Skip to main content
Log in

Proteomic analysis in cancer research: potential application in clinical use

  • Educational Series
  • Red Series
  • Published:
Clinical & Translational Oncology Aims and scope Submit manuscript

Summary

The ultimate goal of cancer proteomics is to adapt proteomic technologies for routine use in clinical laboratories for the purpose of diagnostic and prognostic classification of disease states, as well as in evaluating drug toxicity and efficacy. The novel technologies allows researchers to facilitate the comprehensive analyses of genomes, transcriptomes, and proteomes in health and disease. The information that is expected from such technologies may soon exert a dramatic change in cancer research and impact dramatically on the care of cancer patients. Analysis of tumor-specific proteomic profiles may also allow better understanding of tumor development and the identification of novel targets for cancer therapy. The localization of gene products, which is often difficult to deduce from the sequence, can be determined experimentally. Mechanisms, such as regulation of protein function by proteolysis, recycling, and isolation in cell compartments, affect gene products, not genes. Finally, protein-protein interactions and the molecular composition of cellular structures can be determined only at the protein level. The biological variability among patient samples as well as the great dynamic range of biomarker concentrations are currently the main challenges facing efforts to deduce diagnostic patterns that are unique to specific disease states. While several strategies exist to address this problem, we have tried to offer a wide perspective about the current possibilities.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Ye B, Skates S, Mok SC, et al. Proteomicbased discovery and characterization of glycosylated eosinophil-derived neurotoxin and COOH-terminal osteopontin fragments for ovarian cancer in urine. Clin Cancer Res. 2006;12:432–41.

    Article  PubMed  CAS  Google Scholar 

  2. Grossman HB, Soloway M, Messing E, et al. Surveillance for recurrent bladder cancer using a point-of-care proteomic assay. JAMA. 2006;295:299–305.

    Article  PubMed  CAS  Google Scholar 

  3. Liu Y. Serum proteomic pattern analysis for early cancer detection. Technol Cancer Res Treat. 2006;5:61–6.

    PubMed  Google Scholar 

  4. Maciel CM, Junqueira M, Paschoal ME, et al. Differential proteomic serum pattern of low molecular weight proteins expressed by adenocarcinoma lung cancer patients. J Exp Ther Oncol. 2005;5:31–8.

    PubMed  Google Scholar 

  5. Wu H, Pan CL, Yao, YC, Chang SS, Li SL, Wu TF. Proteomic analysis of the effect of Antrodia camphorata extract on human lung cancer A549 cell. Proteomics. 2006;6: 826–35.

    Article  PubMed  CAS  Google Scholar 

  6. Vasilescu J, Smith JC, Ethier M, Figeys D. Proteomic analysis of ubiquitinated proteins from human MCF-7 breast cancer cells by immunoaffinity purification and mass spectrometry. J Proteome Res. 2005; 4:2192–200.

    Article  PubMed  CAS  Google Scholar 

  7. Rowell C, Carpenter DM, Lamartiniere CA. Chemoprevention of breast cancer, proteomic discovery of genistein action in the rat mammary gland. J Nutr. 2005;155: 2953S-9S.

    Google Scholar 

  8. Varambally S, Yu J, Laxman B, et al. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell, 2005; 8:393–406.

    Article  PubMed  CAS  Google Scholar 

  9. Cheng AJ, Chen LC, Chien KY, et al. Oral cancer plasma tumor marker identified with bead-based affinity-fractionated proteomic technology. Clin Chem. 2005;51: 2236–44.

    Article  PubMed  CAS  Google Scholar 

  10. Kong F, Nicole White C, Xiao X, et al. Using proteomic approaches to identify new biomarkers for detection and monitoring of ovarian cancer. Gynecol Oncol. 2006;100:247–55.

    Article  PubMed  CAS  Google Scholar 

  11. Ahmed N, Oliva KT, Barker G, et al. Proteomic tracking of serum protein isoforms as screening biomarkers of ovarian cancer. Proteomics. 2005;5:4625–56.

    Article  PubMed  CAS  Google Scholar 

  12. Gronborg M, Kristiansen TZ, Iwahori A, et al. Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol Cell Proteomics. 2006;5:157–71.

    Article  PubMed  CAS  Google Scholar 

  13. Melle C, Ernst G, Schimmel B, et al. Characterization of pepsinogen C as a potential biomarker for gastric cancer using a histo-proteomic approach. J Proteome Res. 2005;4:1799–804.

    Article  PubMed  CAS  Google Scholar 

  14. Rajapakse JC, Duan KB, Yeo WK. Proteomic cancer classification with mass spectrometry data. Am J Pharmacogenomics. 2005;5:281–92.

    Article  PubMed  CAS  Google Scholar 

  15. Seike M, Kondo T, Fujii K, et al. Proteomic signatures for histological types of lung cancer. Proteomics. 2005;5:2939–48.

    Article  PubMed  CAS  Google Scholar 

  16. Rehman A, Chahal MS, Tang X, Bruce JE, Pommier Y, Daoud SS. Proteomic identification of heat shock protein 90 as a candidate target for p55 mutation reactivation by PRIMA-1 in breast cancer cells. Breast Cancer Res. 2005;7:R765-R74.

    Article  PubMed  CAS  Google Scholar 

  17. Chen AL, Soman KV, Rychahou PG, Luxon BA, Evers BM. Proteomic analysis of colonic myofibroblasts and effect on colon cancer cell proliferation. Surgery. 2005; 138:382–90.

    Article  PubMed  Google Scholar 

  18. Hood BL, Darfler MM, Guiel TG, et al. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol Cell Proteomics. 2005;4:1741–55.

    Article  PubMed  CAS  Google Scholar 

  19. Srivastava S, Verma M, Gopal-Srivastava, R. Proteomic maps of the cancer-associated infectious agents. J Proteome Res. 2005;4:1171–80.

    Article  PubMed  CAS  Google Scholar 

  20. Zhang D, Tai LK, Wong LL, Chiu LL, Sethi SK, Koay ES. Proteomic study reveals that proteins involved in metabolic and detoxification pathways are highly expressed in HER-2/neu-positive breast cancer. Mol Cell Proteomics. 2005;4:1686–96.

    Article  PubMed  CAS  Google Scholar 

  21. Kim J, Sun P, Lam YW, et al. Changes in serum proteomic patterns by presurgical alpha-tocopherol and L-selenomethionine supplementation in prostate cancer. Cancer Epidemiol Biomarkers Prev. 2005; 14:1697–702.

    Article  PubMed  CAS  Google Scholar 

  22. Yang SY, Xiao XY, Zhang WG, et al. Application of serum SELDI proteomic patterns in diagnosis of lung cancer. BMC Cancer. 2005;5:83.

    Article  PubMed  CAS  Google Scholar 

  23. Goncalves A, Esterni B, Bertucci F, et al. Postoperative serum proteomic profiles may predict metastatic relapse in highrisk primary breast cancer patients receiving adjuvant chemotherapy. Oncogene. 2006;25:981–9.

    Article  PubMed  CAS  Google Scholar 

  24. Karsan A, Eigl BJ, Flibotte S, et al. Analytical and preanalytical biases in serum proteomic pattern analysis for breast cancer diagnosis. Clin Chem. 2005;51: 1525–8.

    Article  PubMed  CAS  Google Scholar 

  25. Basso D, Greco E, Fogar P, et al. Pancretic cancer-associated diabetes mellitus: an open field for proteomic applications. Clin Chim Acta. 2005;557:184–9.

    Article  CAS  Google Scholar 

  26. Alfonso P, Nunez A, Madoz-Gurpide J Lombardia L, Sánchez L, Casal JL. Proteomic expression analysis of colorectal cancer by two-dimensional differential gel electrophoresis Proteomics. 2005;5:2602–11.

    Article  PubMed  CAS  Google Scholar 

  27. Lee KH, Yim EK, Kim CJ, Namkoong SE, Um SJ, Park JS. Proteomic analysis of anti-cancer effects by paclitaxel treatment in cervical cancer cells. Gynecol Oncol. 2005; 98:45–53.

    Article  PubMed  CAS  Google Scholar 

  28. Meyerson M, Carbone D. Genomic and proteomic profiling of lung cancers: lung cancer classification in the age of targeted therapy. J Clin Oncol. 2005;23:3219–26.

    Article  PubMed  CAS  Google Scholar 

  29. Shi P, Huang Z. Proteomic detection of changes in protein synthesis induced by lanthanum in BGC-825 human gastric cancer cells. Biometals, 2005;18:89–95.

    Article  PubMed  CAS  Google Scholar 

  30. Choi, YP, Kang S, Hong S, Xie X, Cho NH. Proteomic analysis of progressive factors in uterine cervical cancer. Proteomics. 2005;5:1481–93.

    Article  PubMed  CAS  Google Scholar 

  31. Lin B, White JT, Lu W, et al. Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease. Cancer Res. 2005;65:3081–91.

    PubMed  CAS  Google Scholar 

  32. Alessandro R, Belluco C, Kohn EC. Proteomic approaches in colon cancer: promising tools for new cancer markers and drug target discovery. Clin Colorectal Cancer. 2005;4:396–402.

    Article  PubMed  CAS  Google Scholar 

  33. Benzinger A, Muster N, Koch HB, Yates JR III, Hermeking H. Targeted proteomic analysis of 14-3-5 sigma, a p55 effector commonly silenced in cancer. Mol Cell Proteomics. 2005;4:785–95.

    Article  PubMed  CAS  Google Scholar 

  34. Baggerly KA, Morris JS, Edmonson SR, Coombes KR. Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst. 2005;97:307–9.

    Article  PubMed  CAS  Google Scholar 

  35. Grossman HB, Messing E, Soloway M, et al. Detection of bladder cancer using a point-of-care proteomic assay. JAMA. 2005; 293:810–6.

    Article  PubMed  CAS  Google Scholar 

  36. Chen R, Pan S, Brentnall TA, Aebersold R. Proteomic profiling of pancreatic cancer for biomarker discovery. Mol Cell Proteomics. 2005;4:523–33.

    Article  PubMed  CAS  Google Scholar 

  37. Posadas EM, Simpkins F, Liotta LA, MacDonald C, Kohn EC. Proteomic analysis for the early detection and rational treatment of cancer-realistic hope? Ann Oncol. 2005;16:16–22.

    Article  PubMed  CAS  Google Scholar 

  38. Rehman I, Azzouzi AR, Catto JW, et al. Proteomic analysis of voided urine after prostatic massage from patients with prostate cancer: a pilot study. Urology. 2004;64:1238–43.

    Article  PubMed  CAS  Google Scholar 

  39. Alexander H, Stegner AL, Wagner-Mann C, Du Bois GC, Alexander S, Sauter ER. Proteomic analysis to identify breast cancer biomarkers in nipple aspirate fluid. Clin Cancer Res. 2004;10:7500–10.

    Article  PubMed  CAS  Google Scholar 

  40. Bhattacharyya S, Siegel ER, Petersen GM, Chari ST, Suva LJ, Haun RS. Diagnosis of pancreatic cancer using serum proteomic profiling. Neoplasia. 2004;6:674–86.

    Article  PubMed  CAS  Google Scholar 

  41. Wulfkuhle J, Espina V, Liotta L, Petricoin E. Genomic and proteomic technologies for individualisation and improvement of cancer treatment. Eur J Cancer. 2004;40:2623–32.

    Article  PubMed  CAS  Google Scholar 

  42. Kuerer HM, Coombes KR, Chen JN, et al. Association between ductal fluid proteomic expression profiles and the presence of lymph node metastases in women with breast cancer. Surgery. 2004;136:1061–9.

    Article  PubMed  Google Scholar 

  43. Chen Y, Shi G, Xia W, et al. Identification of hypoxia-regulated proteins in head and neck cancer by proteomic and tissue array profiling. Cancer Res. 2004;64:7302–10.

    Article  PubMed  CAS  Google Scholar 

  44. Lee K, Kye M, Jang JS, Lee OJ, Kim T, Lim D. Proteomic analysis revealed a strong association of a high level of alpha1-antitrypsin in gastric juice with gastric cancer. Proteomics. 2004;4:3543–52.

    Google Scholar 

  45. Dvorzhinski D, Thalasila A, Thomas PE, et al. A novel proteomic coculture model of prostate cancer cell growth. Proteomics. 2004;4:3268–75.

    Article  PubMed  CAS  Google Scholar 

  46. Ornstein DK, Rayford W, Fusaro VA, et al. Serum proteomic profiling can discriminate prostate cancer from benign prostates in men with total prostate specific antigen levels between 2.5 and 15.0 ng/m. J Urol. 2004;172:1302–5.

    Article  PubMed  CAS  Google Scholar 

  47. Frazier MC, Jackson KM, Jankowska-Stephens E, Anderson MG, Harris WB. Proteomic analysis of proteins altered by dibenzoylmethane in human prostatic cancer LNCaP cells. Proteomics. 2004;4:2814–21.

    Article  PubMed  CAS  Google Scholar 

  48. Seike M, Kondo T, Fujii K, et al. Proteomic signature of human cancer cells. Proteomics. 2004;4:2776–88.

    Article  PubMed  CAS  Google Scholar 

  49. Yokoo H, Kondo T, Fujii K, Yamada T, Todo S, Hirohashi S. Proteomic signature corresponding to alpha fetoprotein expression in liver cancer cells. Hepatology. 2004;40:609–17.

    Article  PubMed  CAS  Google Scholar 

  50. Zhang Z, Bast RC Jr, Yu Y, et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res. 2004; 64:5882–90.

    Article  PubMed  CAS  Google Scholar 

  51. Wong YF, Cheung TH, Lo KW, et al. Protein profiling of cervical cancer by protein-biochips: proteomic scoring to discriminate cervical cancer from normal cervix. Cancer Lett. 2004;211:227–34.

    Article  PubMed  CAS  Google Scholar 

  52. Melle C, Ernst G, Schimmel B, et al. A technical triade for proteomic identification and characterization of cancer biomarkers. Cancer Res. 2004;64:4099–104.

    Article  PubMed  CAS  Google Scholar 

  53. Ahmed N, Barker G, Oliva KT, et al. Proteomic-based identification of haptoglobin-1 precursor as a novel circulating biomarker of ovarian cancer. Br J Cancer. 2004;91:129–40.

    Article  PubMed  CAS  Google Scholar 

  54. Hathout Y, Gehrmann ML, Chertov A, Fenselau C. Proteomic phenotyping: metastatic and invasive breast cancer. Cancer Lett. 2004;210:245–53.

    Article  PubMed  CAS  Google Scholar 

  55. Euslace BK, Sakurai T, Stewart JK, et al. Functional proteomic screens reveal an essential extracellular role for hsp90 alpha in cancer cell invasiveness. Nat Cell Biol. 2004;6:507–14.

    Article  CAS  Google Scholar 

  56. Petricoin EF, Liotta LA. SELDI-TOF-based serum proteomic pattern diagnostics for early detection of cancer. Curr Opin Biotechnol. 2004;15:24–30.

    Article  PubMed  CAS  Google Scholar 

  57. Petricoin EF, Liotta LA. Proteomic approaches in cancer risk and response assessment. Trends Mol Med. 2004;10:59–64.

    Article  PubMed  CAS  Google Scholar 

  58. Fontana S, Pucci-Minafra I, Becchi M, Freyria AM, Minafra S. Effect of collagen substrates on proteomic modulation of breast cancer cells. Proteomics. 2004;4:849–60.

    Article  PubMed  CAS  Google Scholar 

  59. Roberts K, Bhatia K, Stanton P, Lord R. Proteomic analysis of selected prognostic factors of breast cancer. Proteomics. 2004; 4:784–92.

    Article  PubMed  CAS  Google Scholar 

  60. Alexe G, Alexe S, Liotta LA, Petricoin E, Reiss M, Hammer PL. Ovarian cancer detection by logical analysis of proteomic data. Proteomics. 2004;4:766–83.

    Article  PubMed  CAS  Google Scholar 

  61. Hamler RL, Zhu K, Buchanan NS, et al. A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification. Proteomics. 2004; 4:562–77.

    Article  PubMed  CAS  Google Scholar 

  62. Diamandis EP. Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J Natl Cancer Inst. 2004;96:353–6.

    Article  PubMed  Google Scholar 

  63. Kageyama S, Isono T, Iwaki H, et al. Identification by proteomic analysis of calreticulin as a marker for bladder cancer and evaluation of the diagnostic accuracy of its detection in urine. Clin Chem. 2004;50:857–66.

    Article  PubMed  CAS  Google Scholar 

  64. Cho WC, Yip TT, Yip C, et al. Identification of serum amyloid a protein as a potentially useful biomarker to monitor relapse of nasopharyngeal cancer by serum proteomic profiling. Clin Cancer Res. 2004; 10:43–52.

    Article  PubMed  CAS  Google Scholar 

  65. Nishizuka S, Charboneau L, Young L, et al. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysatemicroarrays. Proc Natl Acad Sci USA. 2003;100:14229–34.

    Article  PubMed  CAS  Google Scholar 

  66. Rogers MA, Clarke P, Noble J, et al. Proteomic profiling of urinary proteins in renal cancer by surface enhanced laser desorption ionization and neural-network analysis: identification of key issues affecting potential clinical utility. Cancer Res. 2003;63:6971–83.

    PubMed  CAS  Google Scholar 

  67. Verma M, Kagan J, Sidransky D, Srivastava S. Proteomic analysis of cancer-cell mitochondria. Nat Rev Cancer. 2003;3:789–95.

    Article  PubMed  CAS  Google Scholar 

  68. Yanagisawa K, Shyr Y, Xu BJ, et al. Proteomic patterns of tumour subsets in nonsmall-cell lung cancer. Lancet. 2003;362:433–9.

    Article  PubMed  CAS  Google Scholar 

  69. Yasui Y, Pepe M, Thompson ML, et al. A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection. Biostatistics. 2003;4:449–63.

    Article  PubMed  Google Scholar 

  70. Unwin RD, Craven RA, Harnden P, et al. Proteomic changes in renal cancer and coordinate demonstration of both the glycolytic and mitochondrial aspects of the Warburg effect. Proteomics. 2003;3:1620–32.

    Article  PubMed  CAS  Google Scholar 

  71. Ye B, Cramer DW, Skates SJ, et al. Haptoglobin-alpha subunit as potential serum biomarker in ovarian cancer: identification and characterization using proteomic profiling and mass spectrometry. Clin Cancer Res. 2003;9:2904–11.

    PubMed  CAS  Google Scholar 

  72. Varnum SM, Covington CC, Woodbury RL, et al. Proteomic characterization of nipple aspirate fluid: identification of potential biomarkers of breast cancer. Breast Cancer Res Treat. 2003;80:87–97.

    Article  PubMed  CAS  Google Scholar 

  73. Banez LL, Prasanna P, Sun L, et al. Diagnostic potential of serum proteomic patterns in prostate cancer. J Urol. 2003;170:442–6.

    Article  PubMed  CAS  Google Scholar 

  74. Wu SL, Hancock WS, Goodrich GG, Kunitake ST. An approach to the proteomic analysis of a breast cancer cell line (SKBR-3). Proteomics. 2003;3:1037–46.

    Article  PubMed  CAS  Google Scholar 

  75. Celis JE, Gromov P, Gromova I, et al. Integrating proteomic and functional genomic technologies in discovery-driven translational breast cancer research. Mol Cell Proteomics. 2003;2:369–77.

    PubMed  CAS  Google Scholar 

  76. Sorace JM, Zhan M. A data review and reassessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics. 2003; 4:24.

    Article  PubMed  Google Scholar 

  77. Khan J. Genomic & proteomic technological advances in cancer research. Pharmacogenomics. 2003;4:245–9.

    Article  PubMed  Google Scholar 

  78. Sorace JM, Zhan M. A data review and reassessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics. 2003; 4:24.

    Article  PubMed  Google Scholar 

  79. Odreman F, Vindigni M, Gonzales ML, et al. Proteomic studies on low- and highgrade human brain astrocytomas. J Proteome Res. 2005;4(3):698–708.

    Article  PubMed  CAS  Google Scholar 

  80. Vogel TW, Zhuang Z, Li J, et al. Proteins and protein pattern differences between glioma cell lines and glioblastoma multiforme. Clin Cancer Res. 2005;11(10):3624–32.

    Article  PubMed  CAS  Google Scholar 

  81. Furuta M, Weil RJ, Vortmeyer AO, et al. Protein patterns and proteins that identify subtypes of glioblastoma multiforme. Oncogene. 2004;23(40):6806–14.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jesús García-Foncillas.

Additional information

Supported by an unrestricted educational grant from Astra Zeneca.

Rights and permissions

Reprints and permissions

About this article

Cite this article

García-Foncillas, J., Bandrés, E., Zárate, R. et al. Proteomic analysis in cancer research: potential application in clinical use. Clin Transl Oncol 8, 250–261 (2006). https://doi.org/10.1007/BF02664935

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02664935

Key words

Navigation