Skip to main content
Download PDF

Development of multiplexed protein profiling and detection using near infrared detection of reverse-phase protein microarrays

Clinical Proteomics volume 1, pages 81–89 (2004)Cite this article

Abstract

Protein microarrays have been recently employed for signal pathway profiling and high-throughput protein expression analysis. Reversephase arrays, where the array consists of immobilized analytes and lysates has especially shown promise in low abundance analyte detection and signal pathway profiling using phospho-specific antibodies. A limitation to current reverse phase array methodology is the inability to multiplex proteomic-based endpoints as each array can only report one analyte endpoint. In this study, we report on the use of a dual dye based approach that can effectively double the number of endpoints observed per array allowing, for example, both phosphospecific and total protein levels to be measured and analyzed at once. The method utilizes antibody bound dyes that emit in the infrared spectral region as a means of sensitive and specific detection.

References

  1. Liotta L, Petricoin E. Molecular profiling of human cancer. Nat Rev Genet 2000;1:48–56.

    Article  PubMed  CAS  Google Scholar 

  2. Ideker T, Thorsson V, Ranish JA, et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001;292:929–934.

    Article  PubMed  CAS  Google Scholar 

  3. Schwikowski B, Uetz P. Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol 2000;18: 1257–1261.

    Article  PubMed  CAS  Google Scholar 

  4. Legrain P, Jestin JL, Schachter V. From the analysis of protein complexes to proteome-wide linkage maps. Curr Opin Biotechnol 2000;11:402–407.

    Article  PubMed  CAS  Google Scholar 

  5. Blume-Jensen P, Hunter T. Oncogenic kinase signaling. Nature Insight. Cancer 2001;411:355–365.

    CAS  Google Scholar 

  6. Pawson T. Protein modules and signaling networks. Nature 1995;373:573–580.

    Article  PubMed  CAS  Google Scholar 

  7. Liotta LA, Kohn EC. The microenvironment of the tumour-host interface. Nature 2001;411:375–379.

    Article  PubMed  CAS  Google Scholar 

  8. Gorg A, Obermaier C, Boguth G, et al. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 2000;21:1037–1053.

    Article  PubMed  CAS  Google Scholar 

  9. Hanash SM. Biomedical applications of twodimensional electrophoresis using immobilized pH gradients: current status. Electrophoresis 2000;21:1202–1209.

    Article  PubMed  CAS  Google Scholar 

  10. Li J, Wang C, Kelly JF, Harrison DJ, Thibault P. Rapid and sensitive separation of trace level protein digests using microfabricated devices coupled to a quadrupole-time-of-flight mass spectrometer. Electrophoresis 2000;21:198–210.

    Article  PubMed  CAS  Google Scholar 

  11. Gygi SP, Rist B, Geber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope coded affinity tags. Nature Biotechnol. 1999;17:994–999.

    Article  CAS  Google Scholar 

  12. Washburn MP, Wolters D, Yates JR. Large scale analysis of the yeast proteome by multidi-mensional protein identification technology. Nature Biotechnol. 2001;19:242–247.

    Article  CAS  Google Scholar 

  13. Krutchinsky, AN, Kalkum M, Chait BT. Automatic identification of proteins with a MALDI-quadrupole ion trap mass spectrometer. Anal Chem 2001;73:5066–5077.

    Article  PubMed  CAS  Google Scholar 

  14. Washburn MP, Ulaszek R, Deciu C, Schieltz DM, Yates JR, III. Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal Chem 2002;74:1650–1657.

    Article  PubMed  CAS  Google Scholar 

  15. Zhou H, Ranish JA, Watts JD, Aebersold R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nature Biotechnol 2002;20:512–515.

    Article  CAS  Google Scholar 

  16. Zhou G, Li H, DeCamp D, et al. 2-D differential in-Gel electrophoresis for the identification of human esophageal squamous cell cancer specific protein markers. Mol Cell Proteomics 2002;1:117–123.

    Article  PubMed  CAS  Google Scholar 

  17. Paweletz CP, Charboneau L, Bichsel VE, 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.

    Article  PubMed  CAS  Google Scholar 

  18. Nishizuka S, Charboneau L, Young L, et al. Diagnostic markers that distinguish colon and ovarian adenocarcinomas: Identification by genomic, proteomic, and tissue array profiling. Cancer Res 2003;63:5173–5646.

    Google Scholar 

  19. Espina V, Mehta AI, Winters ME, Wulfkuhle J, Petricoin III E, Liotta L. Protein microarrays: molecular profiling technologies for clinical specimens. Proteomics 2003;3(11):2091–2100.

    Article  PubMed  CAS  Google Scholar 

  20. Grubb RL, Calvert VS, Paweletz CP, et al. Signal pathway profiling of prostate cancer using reverse phase protein arrays. Proteomics 2003;3(11):2142–6.

    Article  PubMed  CAS  Google Scholar 

  21. Wulfkuhle JD, Aquino JA, Calvert VS, et al. Signal pathway profiling of ovarian cancer from human tissue specimens using vererse-phase microarrays. Proteomics 2003;3(11):2085–90.

    Article  PubMed  CAS  Google Scholar 

  22. Herrmann PC, Gillespie J.W., Charboneau L, et al. Mitochondrial Proteome: Altered Cytochrome Oxidase Subunit Levels in Prostate Cancer. Proteomics 2003;3(9):1801–1810.

    Article  PubMed  CAS  Google Scholar 

  23. Liotta LA, Espina V, Mehta AI, et al. Protein microarrays: Meeting analytical challenges for clinical applications. Cancer Cell 2003;3(4): 317–25.

    Article  PubMed  CAS  Google Scholar 

  24. Petricoin EF, Zoon KC, Kohn EC, Barrett JC, Liotta LA. Clinical Proteomics: Translating Benchside Promise into Bedside Reality. Nature Rev Drug Disc 2002;1:683–695.

    Article  CAS  Google Scholar 

  25. Bray D. Molecular networks: the top-down view. Science 2003;301:1864–1865.

    Article  PubMed  CAS  Google Scholar 

  26. Leyland-Jones B. Trastuzumab: hopes and realities. Lancet Oncol 2002;3:137–144.

    Article  PubMed  CAS  Google Scholar 

  27. Sebolt-Leopold JS. Development of anticancer drugs targeting the MAP kinase pathway. Oncogene 2000;19:6594–6599.

    Article  PubMed  CAS  Google Scholar 

  28. Thiesing JT, Ohno-Jones S, Kolibaba KS, Druker B. Efficacy of STI571, an abl tyrosine kinase inhibitor, in conjuction with other antileukemic agents against bcr-abl-positive cells. Blood 2000;96:3195–3199.

    PubMed  CAS  Google Scholar 

  29. Vlahos CJ, Stancato LF. Inhibitors of cellular signaling targets-designs and limitations. Platelets and Megakaryoctyes: Methods and Protocols. In: Gibbons, JM and Mahaut-Smith MP, eds. Humana Press, Totowa, NJ:2002.

    Google Scholar 

  30. Traxler P, Bold G, Buchdunger E, et al. Tyrosine kinase inhibitors: from rational design to clinical trials. Med Res Rev 2001;21:499–512.

    Article  PubMed  CAS  Google Scholar 

  31. Zwick E, Bange J, Ullrich A. Receptor tyrosine kinases as targets for anticancer drugs. Trends Mol Med 2001;8:17–23.

    Article  Google Scholar 

  32. Torhorst J, Bucher C, Kononen J, et al. Tissue microarrays for rapid linking of molecular changes to clinical endpoints. Am J Pathol 2001;159:2249–2256.

    PubMed  CAS  Google Scholar 

  33. Sreekumar A, Nyati MK, Varambally S, et al. Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res 2001;61:7585–7593.

    PubMed  CAS  Google Scholar 

  34. MacBeath G. Proteomics comes to the surface. Nature Biotechnol 2001;19:828–829.

    Article  CAS  Google Scholar 

  35. Walter G, Bussow K, Lueking A, Glokler J. High-throughput protein arrays: prospects for molecular diagnostics. Trends Mol Med 2002; 8:250–253.

    Article  PubMed  CAS  Google Scholar 

  36. Kuruvilla FG, Shamji AF, Sternson SM, Hergenrother PJ, Schreiber SL. Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature 2002; 416:653–657.

    Article  PubMed  CAS  Google Scholar 

  37. Liotta LA, Kohn EC, Petricoin EF. Clinical proteomics: personalized molecular medicine. JAMA 2001;286:2211–2214.

    Article  PubMed  CAS  Google Scholar 

  38. Petricoin EF, Zoon KC, Kohn EC, Barrett JC, Liotta LA. Clinical Proteomics: Translating Benchside Promise into Bedside Reality. Nature Rev Drug Disc 2002;1:683–695.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Office of Cell and Gene Therapy, Center for Biologics Evaluation and Research, Food and Drug Administration, NCI/FDA Clinical Proteomics Program, 20892, Bethesda, Maryland

    Valerie S. Calvert & Emanuel F. Petricoin III

  2. LI-COR Biosciences, 68504, Lincoln, NE

    Yihui Tang, Vince Boveia, Amy Schutz-Geschwender & D. Michael Olive

  3. Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, NCI/FDA Clinical Proteomics Program, 20892, Bethesda, Maryland

    Julie Wulfkuhle & Lance A. Liotta

Authors
  1. Valerie S. Calvert
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yihui Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Vince Boveia
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Julie Wulfkuhle
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Amy Schutz-Geschwender
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. D. Michael Olive
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Lance A. Liotta
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Emanuel F. Petricoin III
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Emanuel F. Petricoin III.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Calvert, V.S., Tang, Y., Boveia, V. et al. Development of multiplexed protein profiling and detection using near infrared detection of reverse-phase protein microarrays. Clin Proteom 1, 81–89 (2004). https://doi.org/10.1385/CP:1:1:081

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1385/CP:1:1:081

Key Words

  • Proteomics
  • signal profiling
  • networks
  • protein microarrays

Clinical Proteomics

ISSN: 1559-0275