Integration of proteomics and genomics in platelets. A profile of platelet proteins and platelet-specific genes

Molecular and Cellular Proteomics

Volumn 3, Issue 2, 2004, Pages 133-144

  McRedmond, J P ^a   Park, S D ^a   Reilly, D F ^a,b   Coppinger, J A ^a   Maguire, P B ^a   Shields, D C ^a   Fitzgerald, D J ^a  

^a ROYAL COLLEGE OF SURGEONS IN IRELAND   (Ireland)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; DNA; ION CHANNEL; MESSENGER RNA; RNA;

ARTICLE; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA MICROARRAY; GENE EXPRESSION; GENETIC ANALYSIS; GENOMICS; HUMAN; MEGAKARYOCYTE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEPLETION; PROTEIN SECRETION; PROTEIN SYNTHESIS; PROTEOMICS; RNA ISOLATION; RNA TRANSLATION; SIGNAL TRANSDUCTION; THROMBOCYTE; THROMBOCYTE DISORDER; THROMBOCYTE FUNCTION; UNINDEXED SEQUENCE;

BLOOD PLATELETS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLATELET ACTIVATION; PROTEOMICS; RNA, MESSENGER;

EID: 2642557064     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M300063-MCP200     Document Type: Article

References (48)

1. Hasegawa, S., Pawankar, R., Suzuki, K., Nakahata, T., Furukawa, S., Okumura, K., and Ra, C. (1999) Functional expression of the high affinity receptor for IgE (FCERI) in human platelets and its intracellular expression in human megakaryocytes. Blood 93, 2543-2551
2. Konkle, B. A., Schick, P. K., He, X., Liu, R. J., and Mazur, E. M. (1993) Plasminogen activator inhibitor-1 mRNA is expressed in platelets and megakaryocytes and the megakaryoblastic cell line CHRF-288. Arterioscler. Thromb. 13, 669-674
3. Chang, J. D., Xu, Y., Raychowdhury, M. K., and Ware, J. A. (1993) Molecular cloning and expression of a cDNA encoding a novel isoenzyme of protein kinase C (nPKC). A new member of the nPKC family expressed in skeletal muscle, megakaryoblastic cells, and platelets. J. Biol. Chem. 268, 14208-14214
4. Power, C. A., Clemetson, J. M., Clemetson, K. J., and Wells, T. N. (1995) Chemokine and chemokine receptor mRNA expression in human platelets, Cytokine 7, 479-482
5. Hsu, T. C., Shore, S. K., Seshsmma, T., Bagasra, O., and Walsh, P. N. (1998) Molecular cloning of platelet factor XI, an alternative splicing product of the plasma factor XI gene. J. Biol. Chem. 273, 13787-13793
6. Shaw, T., Chesterman, C. N., and Morgan, F. J. (1984) In vitro synthesis of low molecular weight proteins in human platelets: absence of labelled release products. Thromb. Res. 36, 619-631
7. Lindemann, S., Tolley, N. D., Dixon, D. A., McIntyre, T. M., Prescott, S. M., Zimmerman, G. A., and Weyrich, A. S. (2001) Activated platelets mediate inflammatory signaling by regulated interleukin 1β synthesis. J. Cell Biol. 154, 485-490
8. Weyrich, A. S., Dixon, D. A., Pabla, R., Elstad, M. R., McIntyre, T. M., Prescott, S. M., and Zimmerman, G. A. (1998) Signal-dependent translation of a regulatory protein, Bcl-3, in activated human platelets. Proc. Natl. Acad. Sci. U. S. A. 95, 5556-5561
9. 3 regulates synthesis of proteins in activated human platelets. J. Cell Biol. 144, 175-184
10. Lindemann, S., Tolley, N. D., Eyre, J. R., Kraiss, L. W., Mahoney, T. M., and Weyrich, A. S. (2001) Integrins regulate the intracellular distribution of eukaryotic initiation factor 4E in platelets. A checkpoint for translational control. J. Biol. Chem. 276, 33947-33951
11. Kieffer, N., Guichard, J., Farcet, J. P., Vainchenker, W., and Breton-Gorius, J. (1987) Biosynthesis of major platelet proteins in human blood platelets. Eur. J. Biochem. 164, 189-195
12. O'Neill, E. E., Brock, C. J., von Kriegsheim, A. F., Pearce, A. C., Dwek, R. A., Watson, S. P., and Hebestreit, H. F. (2002) Towards complete analysis of the platelet proteome. Proteomics 2, 288-305
13. Marcus, K., Immler, D., Sternberger, J., and Meyer, H. E. (2000) Identification of platelet proteins separated by two-dimensional gel electrophoresis and analyzed by matrix assisted laser desorption/ionization-time of flight-mass spectrometry and detection of tyrosine-phosphorylated proteins. Electrophoresis 21, 2622-2636
14. Gnatenko, D. V., Dunn, J. J., McCorkle, S. R., Weissmann, D., Perrotta, P. L., and Bahou, W. F. (2003) Transcript profiling of human platelets using microarray and serial analysis of gene expression. Blood 101, 2285-2293
15. Su, A. I., Cooke, M. P., Ching, K. A., Hakak, Y., Walker, U. R., Wiltshire, T., Orth, A. P., Vega, R. G., Sapinoso, L. M., Moqrich, A., Patapoutian, A., Hampton, G. M., Schultz, P. G., and Hogenesch, J. B. (2002) Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. U. S. A. 99, 4465-4470
16. Maguire, P. B., Wynne, K. J., Harney, D. F., O'Donoghue, N. M., Stephens, G., and Fitzgerald, D. J. (2002) Identification of the phosphotyrosine proteome from thrombin activated platelets. Proteomics 2, 642-648
17. Wolters, D. A., Washburn, M. P., and Yates, J. R., 3rd. (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683-5690
18. Washburn, M. P., Wolters, D., and Yates, J. R., 3rd. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247
19. Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., and Gygi, S. P. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2, 43-50
20. Eng, J. K., McCormack, A. L., and Yates, J. A., 3rd. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989
21. Skrabanek, L., and Campagne, F. (2001) TissueInfo: High-throughput identification of tissue expression profiles and specificity. Nucleic Acids Res. 29, E102-102
22. Huber, W., Von Heydebreck, A., Sultmann, H., Poustka, A., and Vingron, M. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18, (Suppl. 1), S96-S104
23. Angelillo-Scherrer, A., de Frutos, P., Aparicio, C., Melis, E., Savi, P., Lupu, F., Arnout, J., Dewerchin, M., Hoylaerts, M., Herbert, J., Collen, D., Dahlback, B., and Carmeliet, P. (2001) Deficiency or inhibition of Gas6 causes platelet dysfunction and protects mice against thrombosis. Nat. Med. 7, 215-221
24. Kuo, W. P., Jenssen, T. K., Butte, A. J., Ohno-Machado, L., and Kohane, I. S. (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18, 405-412
25. Wilson, S. M., Yip, R., Swing, D. A., O'Sullivan, T. N., Zhang, Y., Novak, E. K., Swank, R. T., Russell, L. B., Copeland, N. G., and Jenkins, N. A. (2000) A mutation in Rab27a causes the vesicle transport defects observed in ashen mice. Proc. Natl. Acad. Sci. U. S. A. 97, 7933-7938
26. Karniguian, A., Zahraoui, A., and Tavitian, A. (1993) Identification of small GTP-binding rab proteins in human platelets: Thrombin-induced phosphorylation of rab3B, rab6, and rab8 proteins. Proc. Natl. Acad. Sci. U. S. A. 90, 7647-7651
27. Bao, X., Fans, A. E., Jang, E. K., and Haslam, R. J. (2002) Molecular cloning, bacterial expression and properties of Rab31 and Rab32. Eur. J. Biochem. 269, 259-271
28. Morris, T. D., Weber, L. A., Hickey, E., Stein, G. S., and Stein, J. L. (1991) Changes in the stability of a human H3 histone mRNA during the HeLa cell cycle. Mol. Cell Biol. 11, 544-553
29. Harris, M. E., Bohni, R., Schneiderman, M. H., Ramamurthy, L., Schumperli, D., and Marzluff, W. F. (1991) Regulation of histone mRNA in the unperturbed cell cycle: Evidence suggesting control at two posttranscriptional steps. Mol. Cell Biol. 11, 241 6-2424
30. Perneger, T. V. (1998) What's wrong with Bonferroni adjustments. Brit. Med. J. 316, 1236-1238
31. Greenbaum, D., Jansen, R., and Gerstein, M. (2002) Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics 18, 585-596
32. Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19, 1720-1730
33. Lian, Z., Kluger, Y., Greenbaum, D. S., Tuck, D., Gerstein, M., Berliner, N., Weissman, S. M., and Newburger, P. E. (2002) Genomic and proteomic analysis of the myeloid differentiation program: Global analysis of gene expression during induced differentiation in the MPRO cell line. Blood 100, 3209-3220
34. Yoshida, K., Kobayashi, K., Miwa, Y., Kang, C. M., Matsunaga, M., Yamaguchi, H., Tojo, S., Yamamoto, M., Nishi, R., Ogasawara, N., Nakayama, T., and Fujita, Y. (2001) Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucleic Acids Res. 29, 683-692
35. Eymann, C., Homuth, G., Scharf, C., and Hecker, M. (2002) Bacillus subtilis functional genomics: Global characterization of the stringent response by proteome and transcriptome analysis. J. Bacteriol. 184, 2500-2520
36. Mader, U., Homuth, G., Scharf, C., Buttner, K., Bode, R., and Hecker, M. (2002) Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability. J. Bacteriol. 184, 4288-4295
37. Wodicka, L., Dong, H., Mittmann, M., Ho, M. H., and Lockhart, D. J. (1997) Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15, 1359-1367
38. Greenbaum, D., Colangelo, C., Williams, K., and Gerstein, M. (2003) Comparing protein abundance and mRNA expression on a genomic scale. Genome Biol. 4, 117.111-117.118
39. Anderson, L., and Seilhamer, J. (1997) A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18, 533-537
40. Chen, G., Gharib, T. G., Huang, C. C., Taylor, J. M., Misek, D. E., Kardia, S. L., Giordano, T. J., Iannettoni, M. D., Orringer, M. B., Hanash, S. M., and Beer, D. G. (2002) Discordant protein and mRNA expression in lung adenocarcinomas. Mol. Cell. Proteomics 1, 304-313
41. You, S. A., Archacki, S. R., Angheloiu, G., Moravec, C. S., Rao, S., Kinter, M., Topol, E. J., and Wang, Q. (2003) Proteomic approach to coronary atherosclerosis shows ferritin light chain as a significant marker: Evidence consistent with iron hypothesis in atherosclerosis. Physiol. Genomics 13, 25-30
42. Piccardoni, P., Evangelists, V., Piccoli, A., de Gaetano, G., Walz, A., and Cerletti, C. (1996) Thrombin-activated human platelets release two NAP-2 variants that stimulate polymorphonuclear leukocytes. Thromb. Haemost. 76, 780-785
43. Aziz, K. A., Cawley, J. C., and Zuzel, M. (1995) Platelets prime PMN via released PF4: Mechanism of priming and synergy with GM-CSF. Br. J. Haematol. 91, 846-853
44. Bustos, M., Saadi, S., and Platt, J. L. (2001) Platelet-mediated activation of endothelial cells: Implications for the pathogenesis of transplant rejection. Transplantation 72, 509-515
45. Kaplanski, G., Porat, R., Aiura, K., Erban, J. K., Gelfand, J. A., and Dinarello, C. A. (1993) Activated platelets induce endothelial secretion of interleukin-8 in vitro via an interleukin-1-mediated event. Blood 81, 2492-2495
46. Hawrylowicz, C. M., Howells, G. L., and Feldmann, M. (1991) Platelet-derived interleukin 1 induces human endothelial adhesion molecule expression and cytokine production. J. Exp. Med. 174, 785-790
47. Hilf, N., Singh-Jasuja, H., Schwarzmaier, P., Gouttefangeas, C., Rammensee, H. G., and Schild, H. (2002) Human platelets express heat shock protein receptors and regulate dendritic cell maturation. Blood 99, 3676-3682
48. Coppinger, J. A., Cagney, G., Toomey, S., Kislinger, T., Belton, O., McRedmond, J. P., Cahill, D. J., Emili, A., Fitzgerald, D. J., and Maguire, P. B. (2004) Characterization of the proteins released from activated platelets leads to localization of novel platelet proteins in human atherosclerotic lesions. Blood, in press