y, Huang K, Cross FR, Cowburn DBT, Chait BT. Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci U S A 1999; 96: 6591–6.

    Article  PubMed  CAS  Google Scholar 

  29. Regnier FE, Riggs L, Zhang R, Xiong L, Liu P, Chakraborty A, et al. Comparative proteomics based on stable isotope labeling and affinity selection. J Mass Spectrom 2002; 37: 133–45.

    Article  PubMed  CAS  Google Scholar 

  30. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotopecoded affinity tags. Nat Biotechnol 1999; 17: 994–9.

    Article  PubMed  CAS  Google Scholar 

  31. Giddings JC. Concepts and comparisons in multidimensional chromatography. J High Resolut Chromatogr 1987; 10: 319–23.

    Article  CAS  Google Scholar 

  32. Washburn MP, Wolters D, Yates JR III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001; 19: 242–7.

    Article  PubMed  CAS  Google Scholar 

  33. Fujii K, Nakano T, Kawamura T, Usui F, Bando F, Wang R, et al. Multi-dimensional protein profiling technology and its application to human plasma proteome. J Proteome Res 2004; 3: 712–8.

    Article  PubMed  CAS  Google Scholar 

  34. Fujii K, Nakano T, Hike H, Usui F, Bando Y, Tojo H, et al. Fully automated online multi-dimensional protein profiling system for complex mixtures. J Chromatogr A 2004 (in press).

  35. Soini Y, Paakko P, Nuorva K, Kamel D, Linnala A, Virtanen I, et al. Tenascin immunoreactivity in lung tumors. Am J Clin Pathol 1993; 100: 145–50.

    PubMed  CAS  Google Scholar 

  36. Patriarca C, Alfano RM, Sonnenberg A, Graziani D, Cassani B, de Melker A, et al. Integrin laminin receptor profile of pulmonary squamous cell and adenocarcinomas. Hum Pathol 1998; 29: 1208–15.

    Article  PubMed  CAS  Google Scholar 

  37. Moriya Y, Niki T, Yamada T, Matsuno Y, Kondo H, Hirohashi S. Increased expression of laminin-5 and its prognostic significance in lung adenocarcinomas of small size. Cancer 2001; 91: 1129–41.

    Article  PubMed  CAS  Google Scholar 

  38. Pavelic K, Banjac Z, Pavelic J, Spaventi S. Evidence for a role of EGF receptor in the progression of human lung carcinoma. Anticancer Res 1993; 13: 1133–7.

    PubMed  CAS  Google Scholar 

  39. Micke P, Hengstler JG, Ros R, Bittinger F, Metz T, Gebhard S, et al. c-erbB-2 expression in small-cell lung cancer is associated with poor prognosis. Int J Cancer 2001; 92: 474–9.

    Article  PubMed  CAS  Google Scholar 

  40. Barr LF, Campbell SE, Bochner BS, Dang CV. Association of the decreased expression of alpha-3-beta-1 integrin with the altered cell: environmental interactions and enhanced soft agar cloning ability of c-myc-overexpressing small cell lung cancer cells. Cancer Res 1998; 58: 5537–45.

    PubMed  CAS  Google Scholar 

  41. Kasprzak A, Przewozna M, Surdyk-Zasada J, Zabel M. The expression of selected neuroendocrine markers and of antineoplastic cytokines (IL-2 and IL-12) in lung cancers. Folia Morphol (Warsz) 2003; 62: 497–9.

    Google Scholar 

  42. Fisher Wilson J. The promise of disease proteomics: faster detection, diagnosis, and drug development. Ann Intern Med 2004; 40: 317–9.

    Google Scholar 

  43. Service RF. Proteomics: a sharper focus. Science 2003; 302: 1318.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Clinical Proteome Center, Tokyo Medical University, Shinjuku Sumitomo Bldg. 17F, 2-6-1 Nishi-shinjuku Shinjuku-ku, 163-0217, Tokyo, Japan

    Toshihide Nishimura, Atsushi Ogiwara, Kiyonaga Fujii, Takao Kawakami, Takeshi Kawamura, Hisae Anyouji & Harubumi Kato

Authors
  1. Toshihide Nishimura
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  2. Atsushi Ogiwara
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  3. Kiyonaga Fujii
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  4. Takao Kawakami
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  5. Takeshi Kawamura
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  6. Hisae Anyouji
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  7. Harubumi Kato
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Nishimura, T., Ogiwara, A., Fujii, K. et al. Disease proteomics toward bedside reality. J Gastroenterol 40 (Suppl 16), 7–13 (2005). https://doi.org/10.1007/BF02990572

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Key words

micro-liquid chromatography (μ-LC)

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