Proteomic analysis of human plasma and blood cells in nutritional studies: Development of biomarkers to aid disease prevention

Expert Review of Proteomics

Volumn 5, Issue 6, 2008, Pages 819-826

  De Roos, Baukje ^a  

^a ROWETT RESEARCH INSTITUTE   (United Kingdom)

Author keywords

Nutritional studies; Peripheral blood mononuclear cell; Plasma; Platelet; Proteomics; Study design

Indexed keywords

BIOLOGICAL MARKER; PLASMA PROTEIN;

DISEASE PREDISPOSITION; HUMAN; NUTRITION; PERIPHERAL BLOOD MONONUCLEAR CELL; PROPHYLAXIS; PROTEIN ISOLATION; PROTEOMICS; REVIEW;

ANIMALS; BIOLOGICAL MARKERS; BLOOD CELLS; DIET; DISEASE; HUMANS; PLASMA; PROTEOMICS;

EID: 58149159875     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.5.6.819     Document Type: Review

References (70)

1. Gerszten RE, Wang TJ. The search for new cardiovascular biomarkers. Nature 451, 949-952 (2008). • Excellent review discussing biomarker discovery in cardiovascular research.
2. van der Greef J, Martin S, Juhasz P et al. The art and practice of systems biology in medicine: mapping patterns of relationships. J. Proteome Res. 6, 1540-1559 (2007). • Provides interesting views on the application of systems biology.
3. de Roos B, McArdle HJ. Proteomics as a tool for the modelling of biological processes and biomarker development in nutrition research. Br. J. Nutr. 99, S66-S71 (2008).
4. Fuchs D, Winkelmann I, Johnson IT et al. Proteomics in nutrition research: principles, technologies and applications. Br. J. Nutr. 94, 302-314 (2005).
5. Kim H, Page GP, Barnes S. Proteomics and mass spectrometry in nutrition research. Nutrition 20, 155-165 (2004).
6. Barnes S, Kim H. Nutriproteomics: identifying the molecular targets of nutritive and non-nutritive components of the diet. J. Biochem. Mol. Biol. 37, 59-74 (2004).
7. Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl Acad. Sci. USA 97, 9390-9395 (2000).
8. Kenyon GL, DeMarini DM, Fuchs E et al. Defining the mandate of proteomics in the post-genomics era: workshop report. Mol. Cell. Proteomics 1, 763-780 (2002).
9. de Roos B, Duivenvoorden I, Rucklidge G et al. Response of apolipoprotein E*3-Leiden transgenic mice to dietary fatty acids: combining liver proteomics with physiological data. FASEB J. 19, 813-815 (2005).
10. -/- mice. J. Proteome Res. 6, 4041-4054 (2007).
11. Issaq HJ, Veenstra TD. The role of electrophoresis in disease biomarker discovery. Electrophoresis 28, 1980-1988 (2007).
12. Kussmann M. How to comprehensively analyse proteins and how this influences nutritional research. Clin. Chem. Lab. Med. 45, 288-300 (2007).
13. Kussmann M, Affolter M. Proteomic methods in nutrition. Curr. Opin. Clin. Nutr. Metab. Care 9, 575-583 (2006).
14. Smolka MB, Zhou H, Purkayastha S, Aebersold R. Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Anal. Biochem. 297, 25-31 (2001).
15. Streckfus CF, Mayorga-Wark O, Arreola D et al. Breast cancer related proteins are present in saliva and are modulated secondary to ductal carcinoma in situ of the breast. Cancer Invest. 26, 159-167 (2008).
16. Duncan MW, Hunsucker SW. Proteomics as a tool for clinically relevant biomarker discovery and validation. Exp. Biol. Med. (Maywood) 230, 808-817 (2005).
17. Echan LA, Tang HY, Ali-Khan N, Lee K, Speicher DW. Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics 5, 3292-3303 (2005).
18. Huang L, Harvie G, Feitelson JS et al. Immunoaffinity separation of plasma proteins by IgY microbeads: meeting the needs of proteomic sample preparation and analysis. Proteomics 5, 3314-3328 (2005).
19. Rai AJ, Gelfand CA, Haywood BC et al. HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 5, 3262-3277 (2005).
20. Omenn GS, States DJ, Adamski M et al. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 5, 3226-3245 (2005).
21. Anderson NL, Anderson NG. Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis 19, 1853-1861 (1998).
22. Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 1, 845-867 (2002).
23. Fang X, Zhang WW. Affinity separation and enrichment methods in proteomic analysis. J. Proteomics 71, 284-303 (2008). • Recent review that provides an excellent overview of affinity separation methods.
24. de Roos B, Duthie SJ, Polley AC et al. Proteomic methodological recommendations for studies involving human plasma, platelets and peripheral blood mononuclear cells. J. Proteome Res. 7, 2280-2290 (2008).
25. de Roos B, Geelen A, Ross K et al. Identification of potential serum biomarkers of inflammation and lipid modulation that are altered by fish oil supplementation in healthy volunteers. Proteomics 8, 1965-1974 (2008).
26. Aldred S, Sozzi T, Mudway I et al. α tocopherol supplementation elevates plasma apolipoprotein A1 isoforms in normal healthy subjects. Proteomics 6, 1695-1703 (2006).
27. Hanash SM, Pitteri SJ, Faca VM. Mining the plasma proteome for cancer biomarkers. Nature 452, 571-579 (2008).
28. Jenkins CS, Phillips DR, Clemetson KJ et al. Platelet membrane glycoproteins implicated in ristocetin-induced aggregation. Studies of the proteins on platelets from patients with Bernard-Soulier syndrome and von Willebrand's disease. J. Clin. Invest. 57, 112-124 (1976).
29. Gravel P, Sanchez JC, Walzer C et al. Human blood platelet protein map established by two-dimensional polyacrylamide gel electrophoresis. Electrophoresis 16, 1152-1159 (1995).
30. Macaulay IC, Carr P, Gusnanto A et al. Platelet genomics and proteomics in human health and disease. J. Clin. Invest. 115, 3370-3377 (2005).
31. Garcia A, Watson SP, Dwek RA, Zitzmann N. Applying proteomics technology to platelet research. Mass Spectrom. Rev. 24, 918-930 (2005). • Discusses several aspects of platelet proteomics.
32. Gnatenko DV, Perrotta PL, Bahou WF. Proteomic approaches to dissect platelet function: half the story. Blood 108, 3983-3991 (2006).
33. O'Neill EE, Brock CJ, von Kriegsheim AF et al. Towards complete analysis of the platelet proteome. Proteomics 2, 288-305 (2002).
34. Garcia A, Prabhakar S, Brock CJ et al. Extensive analysis of the human platelet proteome by two-dimensional gel electrophoresis and mass spectrometry. Proteomics 4, 656-668 (2004).
35. Hartwig JH. The platelet: form and function. Semin. Hematol. 43, S94-S100 (2006).
36. Garcia A, Prabhakar S, Hughan S et al. Differential proteome analysis of TRAP-activated platelets: involvement of DOK-2 and phosphorylation of RGS proteins. Blood 103, 2088-2095 (2004).
37. Maguire PB, Wynne KJ, Harney DF et al. Identification of the phosphotyrosine proteome from thrombin activated platelets. Proteomics 2, 642-648 (2002).
38. Maguire PB, Foy M, Fitzgerald DJ. Using proteomics to identify potential therapeutic targets in platelets. Biochem. Soc. Trans. 33, 409-412 (2005).
39. Zhang H, Li XJ, Martin DB, Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol. 21, 660-666 (2003).
40. Garcia A. Proteome analysis of signaling cascades in human platelets. Blood Cells Mol. Dis. 36, 152-156 (2006).
41. Coppinger JA, Cagney G, Toomey S et al. Characterization of the proteins released from activated platelets leads to localization of novel platelet proteins in human atherosclerotic lesions. Blood 103, 2096-2104 (2004).
42. Moebius J, Zahedi RP, Lewandrowski U et al. The human platelet membrane proteome reveals several new potential membrane proteins. Mol. Cell. Proteomics 4, 1754-1761 (2005).
43. Maynard DM, Heijnen HF, Horne MK, White JG, Gahl WA. Proteomic analysis of platelet α-granules using mass spectrometry. J. Thromb. Haemost. 5, 1945-1955 (2007).
44. Garcia BA, Smalley DM, Cho H et al. The platelet microparticle proteome. J. Proteome Res. 4, 1516-1521 (2005).
45. Dittrich M, Birschmann I, Mietner S et al. Platelet protein interactions: map, signaling components, and phosphorylation groundstate. Arterioscler. Thromb. Vasc. Biol. 28, 1326-1331 (2008).
46. Ruggiero C, Metter EJ, Cherubini A et al. White blood cell count and mortality in the Baltimore Longitudinal Study of Aging. J. Am. Coll. Cardiol. 49, 1841-1850 (2007).
47. Bell DS, O'Keefe JH. White cell count, mortality, and metabolic syndrome in the Baltimore longitudinal study of aging. J. Am. Coll. Cardiol. 50, 1810-1811 (2007).
48. Lau B, Gange SJ, Phair JP et al. Rapid declines in total lymphocyte counts and hemoglobin concentration prior to AIDS among HIV-1-infected men. AIDS 17, 2035-2044 (2003).
49. Yu HH, Wang LC, Lee JH et al. Lymphopenia is associated with neuropsychiatric manifestations and disease activity in paediatric systemic lupus erythematosus patients. Rheumatology (Oxford) 46, 1492-1494 (2007).
50. Maas K, Chan S, Parker J et al. Cutting edge: molecular portrait of human autoimmune disease. J. Immunol. 169, 5-9 (2002).
51. Burczynski ME, Dorner AJ. Transcriptional profiling of peripheral blood cells in clinical pharmacogenomic studies. Pharmacogenomics 7, 187-202 (2006).
52. Bouwens M, Afman LA, Muller M. Fasting induces changes in peripheral blood mononuclear cell gene expression profiles related to increases in fatty acid ?-oxidation: functional role of peroxisome proliferator activated receptor-α in human peripheral blood mononuclear cells. Am. J. Clin. Nutr. 86, 1515-1523 (2007).
53. Fuchs D, Piller R, Linseisen J, Daniel H, Wenzel U. The human peripheral blood mononuclear cell proteome responds to a dietary flaxseed-intervention and proteins identified suggest a protective effect in atherosclerosis. Proteomics 7, 3278-3288 (2007).
54. Fuchs D, Vafeiadou K, Hall WL et al. Proteomic biomarkers of peripheral blood mononuclear cells obtained from postmenopausal women undergoing an intervention with soy isoflavones. Am. J. Clin. Nutr. 86, 1369-1375 (2007).
55. Wilkins MR, Appel RD, Van Eyk JE et al. Guidelines for the next 10 years of proteomics. Proteomics 6, 4-8 (2006).
56. Biron DG, Brun C, Lefevre T et al. The pitfalls of proteomics experiments without the correct use of bioinformatics tools. Proteomics 6, 5577-5596 (2006).
57. Hunt SM, Thomas MR, Sebastian LT et al. Optimal replication and the importance of experimental design for gel-based quantitative proteomics. J. Proteome Res. 4, 809-819 (2005).
58. Carr S, Aebersold R, Baldwin M et al. The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol. Cell. Proteomics 3, 531-533 (2004).
59. Wheelock AM, Goto S. Effects of post-electrophoretic analysis on variance in gel-based proteomics. Expert Rev. Proteomics 3, 129-142 (2006).
60. Vasan RS. Biomarkers of cardiovascular disease: molecular basis and practical considerations. Circulation 113, 2335-2362 (2006).
61. Nielsen UB, Geierstanger BH. Multiplexed sandwich assays in microarray format. J. Immunol. Methods 290, 107-120 (2004).
62. Mariman EC. Nutrigenomics and nutrigenetics: the 'omics' revolution in nutritional science. Biotechnol. Appl. Biochem. 44, 119-128 (2006).
63. Domon B, Aebersold R. Mass spectrometry and protein analysis. Science 312, 212-217 (2006).
64. Anderson L, Hunter CL. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 5, 573-588 (2006).
65. Trayhurn P. Proteomics and nutrition - a science for the first decade of the new millennium. Br. J. Nutr. 83, 1-2 (2000).
66. Xiao Z, Prieto D, Conrads TP, Veenstra TD, Issaq HJ. Proteomic patterns: their potential for disease diagnosis. Mol. Cell. Endocrinol. 230, 95-106 (2005).
67. Veenstra TD, Conrads TP, Hood BL et al. Biomarkers: mining the biofluid proteome. Mol. Cell. Proteomics 4, 409-418 (2005).
68. Jacobs JM, Adkins JN, Qian WJ et al. Utilizing human blood plasma for proteomic biomarker discovery. J. Proteome Res. 4, 1073-1085 (2005).
69. Fu Q, Van Eyk JE. Proteomics and heart disease: identifying biomarkers of clinical utility. Expert Rev. Proteomics 3, 237-249 (2006).
70. Hu S, Loo JA, Wong DT. Human body fluid proteome analysis. Proteomics 6, 6326-6353 (2006).