The human platelet: Strong transcriptome correlations among individuals associate weakly with the platelet proteome

Biology Direct

Volumn 9, Issue 1, 2014, Pages

  Londin, Eric R ^a   Hatzimichael, Eleftheria ^a   Loher, Phillipe ^a   Edelstein, Leonard ^b   Shaw, Chad ^c   Delgrosso, Kathleen ^d   Fortina, Paolo ^d,e   Bray, Paul F ^b   McKenzie, Steven E ^b   Rigoutsos, Isidore ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

^b THOMAS JEFFERSON UNIVERSITY   (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

^d THOMAS JEFFERSON UNIVERSITY   (United States)

^e SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PROTEOME; TRANSCRIPTOME;

ADULT; DNA MICROARRAY; GENETICS; HUMAN; MALE; METABOLISM; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; THROMBOCYTE; YOUNG ADULT;

ADULT; BLOOD PLATELETS; HUMANS; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; PROTEOME; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME; YOUNG ADULT;

EID: 84894611782     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-9-3     Document Type: Article

References (28)

1. Kunicki TJ, Williams SA, Nugent DJ. Genetic variants that affect platelet function. Curr Opin Hematol 2012, 19:371-379. 10.1097/MOH.0b013e3283567526, 22872156.
2. Cecchetti L, Tolley ND, Michetti N, Bury L, Weyrich AS, Gresele P. Megakaryocytes differentially sort mRNAs for matrix metalloproteinases and their inhibitors into platelets: a mechanism for regulating synthetic events. Blood 2011, 118:1903-1911. 10.1182/blood-2010-12-324517, 3158719, 21628401.
3. Denis MM, Tolley ND, Bunting M, Schwertz H, Jiang H, Lindemann S, Yost CC, Rubner FJ, Albertine KH, Swoboda KJ, et al. Escaping the nuclear confines: signal-dependent pre-mRNA splicing in anucleate platelets. Cell 2005, 122:379-391. 10.1016/j.cell.2005.06.015, 16096058.
4. McRedmond JP. Integration of Proteomics and Genomics in Platelets: A PROFILE OF PLATELET PROTEINS AND PLATELET-SPECIFIC GENES. Mol Cell Proteomics 2003, 3:133-144. 10.1074/mcp.M300063-MCP200, 14645502.
5. Rowley JW, Schwertz H, Weyrich AS. Platelet mRNA. Curr Opin Hematol 2012, 19:385-391. 10.1097/MOH.0b013e328357010e, 3670814, 22814651.
6. Rowley JW, Oler AJ, Tolley ND, Hunter BN, Low EN, Nix DA, Yost CC, Zimmerman GA, Weyrich AS. Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes. Blood 2011, 118:e101-111. 10.1182/blood-2011-03-339705, 3193274, 21596849.
7. Weyrich AS, Schwertz H, Kraiss LW, Zimmerman GA. Protein synthesis by platelets: historical and new perspectives. J Thromb Haemost 2009, 7:241-246. 10.1111/j.1538-7836.2008.03211.x, 3027201, 18983498.
8. Gnatenko DV, Perrotta PL, Bahou WF. Proteomic approaches to dissect platelet function: Half the story. Blood 2006, 108:3983-3991. 10.1182/blood-2006-06-026518, 1895451, 16926286.
9. Qureshi AH, Chaoji V, Maiguel D, Faridi MH, Barth CJ, Salem SM, Singhal M, Stoub D, Krastins B, Ogihara M, et al. Proteomic and Phospho-Proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling. PLoS ONE 2009, 4:e7627. 10.1371/journal.pone.0007627, 2762604, 19859549.
10. Bray PF, Mckenzie SE, Edelstein LC, Nagalla S, Delgrosso K, Ertel A, Kupper J, Jing Y, Londin E, Loher P, et al. The complex transcriptional landscape of the anucleate human platelet. BMC Genomics 2013, accepted.
11. Rowley JW, Weyrich AS. Coordinate expression of transcripts and proteins in platelets. Blood 2013, 121:5255-5256.
12. Geiger J, Burkhart JM, Gambaryan S, Walter U, Sickmann A, Zahedi RP. Response: platelet transcriptome and proteome-relation rather than correlation. Blood 2013, 121:5257-5258. 10.1182/blood-2013-04-493403, 23813942.
13. Bruchova H, Yoon D, Agarwal AM, Mendell J, Prchal JT. Regulated expression of microRNAs in normal and polycythemia vera erythropoiesis. Exp Hematol 2007, 35:1657-1667. 10.1016/j.exphem.2007.08.021, 2699372, 17976518.
14. Landry P, Plante I, Ouellet DL, Perron MP, Rousseau G, Provost P. Existence of a microRNA pathway in anucleate platelets. Nat Struct Mol Biol 2009, 16:961-966. 10.1038/nsmb.1651, 2911476, 19668211.
15. Burkhart JM, Vaudel M, Gambaryan S, Radau S, Walter U, Martens L, Geiger J, Sickmann A, Zahedi RP. The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways. Blood 2012, 120:e73-e82. 10.1182/blood-2012-04-416594, 22869793.
16. Nagalla S, Shaw C, Kong X, Kondkar AA, Edelstein LC, Ma L, Chen J, McKnight GS, Lopez JA, Yang L, et al. Platelet microRNA-mRNA co-expression profiles correlate with platelet reactivity. Blood 2011
17. Edelstein LC, Simon LM, Montoya RT, Holinstat M, Chen ES, Bergeron A, Kong X, Nagalla S, Mohandas N, Cohen DE, et al. Racial differences in human platelet PAR4 reactivity reflect expression of PCTP and miR-376c. Nat Med 2013
18. Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol 2009, 5:e1000386. 10.1371/journal.pcbi.1000386, 2678294, 19461883.
19. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing. EMB Net J 2011, 17:10-12.
20. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005, 110:462-467. 10.1159/000084979, 16093699.
21. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
22. Dowal L, Yang W, Freeman MR, Steen H, Flaumenhaft R. Proteomic analysis of palmitoylated platelet proteins. Blood 2011, 118:e62-e73. 10.1182/blood-2011-05-353078, 3186346, 21813449.
23. da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
24. da Huang W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009, 37:1-13. 10.1093/nar/gkn923, 2615629, 19033363.
25. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006, 38:904-909. 10.1038/ng1847, 16862161.
26. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010, 11:R106. 10.1186/gb-2010-11-10-r106, 3218662, 20979621.
27. Anagnou NP, Antonarakis SE, O'Brien SJ, Modi WS, Nienhuis AW. Chromosomal localization and racial distribution of the polymorphic human dihydrofolate reductase pseudogene (DHFRP1). Am J Hum Genet 1988, 42:345-352. 1715258, 3341383.
28. Ple H, Landry P, Benham A, Coarfa C, Gunaratne PH, Provost P. The Repertoire and Features of Human Platelet microRNAs. PLoS ONE 2012, 7:e50746. 10.1371/journal.pone.0050746, 3514217, 23226537.