Cancer proteomics: Many technologies, one goal

Expert Review of Proteomics

Volumn 2, Issue 5, 2005, Pages 693-703

  Conrads, Thomas P ^a   Hood, Brian L ^a   Petricoin III, Emmanuel F ^b   Liotta, Lance A ^b   Veenstra, Timothy D ^a  

^a SAIC FREDERICK INC   (United States)

^b GEORGE MASON UNIVERSITY   (United States)

Author keywords

Biomarkers; Multidimensional separations; Plasma; Proteomic patterns; Proteomics; Serum; Tandem mass spectrometry

Indexed keywords

BIOLOGICAL MARKER;

CANCER; CANCER CENTER; CANCER DIAGNOSIS; CANCER MORTALITY; CANCER PAIN; HUMAN; PLASMA; PROTEOMICS; REVIEW; SERUM; TISSUE; URINE;

ANIMALS; BODY FLUIDS; CYSTITIS, INTERSTITIAL; HUMANS; NEOPLASMS; PROTEIN ARRAY ANALYSIS; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 27144443999     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.2.5.693     Document Type: Review

References (46)

1. von Eschenbach AC. A vision for the National Cancer Program in the United States. Nature Rev. Cancer 4, 820-828 (2004).
2. Cowherd SM, Espina VA, Petricoin EF III et al. Proteomic analysis of human breast cancer tissue with laser-capture microdissection and reverse-phase protein microarrays. Clin. Breast Cancer. 5, 385-392 (2004).
3. Petricoin EF III, Liotta LA. SELDI-TOF-based serum proteomic pattern diagnostics for early detection of cancer. Curr. Opin. Biotechnol. 15, 24-30 (2004).
4. Liotta LA, Espina V, Mehta AI et al. Protein microarrays: meeting analytical challenges for clinical applications. Cancer Cell 3, 317-325 (2003).
5. Miller JC, Zhou H, Kwekel J et al. Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics 3, 56-63 (2003).
6. Espina V, Mehta AI, Winters ME et al. Protein microarrays: molecular profiling technologies for clinical specimens. Proteomics 3, 2091-2100 (2003).
7. Bobrow MN, Harris TD, Shaughnessy KJ et al. Catalyzed reporter deposition, a novel method of signal amplification. Application to immunoassays. J. Immunol. Methods 125, 279-285 (1989).
8. Hunyady B, Krempels K, Harta G et al. Immunohistochemical signal amplification by catalyzed reporter deposition and its application in double immunostaining. J. Histochem. Cytochem. 44, 1353-1362 (1996).
9. King G, Payne S, Walker P et al. A highly sensitive detection method for immunohistochemistry using biotinylated tyramine. J. Pathol. 183, 237-241 (1997).
10. Petricoin EF III, Bichsel V, Calvert V et al. Mapping molecular networks using proteomics: a vision for patient-tailored combination therapy. J. Clin. Oncol. 23, 3614-3621 (2005).
11. Wulfkuhle JD, Aquino JA, Calvert VS et al. Signal pathway profiling of ovarian cancer from human tissue specimens using reverse-phase protein microarrays. Proteomics 3, 2085-2090 (2003).
12. Sheehan KM, Calvert VS, Kay EW et al. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol. Cell. Proteomics 4, 346-355 (2005).
13. 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 20, 1981-1989 (2001).
14. Nishizuka S, Charboneau L, Young L et al. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc. Natl Acad. Sci. USA 100, 14229-14234 (2003).
15. Emmert-Buck MR, Bonner RF, Smith RD et al. Laser capture microdissection. Science 274, 998-1001 (1996).
16. Araujo R, Petricoin EF, Liotta LA. A mathematical model of combination therapy using the EGFR signaling network Biosystems 80, 57-69 (2005).
17. Liotta LA, Kohn EC, Petricoin EF III. Clinical proteomics: personalized molecular medicine. JAMA 286, 2211-2214 (2001).
18. Petricoin EF III, Zoon KC, Kohn EC et al. Clinical proteomics: translating benchside promise into bedside reality. Nature Rev. Drug Discov. 1, 683-695 (2002).
19. Chan SM, Ermann J, Su L et al. Protein microarrays for multiplex analysis of signal transduction pathways. Nature Med. 10, 1390-1396 (2004).
20. Petricoin EF III, Ardekani AM, Hitt BA et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359, 572-577 (2002). Initial demonstration showing the potential of combining proteomic pattern and statistical analysis to diagnose cancer.
21. Srinivas PR, Srivastava S, Hanash S, Wright GL Jr. Proteomics in early detection of cancer. Clin. Chem. 47, 1901-1911 (2001).
22. Adam BL, Davis JW, Ward MD et al. otein profiling of seminal plasma and serum using Ciphergen's SELDI ProteinChip technology for early detection of prostate cancer. Proc. Am. Assoc. Cancer Res. 42, 142 (2001).
23. Veenstra TD, Prieto DA, Conrads TP. Proteomic patterns for early cancer detection. Drug Discov. Today 9, 889-897 (2004).
24. Conrads TP, Fusaro VA, Ross S et al. High-resolution serum proteomic features for ovarian cancer detection, Endocr. Relat. Cancer. 11, 163-178 (2004).
25. Villanueva J, Philip J, Entenberg D et al. Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal Chem. 76, 1560-1570 (2004). Demonstration of a high-resolution matrix-assisted laser desorption/ionization platform for the acquisition of proteomic patterns of serum.
26. Grizzle WE, Semmes OF, Basler J et al. The early detection research network surface-enhanced laser desorption and ionization prostate cancer detection study: a study in biomarker validation in genitourinary oncology. Urol. Oncol. 22, 337-343 (2004).
27. Semmes OJ, Feng Z, Adam BL et al. Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. Clin. Chem. 51, 102-112 (2005).
28. Karsan A, Eigl BJ, Flibotte S et al. Analytical and preanalytical biases in serum proteomic pattern analysis for breast cancer diagnosis. Clin. Chem. 51, 1525-1528 (2005).
29. 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. 64, 5882-5890 (2004). Identification of three potential biomarkers for ovarian cancer using a combination of fractionation and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry.
30. Mok SC, Chao J, Skates S et al. Prostasin, a potential serum marker for ovarian cancer: identification through microarray technology. J. Natl Cancer Inst. 93, 1458-1464 (2001).
31. Malik G, Ward MD, Gupta SK et al. Serum levels of an isoform of apolipoprotein A-II as a potential marker for prostate cancer. Clin. Cancer Res. 11, 1073-85 (2005).
32. Block TM, Communale MA, Lowman M et al. Use of targeted glycoproteomics to identify serum glycoproteins that correlate with liver cancer in woodchucks and humans. Proc. Natl Acad. Sci. USA 102, 779-784 (2005).
33. Pieper R, Gatlin CL, Makusky AJ et al. The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics 3, 1345-1364 (2003).
34. Shen Y, Jacobs JM, Camp DG II et al. Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal. Chem. 76, 1134-1144 (2004).
35. Anderson NL, Polanski M, Pieper R et al. The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol. Cell. Proteomics 3, 311-326 (2004). Summary of serum and plasma profiling studies that expand the understanding of the proteomic content of blood.
36. Chan KC, Lucas DA, Schaefer CF et al. Analysis of the human serum proteome. Clin. Proteomics 1, 101-226 (2004).
37. Gygi SP, Rist B, Gerber SA et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol. 17, 994-999 (1999).
38. 18O stable isotope labeling in a lung tumor xenograft mouse model. J. Am. Soc. Mass Spectrom. 16, 1221-1230 (2005).
39. 18O exchange of truncated peptide substrates. J. Proteome Res. 2, 147-152 (2003).
40. Senger DR, Galli SJ, Dvorak AM et al. Tumor cells secrete a vascular permeability factor that promotes accumulation of ascites fluid. Science 219, 983-985 (1983).
41. 18O labeling and the accurate mass and time tag approach. Mol. Cell. Proteomics. 4, 700-709 (2005). Excellent demonstration of isotopic labeling in the comparison of serum proteomic samples.
42. Gelke M. Renal tubule albumin transport. Ann. Rev. Physiol. 67, 573-594 (2005).
43. Zhou M, Lucas DA, Chan KC et al. An investigation into the human serum 'interactome'. Electrophoresis 25, 1289-1298 (2004). Initial paper showing that low-abundance proteins are bound to higher abundance proteins in serum.
44. Keay SK, Szekely Z, Conrads TP et al. An antiproliferative factor from interstitial cystitis patients is a frizzled 8 protein-related sialoglycopeptide. Proc. Natl Acad. Sci. USA 101, 11803-11808 (2004). Identification of a biomarker for interstitial cystitis. Demonstrates the use of various research tools to discover and validate this sialoglycopeptide biomarker.
45. Warren JW, Keay SK. Interstitial cystitis. Curr. Opin. Urol. 12, 69-74 (2002).
46. 3H-thymidine incorporation by human bladder epithelial cells following exposure to urine from interstitial cystitis patients. J. Urol. 156, 2073-2078 (1996).