Identification of Differentially Expressed Proteins in Pancreatic Cancer Using a Global Proteomic Approach

  • Christophe Rosty
  • Michael Goggins
Part of the Methods in Molecular Medicine™ book series (MIMM, volume 103)


Proteomics is the term used for the large-scale analysis of proteins in biological fluids or cells by biochemical methods. Two approaches are used for proteomics analysis: two-dimensional polyacrylamide gel electrophoresis (2D-PA GE) and a mass-spectrometry-based approach, such as surface-enhanced laser desorption ionization (SELDI). SELDI can be used for large protein profiling or peptide identification after enzymatic digestion. In pancreatic cancer, proteomics analysis can be performed with the aim to identify all differentially expressed proteins in cancer cells vs normal pancreatic cells. Protein profiling of pancreatic juice or serum may also identify biomarkers for pancreatic cancer that could be used as diagnostic markers or therapeutic targets. This chapter outlines the use of 2D-PAGE and SELDI for profiling the protein content of pancreatic juice samples and for identifying proteins differentially expressed in pancreatic cancer patient samples compared to control patient samples.

Key Words

Proteomics two-dimensional polyacrylamide gel electrophoresis mass spec-trometry surface-enhanced laser desorption ionization biomarkers serum pancreatic juice 


  1. 1.
    Pandey, A. and Mann, M. (2000) Proteomics to study genes and genomes. Nature 405, 837–846.PubMedCrossRefGoogle Scholar
  2. 2.
    Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19, 1720–1730.PubMedGoogle Scholar
  3. 3.
    Anderson, L. and Seilhamer, J. (1997) A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18, 533–537.PubMedCrossRefGoogle Scholar
  4. 4.
    Wilkins, M. R., Pasquali, C., Appel, R. D., et al. (1996) From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (NY) 14, 61–65.CrossRefGoogle Scholar
  5. 5.
    Anderson, N. G. and Anderson, N. L. (1996) Twenty years of two-dimensional electrophoresis: Past, present and future. Electrophoresis 17, 443–453.PubMedCrossRefGoogle Scholar
  6. 6.
    Young, D. S. and Tracy, R. P. (1995) Clinical applications of two-dimensional electrophoresis. J. Chromatogr. A 698, 163–179.PubMedCrossRefGoogle Scholar
  7. 7.
    Okuzawa, K., Franzen, B., Lindholm, J., et al. (1994) Characterization of gene expression in clinical lung cancer materials by two-dimensional polyacrylamide gel electrophoresis. Electrophoresis 15, 382–390.PubMedCrossRefGoogle Scholar
  8. 8.
    Franzen, B., Hirano, T., Okuzawa, K., et al. (1995) Sample preparation of human tumors prior to two-dimensional electrophoresis of proteins. Electrophoresis 16, 1087–1089.PubMedCrossRefGoogle Scholar
  9. 9.
    Shevchenko, A., Loboda, A., Ens, W., and Standing, K. G. (2000) MALDI quadrupole time-of-flight mass spectrometry: A powerful tool for proteomic research. Anal. Chem. 72, 2132–2141.PubMedCrossRefGoogle Scholar
  10. 10.
    Hutchens, T. W. and Yip, T. T. (1993) New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Commun. Mass Spectrom. 7, 576–580.CrossRefGoogle Scholar
  11. 11.
    Emmert-Buck, M. R., Gillespie, J. W., Paweletz, C. P., et al. (2000) An approach to proteomic analysis of human tumors. Mol. Carcinog. 27, 158–165.PubMedCrossRefGoogle Scholar
  12. 12.
    Ostergaard, M., Wolf, H., Orntoft, T. F., and Celis, J. E. (1999) Psoriasin (S100A7): A putative urinary marker for the follow-up of patients with bladder squamous cell carcinomas. Electrophoresis 20, 349–354.PubMedCrossRefGoogle Scholar
  13. 13.
    Jungblut, P. R., Zimny-Arndt, U., Zeindl-Eberhart, E., et al. (1999) Proteomics in human disease: Cancer, heart and infectious diseases. Electrophoresis 20, 2100–2110.PubMedCrossRefGoogle Scholar
  14. 14.
    Vlahou, A., Schellhammer, P. F., Mendrinos, S., et al. (2001) Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. Am. J. Pathol. 158, 1491–1502.PubMedCrossRefGoogle Scholar
  15. 15.
    Wright, G. L. Jr., Cazares, L. H., Leung, S. M., et al. (1999) ProteinChip surface enhanced desorption/ionization (SELDI) mass spectrometry: A novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures. Prostate Cancer Prostat. Dis. 2, 264–276.CrossRefGoogle Scholar
  16. 16.
    Petricoin, E. F., Ardekani, A. M., Hitt, B. A., et al. (2002) Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359, 572–577.PubMedCrossRefGoogle Scholar
  17. 17.
    Rosty, C., Christa, L., Kuzdzal, S., et al. (2002) Identification of hepatocarcinoma-intestine-pancreas/pancreatitis-associated protein I as a biomarker for pancreatic ductal adenocarcinoma by protein biochip technology. Cancer Res. 62, 1868–1875.PubMedGoogle Scholar
  18. 18.
    Koopman, J., Zhang, Z., White, N., et al. (2004) Serum diagnosis of pancreatic adenocarcinoma using surface-enhanced laser desorption and ionization mass spectrometry. Clin. Cancer Res. 10, 860–868.CrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2005

Authors and Affiliations

  • Christophe Rosty
    • 1
  • Michael Goggins
    • 2
    • 3
    • 4
  1. 1.Department de PathologieInstitut CurieParisFrance
  2. 2.Department of PathologyThe Johns Hopkins University School of MedicineBaltimore
  3. 3.Department of MedicineThe Johns Hopkins University School of MedicineBaltimore
  4. 4.The Oncology CenterThe Johns Hopkins University School of MedicineBaltimore

Personalised recommendations