Quantitative proteomics for identification of cancer biomarkers

Proteomics - Clinical Applications

Volumn 1, Issue 9, 2007, Pages 1080-1089

  Chaerkady, Raghothama ^a,b   Pandey, Akhilesh ^b  

^a Institute of Bioinformatics   (India)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Multiplexing; Screening; Stable isotope labeling; Validation

Indexed keywords

AMINO ACID; BIOLOGICAL MARKER; OXYGEN 18; TUMOR MARKER;

ANALYTIC METHOD; BODY FLUID; CANCER CELL CULTURE; CANCER TISSUE; EARLY DIAGNOSIS; FLUORESCENCE; HUMAN; IN VITRO STUDY; IN VIVO STUDY; ISOTOPE LABELING; MALIGNANT NEOPLASTIC DISEASE; MONITORING; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN MICROARRAY; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; TWO DIMENSIONAL GEL ELECTROPHORESIS;

EID: 38349159301     PISSN: 18628346     EISSN: None     Source Type: Journal    
DOI: 10.1002/prca.200700284     Document Type: Review

References (66)

1. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B. et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386.
2. Everley, P. A., Krijgsveld, J., Zetter, B. R., Gygi, S. P., Quantitative cancer proteomics: Stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol. Cell. Proteomics 2004, 3, 729-735.
3. Gronborg, M., Kristiansen, T. Z., Iwahori, A., Chang, R. et al., Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol. Cell. Proteomics 2006, 5, 157-171.
4. Liang, X., Zhao, J., Hajivandi, M., Wu, R. et al., Quantification of membrane and membrane-bound proteins in normal and malignant breast cancer cells isolated from the same patient with primary breast carcinoma. J. Proteome Res. 2006, 5, 2632-2641.
5. Hoogland, C., Mostaguir, K., Sanchez, J. C., Hochstrasser, D. F. et al., SWISS-2DPAGE, ten years later. Proteomics 2004, 4, 2352-2356.
6. Ong, S. E., Pandey, A., An evaluation of the use of two-dimensional gel electrophoresis in proteomics. Biomol. Eng. 2001, 18, 195-205.
7. Marouga, R., David, S., Hawkins, E., The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal. Bioanal. Chem. 2005, 382, 669-678.
8. Karp, N. A., Kreil, D. P., Lilley, K. S., Determining a significant change in protein expression with DeCycler during a pairwise comparison using two-dimensional difference gel electrophoresis. Proteomics 2004, 4, 1421-1432.
9. Anderson, T. J., Tchernyshyov, I., Diez, R., Cole, R. N. et al., Discovering robust protein biomarkers for disease from relative expression reversals in 2-D DIGE data. Proteomics 2007, 7, 1197-1207.
10. Kondo, T., Hirohashi, S., Application of highly sensitive fluorescent dyes (CyDye DIGE Fluor saturation dyes) to laser microdissection and two-dimensional difference gel electrophoresis (2D-DIGE) for cancer proteomics. Nat. Protoc. 2006, 1, 2940-2956.
11. Mustafa, D. A., Bergers, P. C., Dekker, L. J., Charif, H. et al., Identification of glioma neovascularisation-related proteins by using MALDI-FTMS and nano-LC fractionation to micro-dissected tumor vessels. Mol. Cell. Proteomics 2007, 6, 1147-1157.
12. Bi, X., Lin, Q., Foo, T. W., Joshi, S. et al., Proteomic analysis of colorectal cancer reveals alterations in metabolic pathways: Mechanism of tumorigenesis. Mol. Cell. Proteomics 2006, 5, 1119-1130.
13. Celis, J. E., Gel-based proteomics: What does MCP expect?. Mol. Cell. Proteomics 2004, 3, 949.
14. Ohlsson, G., Moreira, J. M., Gromov, P., Sauter, G. et al., Loss of expression of the adipocyte-type fatty acid-binding protein (A-FABP) is associated with progression of human urothelial carcinomas. Mol. Cell. Proteomics 2005, 4, 570-581.
15. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F. et al., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17, 994-999.
16. Li, J., Steen, H., Gygi, S. P., Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: The yeast salinity stress response. Mol. Cell. Proteomics 2003, 2, 1198-1204.
17. Chen, R., Pan, S., Yi, E. C., Donohoe, S. et al., Quantitative proteomic profiling of pancreatic cancer juice. Proteomics 2006, 6, 3871-3879.
18. Miseta, A., Csutora, P., Relationship between the occurrence of cysteine in proteins and the complexity of organisms. Mol. Biol. Evol. 2000, 17, 1232-1239.
19. Schnolzer, M., Jedrzejewski, P., Lehmann, W. D., Protease-catalyzed incorporation of 180 into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ ionization mass spectrometry. Electrophoresis 1996, 17, 945-953.
20. Zang, L., Palmer Toy, D., Hancock, W. S., Sgroi, D. C. et al., Proteomic analysis of ductal carcinoma of the breast using laser capture microdissection, LC-MS, and 16O/18O isotopic labeling. J. Proteome Res. 2004, 3, 604-612.
21. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents, Mol. Cell. Proteomics 2004, 3, 1154-1169.
22. Keshamouni, V. G., Michailidis, G., Grasso, C. S., Anthwal, S. et al., Differential protein expression profiling by iTRAQ-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype. J. Proteome Res. 2006, 5, 1143-1154.
23. Sechi, S., A method to identify and simultaneously determine the relative quantities of proteins isolated by gel electrophoresis. Rapid Commun. Mass Spectrom. 2002, 16, 1416-1424.
24. Chakraborty, A., Regnier, F. E., Global internal standard technology for comparative proteomics. J Chromatogr. A 2002, 949, 173-184.
25. Ji, C., Guo, N., Li, L., Differential dimethyl labeling of N-termini of peptides after guanidination for proteome analysis. J. Proteome Res. 2005, 4, 2099-2108.
26. Ji, C., Li, L., Quantitative proteome analysis using differential stable isotopic labeling and microbore LC-MALDI MS and MS/MS. J. Proteome Res. 2005, 4, 734-742.
27. Kirkpatrick, D. S., Gerber, S. A., Gygi, S. P., The absolute quantification strategy: A general procedure for the quantification of proteins and post-translational modifications. Methods 2005, 35, 265-273.
28. Barnidge, D. R., Goodmanson, M. K., Kies, G. G., Muddiman, D. C., Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry. J. Proteome Res. 2004, 3, 644-652.
29. Beynon, R. J., Doherty, M. K., Pratt, J. M., Gaskell, S. J., Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods 2005, 2, 587-589.
30. Le Bihan, T., Goh, T., Stewart, II, Salter, A. M. et al., Differential analysis of membrane proteins in mouse fore- and hindbrain using a label-free approach. J. Proteome Res. 2006, 5, 2701-2710.
31. Ono, M., Shitashige, M., Honda, K., Isobe, T. et al., Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry. Mol. Cell. Proteomics 2006, 5, 1338-1347.
32. Liu, H., Sadygov, R. G., Yates, J. R., 3rd, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
33. Schmidt, M. W., Houseman, A., Ivanov, A. R., Wolf, D. A., Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Mol. Syst. Biol. 2007, 3, 79.
34. Bondarenko, P. V., Chelius, D., Shaler, T. A., Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal. Chem. 2002, 74, 4741-4749.
35. Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G. et al., Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 2005, 4, 1487-1502.
36. Wiener, M. C., Sachs, J. R., Deyanova, E. G., Yates, N. A., Differential mass spectrometry: A label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal. Chem. 2004, 76, 6085-6096.
37. Shafer, M. W., Mangold, L., Partin, A. W., Haab, B. B., Antibody array profiling reveals serum TSP-1 as a marker to distinguish benign from malignant prostatic disease. Prostate 2007, 67, 255-267.
38. Li, Y., Lee, H. J., Corn, R. M., Detection of protein biomarkers using RNA aptamer microarrays and enzymatically amplified surface plasmon resonance imaging. Anal. Chem. 2007, 79, 1082-1088.
39. Shangguan, D., Cao, Z. C., Li, Y., Tan, W., Aptamers evolved from cultured cancer cells reveal molecular differences of cancer cells in patient samples. Clin. Chem. 2007, 53, 1153-1155.
40. Joos, T. O., Berger, H., The long and difficult road to the diagnostic market: Protein microarrays. Drug Discov. Today 2006,11, 959-961.
41. Schweitzer, B., Roberts, S., Grimwade, B., Shao, W. et al., Multiplexed protein profiling on microarrays by rolling-circle amplification. Nat. Biotechnol. 2002, 20, 359-365.
42. Geho, D., Lahar, N., Gurnani, P., Huebschman, M. et al., Pegylated, steptavidin-conjugated quantum dots are effective detection elements for reverse-phase protein microarrays. Bioconjug. Chem. 2005, 16, 559-566.
43. Kattah, M. G., Alemi, G. R., Thibault, D. L., Balboni, I. et al., A new two-color Fab labeling method for autoantigen protein microarrays. Nat. Methods 2006, 3, 745-751.
44. Gulmann, C., Sheehan, K. M., Kay, E. W., Liotta, L. A. et al., Array-based proteomics: Mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancer. J. Pathol. 2006, 208, 595-606.
45. Schwenk, J. M., Lindberg, J., Sundberg, M., Uhlen, M. et al., Determination of binding specificities in highly multiplexed bead-based assays for antibody proteomics. Mol. Cell. Proteomics 2007, 6, 125-132.
46. Waterboer, T., Sehr, P., Michael, K. M., Franceschi, S. et al., Multiplex human papillomavirus serology based on in situ-purified glutathione s-transferase fusion proteins. Clin. Chem. 2005, 51, 1845-1853.
47. Gorelik, E., Landsittel, D. P., Marrangoni, A. M., Modugno, F. et al., Multiplexed immunobead-based cytokine profiling for early detection of ovarian cancer. Cancer Epidemiol. Biomarkers Prev. 2005, 14, 981-987.
48. Linkov, F., Lisovich, A., Yurkovetsky, Z., Marrangoni, A. et al., Early detection of head and neck cancer: Development of a novel screening tool using multiplexed immunobead-based biomarker profiling. Cancer Epidemiol. Biomarkers Prev. 2007, 16, 102-107.
49. Emmert-Buck, M. R., Bonner, R. F., Smith, P. D., Chuaqui, R. F. et al., Laser capture microdissection. Science 1996, 274, 998-1001.
50. Milchgrub, S., Wistuba, II, Kim, B. K., Rutherford, C. et al., Molecular identification of metastatic cancer to the skin using laser capture microdissection: A case report. Cancer 2000, 88, 749-754.
51. Kuick, R., Misek, D. E., Monsma, D. J., Webb, C. R et al., Discovery of cancer biomarkers through the use of mouse models. Cancer Lett. 2007, 249, 40-48.
52. Srinivasan, V., Pamula, V. K., Fair, R. B., An integrated digital microfluidic lab-on-a-chip for clinical diagnostics on human physiological fluids. Lab Chip 2004, 4, 310-315.
53. Chaurand, P., Schriver, K. E., Caprioli, R. M., Instrument design and characterization for high resolution MALDI-MS imaging of tissue sections. J. Mass Spectrom. 2007, 42, 476-489.
54. Hoffman, S. A., Joo, W. A., Echan, L. A., Speicher, D. W., Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007, 849, 43-52.
55. Chignard, N., Shang, S., Wang, H., Marrero, J. et al., Cleavage of endoplasmic reticulum proteins in hepatocellular carcinoma: Detection of generated fragments in patient sera. Gastroenterology 2006, 130, 2010-2022.
56. Zhou, G., Li, H., DeCamp, D., Chen, S. et al., 2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers. Mol. Cell. Proteomics 2002, 1, 117-124.
57. Yu, K. H., Rustgi, A. K., Blair, I. A., Characterization of proteins in human pancreatic cancer serum using differential gel electrophoresis and tandem mass spectrometry. J. Proteome Res. 2005, 4, 1742-1751.
58. Seshi, B., An integrated approach to mapping the proteome of the human bone marrow stromal cell. Proteomics 2006, 6, 5169-5182
59. Pawlik, T. M., Hawke, D. H., Liu, Y., Krishnamurthy, S. et al., Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein. BMC Cancer 2006, 6, 68
60. DeSouza, L., Diehl, G., Rodrigues, M. J., Guo, J. et al, Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J. Proteome Res. 2005, 4, 377-386.
61. Li, C., Hong, Y., Tan, Y. X., Zhou, H. et al., Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry. Mol. Cell. Proteomics 2004, 3, 399-409.
62. Hood, B. L., Lucas, D. A., Kim, G., Chan, K. C. et al., Quantitative analysis of the low molecular weight serum proteome using 18O stable isotope labeling in a lung tumor xenograft mouse model. J. Am. Soc. Mass Spectrom. 2005, 16, 1221-1230.
63. Brown, K. J., Fenselau, C., Investigation of doxorubicin resistance in MCF-7 breast cancer cells using shot-gun comparative proteomics with proteolytic 18O labeling. J. Proteome Res. 2004, 3, 455-462.
64. Ru, Q. C., Zhu, L. A., Silberman, J., Shriver, C. D., Label-free serniquantitative peptide feature profiling of human breast cancer and breast disease sera via two-dimensional liquid chromatography-mass spectrometry. Mol. Cell. Proteomics 2006, 5, 1095-1104.
65. Patwardhan, A. J., Strittmatter, E. F., Camp, D. G., 2nd, Smith, R. D. et al., Quantitative proteome analysis of breast cancer cell lines using 18O-labeling and an accurate mass and time tag strategy. Proteomics 2006, 6, 2903-2915.
66. Lokshin, A. E., Winans, M., Landsittel, D., Marrangoni, A. M. et al., Circulating IL-8 and anti-IL-8 autoantibody in patients with ovarian cancer. Gynecol. Oncol. 2006, 102, 244-251.