Role of proteomic technologies in understanding risk of arterial thrombosis

Expert Review of Proteomics

Volumn 6, Issue 5, 2009, Pages 539-550

  Polkinghorne, Victoria R ^a   Standeven, Kristina F ^a   Schroeder, Verena ^a   Carter, Angela M ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

Arterial thrombosis; Cardiovascular disease; Endothelial cell; Fibrin; Leukocyte; Plasma; Platelet; Proteomics; Vascular smooth muscle cell

Indexed keywords

BLOOD CLOTTING FACTOR; CELL PROTEIN; CHEMOKINE; CYTOKINE; ENDOTHELIAL LEUKOCYTE ADHESION MOLECULE 1; GLYCOPROTEIN; INTERCELLULAR ADHESION MOLECULE 1; PLASMA PROTEIN; PROTEOME; VASCULAR CELL ADHESION MOLECULE 1;

ARTERY THROMBOSIS; CARDIOVASCULAR RISK; CELL ACTIVATION; CYTOKINE PRODUCTION; DEEP VEIN THROMBOSIS; ENDOTHELIUM CELL; FUNCTIONAL PROTEOMICS; HUMAN; LEUKOCYTE; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; POLYACRYLAMIDE GEL ELECTROPHORESIS; REVIEW; SMOOTH MUSCLE FIBER; TANDEM MASS SPECTROMETRY; THROMBOCYTE; THROMBOGENESIS; TWO DIMENSIONAL ELECTROPHORESIS; VASCULAR SMOOTH MUSCLE;

BLOOD PLATELETS; BLOOD PROTEINS; HUMANS; LEUKOCYTES; MUSCLE, SMOOTH, VASCULAR; PROTEOMICS; RISK; THROMBOSIS;

EID: 70350443063     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/epr.09.75     Document Type: Review

References (87)

1. Nagata Y, Usuda K, Uchiyama A et al. Characteristics of the pathological images of coronary artery thrombi according to the infarct-related coronary artery in acute myocardial infarction. Circ. J. 68(4), 308-314 (2004). (Pubitemid 38470703)
2. Aebersold R. A mass spectrometric journey into protein and proteome research. J. Am. Soc. Mass Spectrom. 14(7), 685-695 (2003). (Pubitemid 36870951)
3. Matt P, Fu Z, Fu Q, Van Eyk JE. Biomarker discovery: proteome fractionation and separation in biological samples. Physiol. Genomics 33(1), 12-17 (2008).
4. Kislinger T, Emili A. Multidimensional protein identification technology: current status and future prospects. Expert Rev. Proteomics 2(1), 27-39 (2005). (Pubitemid 40292577)
5. Zhang G, Neubert TA. Use of stable isotope labeling by amino acids in cell culture (SILAC) for phosphotyrosine protein identification and quantitation. Methods Mol. Biol. 527, 79-92, xi (2009).
6. Lilley KS, Friedman DB. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev. Proteomics 1(4), 401-409 (2004).
7. Drake TA, Ping P. Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Proteomics approaches to the systems biology of cardiovascular diseases. J. Lipid Res. 48(1), 1-8 (2007).
8. Meilhac O, Delbosc S, Michel JB. Cardiovascular biomarker discovery by SELDI-TOF mass spectrometry. Methods Mol. Biol. 357, 331-341 (2007). (Pubitemid 350183258)
9. Fournier I, Wisztorski M, Salzet M. Tissue imaging using MALDI-MS: a new frontier of histopathology proteomics. Expert Rev. Proteomics 5(3), 413-424 (2008). (Pubitemid 351871117)
10. Franck J, Arafah K, Elayed M et al. MALDI imaging: State of the art technology in clinical proteomics. Mol. Cell Proteomics DOI: 10.1007/s00418-008-0469-0469 (2009) (Epub ahead of print).
11. Duran MC, Mas S, Martin-Ventura JL et al. Proteomic analysis of human vessels: application to atherosclerotic plaques. Proteomics 3(6), 973-978 (2003). (Pubitemid 36801685)
12. Libby P, Theroux P. Pathophysiology of coronary artery disease. Circulation 111(25), 3481-3488 (2005).
13. Karabina SA, Brocheriou I, Le Naour G et al. Atherogenic properties of LDL particles modified by human group X secreted phospholipase A2 on human endothelial cell function. FASEB J. 20(14), 2547-2549 (2006).
14. Chen CY, Lee CM, Hsu HC, Yang CY, Chow LP, Lee YT. Proteomic approach to study the effects of various oxidatively modified low-density lipoprotein on regulation of protein expression in human umbilical vein endothelial cell. Life Sci. 80(26), 2469-2480 (2007).
15. Xu C, Bailly-Maitre B, Reed JC. Endoplasmic reticulum stress: cell life and death decisions. J. Clin. Invest. 115(10), 2656-2664 (2005). (Pubitemid 41434389)
16. Wang XL, Fu A, Raghavakaimal S, Lee HC. Proteomic analysis of vascular endothelial cells in response to laminar shear stress. Proteomics 7(4), 588-596 (2007). (Pubitemid 46362622)
17. Wu J, Liu W, Sousa E et al. Proteomic identification of endothelial proteins isolated in situ from atherosclerotic aorta via systemic perfusion. J. Proteome Res. 6(12), 4728-4736 (2007). • Elegant paper employing a functional proteomics approach to specifically isolate endothelial cell membrane proteins in an in vivo model.
18. Aird WC. Spatial and temporal dynamics of the endothelium. J. Thromb. Haemost. 3(7), 1392-1406 (2005).
19. Banfi C, Brioschi M, Wait R et al. Proteome of endothelial cell-derived procoagulant microparticles. Proteomics 5(17), 4443-4455 (2005). (Pubitemid 41739922)
20. van Mourik JA, Romani dW, Voorberg J. Biogenesis and exocytosis of Weibel-Palade bodies. Histochem. Cell. Biol. 117(2), 113-122 (2002).
21. Carter AM. Inflammation, thrombosis and acute coronary syndromes. Diab. Vasc. Dis. Res. 2(3), 113-121 (2005).
22. Libby P, Theroux P. Pathophysiology of coronary artery disease. Circulation 111(25), 3481-3488 (2005).
23. Jin M, Opalek JM, Marsh CB, Wu HM. Proteome comparison of alveolar macrophages with monocytes reveals distinct protein characteristics. Am. J. Respir. Cell Mol. Biol. 31(3), 322-329 (2004). (Pubitemid 39180302)
24. Barderas MG, Tunon J, Darde VM et al. Atorvastatin modifies the protein profile of circulating human monocytes after an acute coronary syndrome. Proteomics 9(7), 1982-1993 (2009).
25. Barderas MG, Darde VM, Duran MC, Egido J, Vivanco F. Characterization of circulating human monocytes by proteomic analysis. Methods Mol. Biol. 357, 319-328 (2007). (Pubitemid 350183257)
26. Barderas MG, Tunon J, Darde VM et al. Circulating human monocytes in the acute coronary syndrome express a characteristic proteomic profile. J. Proteome Res. 6(2), 876-886 (2007). (Pubitemid 46340192)
27. Vergara D, Chiriaco F, Acierno R, Maffia M. Proteomic map of peripheral blood mononuclear cells. Proteomics 8(10), 2045-2051 (2008). (Pubitemid 351775784)
28. Jin M, Diaz PT, Bourgeois T et al. 2D gel proteome reference map of blood monocytes. Proteome Sci. 4, 16 (2006). (Pubitemid 44420324)
29. Dotzlaw H, Schulz M, Eggert M, Neeck G. A pattern of protein expression in peripheral blood mononuclear cells distinguishes rheumatoid arthritis patients from healthy individuals. Biochim. Biophys. Acta 1696(1), 121-129 (2004). (Pubitemid 38223892)
30. 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(18), 3278-3288 (2007). (Pubitemid 47517943)
31. Skopeliti M, Kratzer U, Altenberend F et al. Proteomic exploitation on prothymosin alpha-induced mononuclear cell activation. Proteomics. 7(11), 1814-1824 (2007).
32. Kang JH, Ryu HS, Kim HT et al. Proteomic analysis of human macrophages exposed to hypochlorite-oxidized low-density lipoprotein. Biochim. Biophys. Acta 1794(3), 446-458 (2009).
33. Dupont A, Chwastyniak M, Beseme O et al. Application of saturation dye 2D-DIGE proteomics to characterize proteins modulated by oxidized low density lipoprotein treatment of human macrophages. J. Proteome Res 7(8), 3572-3582 (2008).
34. Rosengren AT, Nyman TA, Lahesmaa R. Proteome profiling of interleukin-12 treated human T helper cells. Proteomics 5(12), 3137-3141 (2005). (Pubitemid 41176481)
35. Nyman TA, Rosengren A, Syyrakki S, Pellinen TP, Rautajoki K, Lahesmaa R. A proteome database of human primary T helper cells. Electrophoresis 22(20), 4375-4382 (2001). (Pubitemid 34065757)
36. Rautajoki K, Nyman TA, Lahesmaa R. Proteome characterization of human T helper 1 and 2 cells. Proteomics 4(1), 84-92 (2004). (Pubitemid 38140877)
37. Loyet KM, Ouyang W, Eaton DL, Stults JT. Proteomic profiling of surface proteins on Th1 and Th2 cells. J. Proteome Res. 4(2), 400-409 (2005). (Pubitemid 40548145)
38. McGregor E, Kempster L, Wait R et al. Identification and mapping of human saphenous vein medial smooth muscle proteins by two-dimensional polyacrylamide gel electrophoresis. Proteomics 1(11), 1405-1414 (2001). (Pubitemid 33587896)
39. Dupont A, Corseaux D, Dekeyzer O et al. The proteome and secretome of human arterial smooth muscle cells. Proteomics 5(2), 585-596 (2005). (Pubitemid 40262075)
40. Boccardi C, Cecchettini A, Caselli A et al. A proteomic approach to the investigation of early events involved in vascular smooth muscle cell activation. Cell Tissue Res. 328(1), 185-195 (2007). (Pubitemid 46411920)
41. Van Craeyveld E, Lievens J, Jacobs F, Feng Y, Snoeys J, De Geest B. Apolipoprotein A-I and lecithin:cholesterol acyltransferase transfer induce cholesterol unloading in complex atherosclerotic lesions. Gene Ther. 16(6), 757-765. (2009).
42. Trivedi V, Boire A, Tchernychev B et al. Platelet matrix metalloprotease-1 mediates thrombogenesis by activating PAR1 at a cryptic ligand site. Cell 137(2), 332-343 (2009).
43. Diebold I, Kraicun D, Bonello S, Gorlach A. The 'PAI-1 paradox' in vascular remodeling. Thromb. Haemost. 100(6), 984-991 (2008).
44. Cosemans JM, Iserbyt BF, Deckmyn H, Heemskerk JW. Multiple ways to switch platelet integrins on and off. J. Thromb. Haemost. 6(8), 1253-1261 (2008). (Pubitemid 352016302)
45. Rivera J, Lozano ML, Navarro-Nunez L, Vicente V. Platelet receptors and signaling in the dynamics of thrombus formation. Haematologica 94(5), 700-711 (2009).
46. Garcia A, Watson SP, Dwek RA, Zitzmann N. Applying proteomics technology to platelet research. Mass Spectrom. Rev. 24(6), 918-930 (2005).
47. 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(6), 2088-2095 (2004). (Pubitemid 38326224)
48. Garcia A, Senis YA, Antrobus R et al. A global proteomics approach identifies novel phosphorylated signaling proteins in GPVI-activated platelets: involvement of G6f, a novel platelet Grb2-binding membrane adapter. Proteomics 6(19), 5332-5343 (2006). (Pubitemid 44547170)
49. Maguire PB, Wynne KJ, Harney DF, O'Donoghue NM, Stephens G, Fitzgerald DJ. Identification of the phosphotyrosine proteome from thrombin activated platelets. Proteomics 2(6), 642-648 (2002). (Pubitemid 34693562)
50. Guerrier L, Claverol S, Fortis F et al. Exploring the platelet proteome via combinatorial, hexapeptide ligand libraries. J. Proteome Res 6(11), 4290-4303 (2007). • Interesting paper illustrating the use of hexapeptide libraries for improved detection of low-abundance proteins. (Pubitemid 350158505)
51. Zahedi RP, Lewandrowski U, Wiesner J et al. Phosphoproteome of resting human platelets. J. Proteome Res 7(2), 526-534 (2008).
52. Gevaert K, Goethals M, Martens L et al. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotechnol. 21(5), 566-569 (2003). (Pubitemid 36532024)
53. Martens L, Van Damme P, Van Damme J et al. The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile. Proteomics 5(12), 3193-3204 (2005). (Pubitemid 41176487)
54. Blair P, Flaumenhaft R. Platelet a-granules: Basic biology and clinical correlates. Blood Rev. 23(4), 177-189 (2009).
55. Smith SA, Mutch NJ, Baskar D, Rohloff P, Docampo R, Morrissey JH. Polyphosphate modulates blood coagulation and fibrinolysis. Proc. Natl Acad. Sci. USA 103(4), 903-908 (2006). (Pubitemid 43212194)
56. 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(6), 2096-2104 (2004). • Landmark paper describing the proteins released from activated platelets. (Pubitemid 38326225)
57. Maynard DM, Heijnen HF, Horne MK, White JG, Gahl WA. Proteomic analysis of platelet α-granules using mass spectrometry. J. Thromb. Haemost. 5(9), 1945-1955 (2007). • Interesting paper that identifies novel α-granule proteins likely to be important in thrombosis.
58. Italiano JE, Jr., Richardson JL, Patel-Hett S et al. Angiogenesis is regulated by a novel mechanism: pro- and antiangiogenic proteins are organized into separate platelet a granules and differentially released. Blood 111(3), 1227-1233 (2008). (Pubitemid 351213404)
59. Sehgal S, Storrie B. Evidence that differential packaging of the major platelet granule proteins von Willebrand factor and fibrinogen can support their differential release. J. Thromb. Haemost. 5(10), 2009-2016 (2007). (Pubitemid 47450016)
60. Hernandez-Ruiz L, Valverde F, Jimenez-Nunez MD et al. Organellar proteomics of human platelet dense granules reveals that 14-13-3ζ is a granule protein related to atherosclerosis. J. Proteome Res. 6(11), 4449-4457 (2007). • Interesting paper that identifies novel dense-granule proteins likely to be important in thrombosis. (Pubitemid 350158520)
61. Garcia BA, Smalley DM, Cho H, Shabanowitz J, Ley K, Hunt DF. The platelet microparticle proteome. J. Proteome Res 4(5), 1516-1521 (2005).
62. Moebius J, Zahedi RP, Lewandrowski U, Berger C, Walter U, Sickmann A. The human platelet membrane proteome reveals several new potential membrane proteins. Mol. Cell Proteomics 4(11), 1754-1761 (2005). (Pubitemid 41749268)
63. Hartinger J, Stenius K, Hogemann D, Jahn R. 16-BAC/SDS-PAGE: a two-dimensional gel electrophoresis system suitable for the separation of integral membrane proteins. Anal. Biochem. 240(1), 126-133 (1996). (Pubitemid 26292931)
64. Senis YA, Tomlinson MG, Garcia A et al. A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein. Mol. Cell. Proteomics 6(3), 548-564 (2007). (Pubitemid 46554548)
65. Lewandrowski U, Wortelkamp S, Lohrig K et al. Platelet membrane proteomics: a novel repository for functional research. Blood 114(1), E10-19 (2009).
66. Standeven KF, Ariens RA, Grant PJ. The molecular physiology and pathology of fibrin structure/function. Blood Rev. 19(5), 275-288 (2005).
67. Fatah K, Hamsten A, Blomback B, Blomback M. Fibrin gel network characteristics and coronary heart disease: relations to plasma fibrinogen concentration, acute phase protein, serum lipoproteins and coronary atherosclerosis. Thromb. Haemost. 68(2), 130-135 (1992).
68. Fatah K, Silveira A, Tornvall P, Karpe F, Blomback M, Hamsten A. Proneness to formation of tight and rigid fibrin gel structures in men with myocardial infarction at a young age. Thromb. Haemost. 76(4), 535-540 (1996). (Pubitemid 26372007)
69. Carter AM, Cymbalista CM, Spector TD, Grant PJ. Heritability of clot formation, morphology, and lysis: the EuroCLOT study. Arterioscler. Thromb. Vasc. Biol. 27(12), 2783-2789 (2007).
70. Bhasin N, Ariens RA, West RM, Parry DJ, Grant PJ, Scott DJ. Altered fibrin clot structure and function in the healthy first-degree relatives of subjects with intermittent claudication. J. Vasc. Surg. 48(6), 1497-1503, 1503 (2008).
71. Carr ME. Fibrin formed in plasma is composed of fibers more massive than those formed from purified fibrinogen. Thromb. Haemost. 59(3), 535-539 (1988).
72. Saha S, Harrison SH, Shen C et al. HIP2: an online database of human plasma proteins from healthy individuals. BMC Med. Genomics 1, 12 (2008).
73. Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 1(11), 845-867 (2002).
74. 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(13), 3226-3245 (2005). (Pubitemid 41192032)
75. Guerrier L, Thulasiraman V, Castagna A et al. Reducing protein concentration range of biological samples using solid-phase ligand libraries. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 833(1), 33-40 (2006).
76. Restuccia U, Boschetti E, Fasoli E et al. pI-based fractionation of serum proteomes versus anion exchange after enhancement of low-abundance proteins by means of peptide libraries. J. Proteomics 72(6), 1061-1070 (2009).
77. Pernemalm M, Lewensohn R, Lehtiö J. Affinity prefractionation for MS-based plasma proteomics. Proteomics 9(6), 1420-1427 (2009).
78. Misek DE, Kuick R, Wang H et al. A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system. Proteomics 5(13), 3343-3352 (2005). • Identifies protein isoforms that differ between serum and plasma, which are likely to be relevant in the process of thrombosis. (Pubitemid 41192040)
79. Tammen H, Schulte I, Hess R et al. Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display. Proteomics 5(13), 3414-3422 (2005). • Identifies and shows abundance of serum-specific peptides from proteins that are likely to be relevant in the process of thrombosis. (Pubitemid 41192047)
80. Marshall J, Kupchak P, Zhu W et al. Processing of serum proteins underlies the mass spectral fingerprinting of myocardial infarction. J. Proteome Res. 2(4), 361-372 (2003). (Pubitemid 36988415)
81. Donahue MP, Rose K, Hochstrasser D et al. Discovery of proteins related to coronary artery disease using industrial-scale proteomics analysis of pooled plasma. Am. Heart J. 152(3), 478-485 (2006). (Pubitemid 44233432)
82. Hong M, Zhang X, Hu Y et al. The potential biomarkers for thromboembolism detected by SELDIT-OF-MS. Thromb. Res. 123(3), 556-564 (2009).
83. Howes J-M, Keen JN, Findlay JB, Carter AM. The application of proteomics technology to thrombosis research: the identification of potential therapeutic targets in cardiovascular disease. Diab. Vasc. Dis. Res. 5(3), 205-212 (2008).
84. Rijken DC, Dirkx SP, Luider TM, Leebeek FW. Hepatocyte-derived fibrinogen-related protein-1 is associated with the fibrin matrix of a plasma clot. Biochem. Biophys. Res. Commun. 350(1), 191-194 (2006).
85. Howes J-M, Kenn JN, Findlay JBC, Grant PJ, Carter AM. Deciphering the plasma clot proteome. Mol. Cell. Proteomics 3, S218 (2004).
86. Orru S, Caputo I, D'Amato A, Ruoppolo M, Esposito C. Proteomics identification of acyl-acceptor and acyl-donor substrates for transglutaminase in a human intestinal epithelial cell line. Implications for celiac disease. J. Biol. Chem. 278(34), 31766-31773 (2003). (Pubitemid 37048357)
87. Ruoppolo M, Orru S, D'Amato A et al. Analysis of transglutaminase protein substrates by functional proteomics. Protein Sci. 12(6), 1290-1297 (2003). (Pubitemid 36597516)