A quantitative proteomic approach to prion disease biomarker research: Delving into the glycoproteome

Journal of Proteome Research

Volumn 10, Issue 6, 2011, Pages 2687-2702

  Wei, Xin ^a   Herbst, Allen ^b,c   Ma, Di ^a   Aiken, Judd ^b,c   Li, Lingjun ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF ALBERTA   (Canada)

^c UNIVERSITY OF ALBERTA   (Canada)

Author keywords

biomarkers; glycoprotein; mass spectrometry; multidimensional separation; prion disease; proteomics; quantitation

Indexed keywords

BIOLOGICAL MARKER; GLYCOPROTEIN; LECTIN;

AFFINITY CHROMATOGRAPHY; ANIMAL EXPERIMENT; ARTICLE; DEGENERATIVE DISEASE; DISEASE MARKER; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMA; PRION DISEASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ISOLATION; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; TANDEM MASS SPECTROMETRY; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; ANIMALS; BIOLOGICAL MARKERS; CARRIER PROTEINS; CHROMATOGRAPHY, AFFINITY; GLYCOPROTEINS; LECTINS; MICE; MICE, INBRED C57BL; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PRION DISEASES; PROTEOMICS; REPRODUCIBILITY OF RESULTS; TANDEM MASS SPECTROMETRY;

EID: 79958200862     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr2000495     Document Type: Article

References (55)

1. Borchelt, D. R.; Scott, M.; Taraboulos, A.; Stahl, N.; Prusiner, S. B. Scrapie and Cellular Prion Proteins Differ in Their Kinetics of Synthesis and Topology in Cultured-Cells J. Cell Biol. 1990, 110 (3) 743-752
2. Caughey, B.; Race, R. E.; Ernst, D.; Buchmeier, M. J.; Chesebro, B. Prion Protein-Biosynthesis in Scrapie-Infected and Uninfected Neuro-Blastoma Cells J. Virol. 1989, 63 (1) 175-181 (Pubitemid 19028095)
3. Chesebro, B.; Race, R.; Wehrly, K.; Nishio, J.; Bloom, M.; Lechner, D.; Bergstrom, S.; Robbins, K.; Mayer, L.; Keith, J. M. Nature 1985, 315, 331
4. Oesch, B.; Westaway, D.; Walchli, M.; McKinley, M. P.; Kent, S. B.; Aebersold, R.; Barry, R. A.; Tempst, P.; Teplow, D. B.; Hood, L. E. Cell 1985, 40, 735
5. Schaller, O.; Fatzer, R.; Stack, M.; Clark, J.; Cooley, W.; Biffiger, K.; Egli, S.; Doherr, M.; Vandevelde, M.; Heim, D.; Oesch, B.; Moser, M. Validation of a western immunoblotting procedure for bovine PrP(Sc) detection and its use as a rapid surveillance method for the diagnosis of bovine spongiform encephalopathy (BSE) Acta Neuropathol. 1999, 98, 7
6. Burkhard, P. R.; Sanchez, J. C.; Landis, T.; Hochstrasser, D. F. Neurology 2001, 56, 1528
7. Choe, L. H.; Green, A.; Knight, R. S.; Thompson, E. J.; Lee, K. H. Electrophoresis 2002, 23, 2242
8. Otto, M.; Wiltfang, J.; Cepek, L.; Neumann, M.; Mollenhauer, B.; Steinacker, P.; Ciesielczyk, B.; Schulz-Schaeffer, W.; Kretzschmar, H. A.; Poser, S. Neurology 2002, 58, 192
9. Parveen, I.; Moorby, J.; Allison, G.; Jackman, R. Vet. Res. 2005, 36, 665
10. Sanchez, J. C.; Guillaume, E.; Lescuyer, P.; Allard, L.; Carrette, O.; Scherl, A.; Burgess, J.; Corthals, G. L.; Burkhard, P. R.; Hochstrasser, D. F. Proteomics 2004, 4, 2229
11. Van Everbroeck, B.; Boons, J.; Cras, P. Clin. Neurol. Neurosurg. 2005, 107, 355
12. Zerr, I.; Bodemer, M.; Otto, M.; Poser, S.; Windl, O.; Kretzschmar, H. A.; Gefeller, O.; Weber, T. Lancet 1996, 348, 846
13. Rifai, N.; Gillette, M. A.; Carr, S. A. Protein biomarker discovery and validation: the long and uncertain path to clinical utility Nat. Biotechnol. 2006, 24 (8) 971-983 (Pubitemid 44215392)
14. Madera, M.; Mechref, Y.; Klouckova, I.; Novotny, M. V. High-sensitivity profiling of glycoproteins from human blood serum through multiple-lectin affinity chromatography and liquid chromatography/tandem mass spectrometry J Chromatogr B 2007, 845 (1) 121-137 (Pubitemid 44839305)
15. Yang, Z.; Harris, L. E.; Palmer-Toy, D. E.; Hancock, W. S. Multilectin Affinity Chromatography for Characterization of Multiple Glycoprotein Biomarker Candidates in Serum from Breast Cancer Patients Clin Chem 2006, 52 (10) 1897-1905 (Pubitemid 44470697)
16. Qiu, R.; Regnier, F. E. Use of Multidimensional Lectin Affinity Chromatography in Differential Glycoproteomics Anal. Chem. 2005, 77 (9) 2802-2809 (Pubitemid 40617327)
17. Bertozzi, C. R.; Kiessling, L. L. Chemical Glycobiology Science 2001, 291 (5512) 2357-2364 (Pubitemid 32231790)
18. Wei, X.; Li, L. Comparative glycoproteomics: approaches and applications Brief. Funct. Genomic Proteomic 2009, 8 (2) 104-113
19. Diamandis, E. P. Mass Spectrometry as a Diagnostic and a Cancer Biomarker Discovery Tool: Opportunities and Potential Limitations Mol. Cell. Proteomics 2004, 3 (4) 367-378 (Pubitemid 38702090)
20. Liu, F.; Iqbal, K.; Grundke-Iqbal, I.; Hart, G. W.; Gong, C.-X. O-GlcNAcylation regulates phosphorylation of tau: A mechanism involved in Alzheimer's disease Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (29) 10804-10809 (Pubitemid 38955823)
21. Botella-Lopez, A.; Burgaya, F.; Gavin, R.; Garcia-Ayllon, M. S.; Gomez-Tortosa, E.; Pena-Casanova, J.; Urena, J. M.; Del Rio, J. A.; Blesa, R.; Soriano, E.; Saez-Valero, J. Reelin expression and glycosylation patterns are altered in Alzheimer's disease Proc. Natl. Acad. Sci. U.S.A. 2006, 103 (14) 5573-5578
22. Rudd, P. M.; Endo, T.; Colominas, C.; Groth, D.; Wheeler, S. F.; Harvey, D. J.; Wormald, M. R.; Serban, H.; Prusiner, S. B.; Kobata, A.; Dwek, R. A. Glycosylation differences between the normal and pathogenic prion protein isoforms Proc. Natl. Acad. Sci. U.S.A. 1999, 96 (23) 13044-13049
23. Hutchinson, W. L.; Noble, G. E.; Hawkins, P. N.; Pepys, M. B. The pentraxins, C-reactive protein and serum amyloid P component, are cleared and catabolized by hepatocytes in vivo J. Clin. Invest. 1994, 94 (4) 1390-1306
24. Mold, C.; Baca, R.; Du Clos, T. W. Serum amyloid P component and C-reactive protein opsonize apoptotic cells for phagocytosis through Fcgamma receptors J. Autoimmun. 2002, 19 (3) 147-154 (Pubitemid 35341864)
25. Togashi, S.; Lim, S. K.; Kawano, H.; Ito, S.; Ishihara, T.; Okada, Y.; Nakano, S.; Kinoshita, T.; Horie, K.; Episkopou, V.; Gottesman, M. E.; Costantini, F.; Shimada, K.; Maeda, S. Serum amyloid P component enhances induction of murine amyloidosis Lab. Invest. 1997, 77 (5) 525-531 (Pubitemid 27508623)
26. Han, D. K.; Eng, J.; Zhou, H.; Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry Nat. Biotechnol. 2001, 19 (10) 946-951 (Pubitemid 32947573)
27. Geer, L. Y.; Markey, S. P.; Kowalak, J. A.; Wagner, L.; Xu, M.; Maynard, D. M.; Yang, X.; Shi, W.; Bryant, S. H. Open Mass Spectrometry Search Algorithm J. Proteome Res. 2004, 3 (5) 958-964 (Pubitemid 39425651)
28. Khatri, P.; Draghici, S.; Ostermeier, G. C.; Krawetz, S. A. Profiling Gene Expression Using Onto-Express Genomics 2002, 79 (2) 266-270
29. Ramstrom, M.; Hagman, C.; Mitchell, J. K.; Derrick, P. J.; Hakansson, P.; Bergquist, J. Depletion of high-abundant proteins in body fluids prior to liquid chromatography fourier transform ion cyclotron resonance mass spectrometry J. Proteome Res. 2005, 4 (2) 410-416 (Pubitemid 40548146)
30. Brzeski, H.; Katenhusen, R. A.; Sullivan, A. G.; Russell, S.; George, A.; Somiari, R. I.; Shriver, C. Albumin depletion method for improved plasma glycoprotein analysis by two-dimensional difference gel electrophoresis Biotechniques 2003, 35 (6) 1128-32 (Pubitemid 37517487)
31. Baron, A. T.; Lafky, J. M.; Boardman, C. H.; Balasubramaniam, S.; Suman, V. J.; Podratz, K. C.; Maihle, N. J. Serum sErbB1 and epidermal growth factor levels as tumor biomarkers in women with stage III or IV epithelial ovarian cancer Cancer Epidemiol. Biomarkers Prevention 1999, 8 (2) 129-137 (Pubitemid 29085379)
32. Edmund, A. W.; Brice, M. B.; Friedlander, W.; Bateman, E. D.; Kirsch, R. E. Serum Angiotensin-Converting Enzyme Activity, Concentration, and Specific Activity in Granulomatous Interstitial Lung Disease, Tuberculosis, and COPD Chest 1995, 107 (3) 706-710
33. Hiroaki, S.; Shunichi, T.; Kuniyuki, K.; Masahide, I.; Michio, M.; Nobuaki, K. Serum concentration of CD44 variant 6 and its relation to prognosis in patients with gastric carcinoma Cancer 1998, 83 (6) 1094-1101
34. Hunter, N.; Foster, J.; Chong, A.; McCutcheon, S.; Parnham, D.; Eaton, S.; MacKenzie, C.; Houston, F. Transmission of prion diseases by blood transfusion J. Gen. Virol. 2002, 83, 2897-2905 (Pubitemid 35276989)
35. Chang, B. G.; Cheng, X.; Yin, S. M.; Pan, T.; Zhang, H. T.; Wong, P. K.; Kang, S. C.; Xiao, F.; Yan, H. M.; Li, C. Y.; Wolfe, L. L.; Miller, M. W.; Wisniewski, T.; Greene, M. I.; Sy, M. S. Test for detection of disease-associated prion aggregate in the blood of infected but asymptomatic animals Clin. Vaccine Immunol. 2007, 14 (1) 36-43
36. Rudd, P. M.; Merry, A. H.; Wormald, M. R.; Dwek, R. A. Glycosylation and prion protein Curr. Opin. Struct. Biol. 2002, 12 (5) 578-586 (Pubitemid 35449064)
37. Fournier, M. L.; Gilmore, J. M.; Martin-Brown, S. A.; Washburn, M. P. Multidimensional separations-based shotgun proteomics Chem. Rev. 2007, 107 (8) 3654-3686 (Pubitemid 47322747)
38. Dowell, J. A.; VanderHeyden, W.; Li, L. Rat Neuropeptidomics by LC-MS/MS and MALDI-FTMS: Enhanced Dissection and Extraction Techniques Coupled with 2D RP-RP HPLC J. Proteome Res. 2006, 5 (12) 3368-3375 (Pubitemid 44904328)
39. Gilar, M.; Olivova, P.; Daly, A. E.; Gebler, J. C. Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions J. Sep. Sci. 2005, 28 (14) 1694-1703 (Pubitemid 43055013)
40. Hsu, J. L.; Huang, S. Y.; Chow, N. H.; Chen, S. H. Stable-Isotope Dimethyl Labeling for Quantitative Proteomics Anal. Chem. 2003, 75 (24) 6843-6852
41. Song, X.; Bandow, J.; Sherman, J.; Baker, J. D.; Brown, P. W.; McDowell, M. T.; Molloy, M. P. iTRAQ Experimental Design for Plasma Biomarker Discovery J. Proteome Res. 2008, 7 (7) 2952-2958
42. Zybailov, B.; Coleman, M. K.; Florens, L.; Washburn, M. P. Correlation of Relative Abundance Ratios Derived from Peptide Ion Chromatograms and Spectrum Counting for Quantitative Proteomic Analysis Using Stable Isotope Labeling Anal. Chem. 2005, 77 (19) 6218-6224 (Pubitemid 41436955)
43. Watanabe, J.; Grijalva, V.; Hama, S.; Barbour, K.; Berger, F. G.; Navab, M.; Fogelman, A. M.; Reddy, S. T. Hemoglobin and Its Scavenger Protein Haptoglobin Associate with ApoA-1-containing Particles and Influence the Inflammatory Properties and Function of High Density Lipoprotein J. Biol. Chem. 2009, 284 (27) 18292-18301
44. Wei, X.; Herbst, A.; Schmidt, J.; Aikent, J.; Li, L. J. Facilitating Discovery of Prion Disease Biomarkers by Quantitative Glycoproteomics LC GC North Am. 2009, 27 (2) 154-162
45. Edelman, G. M.; Wang, J. L. Binding and functional properties of concanavalin A and its derivatives. III. Interactions with indoleacetic acid and other hydrophobic ligands J. Biol. Chem. 1978, 253 (9) 3016-3022 (Pubitemid 8353171)
46. Holtzman, D. M.; Pitas, R. E.; Kilbridge, J.; Nathan, B.; Mahley, R. W.; Bu, G.; Schwartz, A. L. Low density lipoprotein receptor-related protein mediates apolipoprotein E-dependent neurite outgrowth in a central nervous system-derived neuronal cell line Proc. Natl. Acad. Sci. U.S.A. 1995, 92 (21) 9480-9484
47. Jiang, Q.; Lee, C. Y. D.; Mandrekar, S.; Wilkinson, B.; Cramer, P.; Zelcer, N.; Mann, K.; Lamb, B.; Willson, T. M.; Collins, J. L.; Richardson, J. C.; Smith, J. D.; Comery, T. A.; Riddell, D.; Holtzman, D. M.; Tontonoz, P.; Landreth, G. E. ApoE Promotes the Proteolytic Degradation of Aβ Neuron 2008, 58 (5) 681-693
48. Diedrich, J. F.; Minnigan, H.; Carp, R. I.; Whitaker, J. N.; Race, R.; Frey, W.; Haase, A. T. Neuropathological Changes in Scrapie and Alzheimers-Disease Are Associated with Increased Expression of Apolipoprotein-E and Cathepsin-D in Astrocytes J. Virol. 1991, 65 (9) 4759-4768
49. Leila, H. C.; Alison, G.; Richard, S. G. K.; Edward, J. T.; Kelvin, H. L. Apolipoprotein E and other cerebrospinal fluid proteins differentiate ante mortem variant Creutzfeldt-Jakob disease from ante mortem sporadic Creutzfeldt-Jakob disease Electrophoresis 2002, 23 (14) 2242-2246
50. Pepys, M. B.; Booth, D. R.; Hutchinson, W. L.; Gallimore, J. R.; Collins, P. M.; Hohenester, E. Amyloid P component. A critical review Amyloid-J. Protein Folding Disorders 1997, 4 (4) 274-295 (Pubitemid 127716144)
51. Kalaria, R. N.; Golde, T. E.; Cohen, M. L.; Younkin, S. G. Serum Amyloid-P in Alzheimers-Disease-Implications for Dysfunction of the Blood-Brain-Barrier Ann. N.Y. Acad. Sci. 1991, 640, 145-148
52. Akiyama, H.; Yamada, T.; Kawamata, T.; McGeer, P. L. Association of Amyloid-P Component with Complement Proteins in Neurologically Diseased Brain-Tissue Brain Res. 1991, 548 (1-2) 349-352
53. Coria, F.; Castano, E.; Prelli, F.; Larrondolillo, M.; Vanduinen, S.; Shelanski, M. L.; Frangione, B. Isolation and Characterization of Amyloid P-Component from Alzheimers-Disease and Other Types of Cerebral Amyloidosis Lab. Invest. 1988, 58 (4) 454-458
54. Pepys, M. B.; Herbert, J.; Hutchinson, W. L.; Tennent, G. A.; Lachmann, H. J.; Gallimore, J. R.; Lovat, L. B.; Bartfai, T.; Alanine, A.; Hertel, C.; Hoffmann, T.; Jakob-Roetne, R.; Norcross, R. D.; Kemp, J. A.; Yamamura, K.; Suzuki, M.; Taylor, G. W.; Murray, S.; Thompson, D.; Purvis, A.; Kolstoe, S.; Wood, S. P.; Hawkins, P. N. Targeted pharmacological depletion of serum amyloid P component for treatment of human amyloidosis Nature 2002, 417 (6886) 254-259 (Pubitemid 34534701)
55. Omtvedt, L. A.; Wien, T. N.; Myran, T.; Sletten, K.; Husby, G. Serum amyloid P component in mink, a non-glycosylated protein with affinity for phosphorylethanolamine and phosphorylcholine Amyloid-J. Protein Folding Disorders 2004, 11 (2) 101-108 (Pubitemid 39232095)