Integration of Proteomics and Genomics in PlateletsJames McRedmond, Soon Deok Park, Dermot F. Reilly et al.|Molecular & Cellular Proteomics|2003 Platelets, while anucleate, contain RNA, some of which is translated into protein upon activation. Hypothesising that the platelet proteome is reflected in the transcriptome, we identified 82 proteins secreted from activated platelets and compared these, as well as published proteomic data, to the transcriptional profile. We also compared the transcriptome of platelets to other tissues to identify platelet-specific genes and used ontology to determine gene categories over-represented in platelets. RNA was isolated from highly pure platelet preparations for hybridization to Affymetrix oligonucleotide arrays. We identified 2,928 distinct messages as being present in platelets. The platelet transcriptome was compared with the proteome by relating both to UniGene clusters. Platelet proteomic data correlated well with the transcriptome, with 69% of secreted proteins detectable at the mRNA level, and similar concordance was obtained using two published datasets. While many of the most abundant mRNAs are for known platelet proteins, messages were detected for proteins not previously reported in platelets. Some of these may represent residual megakaryocyte messages; however, proteomic analysis confirmed the expression of many previously unreported genes in platelets. Transcripts for well-described platelet proteins are among the most platelet-specific messages. Ontological categories related to signal transduction, receptors, ion channels, and membranes are over-represented in platelets, while categories involved in protein synthesis are depleted. Despite the absence of gene transcription, the platelet proteome is mirrored in the transcriptome. Conversely, transcriptional analysis predicts the presence of novel proteins in the platelet. Transcriptional analysis is relevant to platelet biology, providing insights into platelet function and the mechanisms of platelet disorders. Platelets, while anucleate, contain RNA, some of which is translated into protein upon activation. Hypothesising that the platelet proteome is reflected in the transcriptome, we identified 82 proteins secreted from activated platelets and compared these, as well as published proteomic data, to the transcriptional profile. We also compared the transcriptome of platelets to other tissues to identify platelet-specific genes and used ontology to determine gene categories over-represented in platelets. RNA was isolated from highly pure platelet preparations for hybridization to Affymetrix oligonucleotide arrays. We identified 2,928 distinct messages as being present in platelets. The platelet transcriptome was compared with the proteome by relating both to UniGene clusters. Platelet proteomic data correlated well with the transcriptome, with 69% of secreted proteins detectable at the mRNA level, and similar concordance was obtained using two published datasets. While many of the most abundant mRNAs are for known platelet proteins, messages were detected for proteins not previously reported in platelets. Some of these may represent residual megakaryocyte messages; however, proteomic analysis confirmed the expression of many previously unreported genes in platelets. Transcripts for well-described platelet proteins are among the most platelet-specific messages. Ontological categories related to signal transduction, receptors, ion channels, and membranes are over-represented in platelets, while categories involved in protein synthesis are depleted. Despite the absence of gene transcription, the platelet proteome is mirrored in the transcriptome. Conversely, transcriptional analysis predicts the presence of novel proteins in the platelet. Transcriptional analysis is relevant to platelet biology, providing insights into platelet function and the mechanisms of platelet disorders. Platlelets are anucleate cells formed from budding of megakaryocytes, from which they inherit much of their cytoplasmic contents. Messages for many platelet proteins are present in platelet RNA, including Fc receptors (1Hasegawa S. Pawankar R. Suzuki K. Nakahata T. Furukawa S. Okumura K. Ra C. Functional expression of the high affinity receptor for IgE (FcϵRI) in human platelets and its intracellular expression in human megakaryocytes..Blood. 1999; 93: 2543-2551Google Scholar), plasminogen activator inhibitor-1 (2Konkle B.A. Schick P.K. He X. Liu R.J. Mazur E.M. Plasminogen activator inhibitor-1 mRNA is expressed in platelets and megakaryocytes and the megakaryoblastic cell line CHRF-288..Arterioscler. Thromb. 1993; 13: 669-674Google Scholar), protein kinase C isoforms (3Chang J.D. Xu Y. Raychowdhury M.K. Ware J.A. 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. 1993; 268: 14208-14214Google Scholar), and chemokines (4Power C.A. Clemetson J.M. Clemetson K.J. Wells T.N. Chemokine and chemokine receptor mRNA expression in human platelets..Cytokine. 1995; 7: 479-482Google Scholar). Indeed, coagulation factor XI is present in platelets as a platelet/megakaryocyte-specific splice variant (5Hsu T.C. Shore S.K. Seshsmma T. Bagasra O. Walsh P.N. Molecular cloning of platelet factor XI, an alternative splicing product of the plasma factor XI gene..J. Biol. Chem. 1998; 273: 13787-13793Google Scholar). However, RNA in platelets was long regarded as a vestige of protein synthesis in the megakaryocyte (6Shaw T. Chesterman C.N. Morgan F.J. In vitro synthesis of low molecular weight proteins in human platelets: absence of labelled release products..Thromb. Res. 1984; 36: 619-631Google Scholar). Nevertheless, at least some platelet mRNA is functional: activated platelets synthesize proteins in a regulated manner, dependent on platelet activation and integrin engagement (7Lindemann S. Tolley N.D. Dixon D.A. McIntyre T.M. Prescott S.M. Zimmerman G.A. Weyrich A.S. Activated platelets mediate inflammatory signaling by regulated interleukin 1β synthesis..J. Cell Biol. 2001; 154: 485-490Google Scholar, 8Weyrich A.S. Dixon D.A. Pabla R. Elstad M.R. McIntyre T.M. Prescott S.M. Zimmerman G.A. Signal-dependent translation of a regulatory protein, Bcl-3, in activated human platelets..Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 5556-5561Google Scholar, 9Pabla R. Weyrich A.S. Dixon D.A. Bray P.F. McIntyre T.M. Prescott S.M. Zimmerman G.A. Integrin-dependent control of translation: Engagement of integrin αIIbβ3 regulates synthesis of proteins in activated human platelets..J. Cell Biol. 1999; 144: 175-184Google Scholar, 10Lindemann S. Tolley N.D. Eyre J.R. Kraiss L.W. Mahoney T.M. Weyrich A.S. Integrins regulate the intracellular distribution of eukaryotic initiation factor 4E in platelets. A checkpoint for translational control..J. Biol. Chem. 2001; 276: 33947-33951Google Scholar). These translated proteins include many of the more abundant proteins (11Kieffer N. Guichard J. Farcet J.P. Vainchenker W. Breton-Gorius J. Biosynthesis of major platelet proteins in human blood platelets..Eur. J. Biochem. 1987; 164: 189-195Google Scholar), but also the cytokine IL-1β (7Lindemann S. Tolley N.D. Dixon D.A. McIntyre T.M. Prescott S.M. Zimmerman G.A. Weyrich A.S. Activated platelets mediate inflammatory signaling by regulated interleukin 1β synthesis..J. Cell Biol. 2001; 154: 485-490Google Scholar) and the transcriptional regulator Bcl-3 (8Weyrich A.S. Dixon D.A. Pabla R. Elstad M.R. McIntyre T.M. Prescott S.M. Zimmerman G.A. Signal-dependent translation of a regulatory protein, Bcl-3, in activated human platelets..Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 5556-5561Google Scholar). Rather than merely representing residual messages for megakaryocyte/platelet proteins, the profile of platelet mRNA may provide valuable insights into the biology of platelets and megakaryocytes, including information on the nonthrombotic functions of platelets. We have interrogated gene arrays with platelet RNA and compared the results with a proteomic analysis of proteins secreted from platelets, as well as data from two previously published platelet proteomic studies (12O’Neill E.E. Brock C.J. von Kriegsheim A.F. Pearce A.C. Dwek R.A. Watson S.P. Hebestreit H.F. Towards complete analysis of the platelet proteome..Proteomics. 2002; 2: 288-305Google Scholar, 13Marcus K. Immler D. Sternberger J. Meyer H.E. 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. 2000; 21: 2622-2636Google Scholar), to address whether the profile of platelet mRNA correlates with protein expression. Our findings confirm the general description of the platelet transcriptome provided by Gnatenko et al. (14Gnatenko D.V. Dunn J.J. McCorkle S.R. Weissmann D. Perrotta P.L. Bahou W.F. Transcript profiling of human platelets using microarray and serial analysis of gene expression..Blood. 2003; 101: 2285-2293Google Scholar). We also compare the platelet transcriptome with publicly available gene expression data from multiple tissues. We have identified individual messages that are relatively and absolutely platelet-specific as well as ontological categories over-represented in platelets. Blood was drawn into one-sixth volume of buffer (38 mm citric acid, mm and mm at for and the plasma used expressed protein platelet factor platelet regulated on activation cell expressed and was at in in a to and Platelet were platelets from of these preparations to of the and platelets were at for and in of RNA was isolated as the and in of RNA from of blood were was used to of individual RNA of the platelet was used as an of platelet RNA, while the of the cell was used as a of cell in which cell was detected were Platelet cDNA preparations were also for the not RNA was for hybridization to the as the of RNA from was and using an to of cDNA was and used to in vitro transcription, of was and to the to the A hybridization was using the data was analyzed in the of and oligonucleotide that the for the of was to as in the Y. J.R. T. A. A. analysis of the human and Natl. Acad. Sci. U. S. A. 2002; Scholar). platelets were as previously K.J. Identification of the proteome from activated 2002; 2: Scholar). platelets were with for and on were by at for The was of by for at at using a The platelet was in and at for The was in mm at and with mm by with mm for at The were to with mm and with a of at The were to with mm with mm and with at while The were with to the and at A was as D.A. J.R. protein for Chem. 2001; Scholar, D. J.R. analysis of the proteome by protein 2001; Scholar). a was with an ion A was to a using a laser and with of and with of were using a was as J. S.P. of with spectrometry for protein the Res. 2003; 2: Scholar). The J.R. to data of with in a protein Scholar) was used to identify proteins from and were gene and protein expression data and to ontological were to UniGene clusters. in the were with UniGene for of the Affymetrix while for a were by gene in the with The were by of multiple for genes on the Affymetrix in a of distinct data were to arrays with proteins from the These were to UniGene previously to with genes expressed highly in individual we expressed data for a of obtained from the of expression and Res. 2001; Scholar). and were from the were and the to UniGene tissues with and to UniGene clusters. for of the of of the and at least two were highly In of the on the were from the of platelet-specific identify genes expressed relatively in platelets, we compared gene expression data to distinct human tissues in the expression were using a W. A. A. to microarray data and to the of 2002; Scholar) that signal into for which is the signal the of the genes were to expressed the of for of the were The platelet were to and the for tissues were to a The in platelet and was for A high a gene expressed at a in platelets than the other tissues in the ontology genes the of into categories to were ontological by the to UniGene was two with were obtained from the The were cDNA to The to UniGene from for and from were used to the were to gene ontology for which the were expressed at in platelets than in other human tissues. for of the were as and gene ontology the in platelets and in the data for were compared using a In we isolated platelet RNA for the presence of messages. using the of cDNA in with we detected of including the platelet integrin and as well as the of A. C. J. J. D. of platelet and 2001; 7: Scholar), and The signal of a with platelet was than that with other in to the of RNA in platelets D.V. Dunn J.J. McCorkle S.R. Weissmann D. Perrotta P.L. Bahou W.F. Transcript profiling of human platelets using microarray and serial analysis of gene expression..Blood. 2003; 101: 2285-2293Google and may have much of the on a in a distribution of signal Platelet hybridization data was as in and to with other the of we detected of on the in two with the to UniGene that to 2,928 of are on the distinct on the However, as a similar of messages in may in an of the of the platelet transcriptome. two other from and messages for of the genes were detected in platelet RNA not The of these of mRNA from two microarray 2002; Scholar). The on Affymetrix arrays may to platelet RNA, which a of from genes (14Gnatenko D.V. Dunn J.J. McCorkle S.R. Weissmann D. Perrotta P.L. Bahou W.F. Transcript profiling of human platelets using microarray and serial analysis of gene expression..Blood. 2003; 101: 2285-2293Google Scholar) a on the The may for the most abundant detected in platelets, for which a protein was in platelets among the with messages for proteins as and are proteins known to highly expressed in platelets, as platelet factor platelet protein the von factor receptor the cytokine and as well as platelet et et chemokine protein factor family chemokine member receptor receptor chemokine protein member protein member member similar to in a new The most abundant platelet in a by Gnatenko et al. (14Gnatenko D.V. Dunn J.J. McCorkle S.R. Weissmann D. Perrotta P.L. Bahou W.F. Transcript profiling of human platelets using microarray and serial analysis of gene expression..Blood. 2003; 101: 2285-2293Google Scholar) are in with Indeed, of the and of the genes are to both a of the of Gnatenko et al. in the on analysis of platelet RNA is highly in analysis of proteins secreted from platelets that a of abundant proteins and the platelet J.A. S. T. O. J.P. A. of the proteins from activated platelets to of novel platelet proteins in human Scholar). we used protein to a of the platelet and a more of proteins present at a In from proteins were with 82 in at least two of These 82 proteins formed platelet the Affymetrix and the proteins identified in the platelet proteome to UniGene the of results with proteomic the 82 identified proteins in the platelet on the these proteins, messages to were detected in platelet mRNA and of the platelet messages were detected at the protein in the platelet of platelet proteomic and of distinct on in from et et in a new was the mRNA and protein for two other proteomic of platelets. et al. (12O’Neill E.E. Brock C.J. von Kriegsheim A.F. Pearce A.C. Dwek R.A. Watson S.P. Hebestreit H.F. Towards complete analysis of the platelet proteome..Proteomics. 2002; 2: 288-305Google Scholar) identified protein in the to UniGene clusters. the on the 82 were present in platelets and A proteomic by et al. K. Immler D. Sternberger J. Meyer H.E. 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. 2000; 21: 2622-2636Google Scholar) reported tyrosine-phosphorylated platelet proteins that we to UniGene of which were on the these, were present in platelets at the and The a of for which a protein was The proteomic and transcriptional are While the proteomic data used was not to proteins detected in platelet have much than messages on the as a for proteomic Conversely, the presence of in platelets the of We have detected proteins by analysis of platelet on the of analysis of platelet RNA not of gene expression analysis is as platelet messages and are known to contain proteins that are to involved in regulated of and S.M. R. D.A. T.N. Y. A in the in Natl. Acad. Sci. U. S. A. 2000; Scholar). including and have to present in platelets A. A. A. Identification of proteins in human platelets: of and Natl. Acad. Sci. U. S. A. 1993; Scholar), mRNA for and have identified X. R.J. Molecular expression and of and J. Biochem. 2002; Scholar). We of the family proteins and and proteins among the 2,928 mRNA of these including that for protein, have not reported in platelets. A and identified in the platelet proteome by et al. are in the platelet transcriptome Messages expressed in platelets, at a in platelets than in other to relevant to platelet for A of were used to identify platelet-specific genes A of Affymetrix were to UniGene clusters. these, were to highly expressed that of transcriptome and at least two in at least of the were in platelets to these, a expression in platelets than in other tissues these in of a of platelet-specific the of which are in most platelet-specific member receptor chemokine and of chemokine factor chemokine member to signaling to member protein member protein protein factor mRNA member factor variant factor member member to protein protein of in a new of the most abundant platelet genes are platelet-specific most In platelet analysis the known platelet genes variant and the receptor genes are also by The presence of messages in platelets is platelets are anucleate, we not to contain protein, and was in proteomic messages are in other tissues in the of a human mRNA the cell Cell Biol. Scholar), their absence from other cell in the in platelet RNA may to the of the cell megakaryocytes are to multiple of the cell is with a of mRNA synthesis and R. D. W.F. of mRNA in the cell control at two Cell Biol. Scholar). While they for platelet-specific we are as to the of the of messages in platelets. We identified to at least UniGene on the the were to at least were by at least on the were to identify the of these for which the genes of expression the tissues and platelets. A of and in platelets to the tissues of gene expression in platelets and in in to to plasma to to protein signaling factor signaling to to ion to protein of regulator ion factor of of of to ion initiation cytokine in a new The of in ontological categories the of However, for multiple in as not ontology categories are with J. 1998; Scholar). a a of is ontology are compared platelets and other to gene expression by at the level, we to The gene ontology used a The and of the for which the genes are over-represented in platelets include and the present at in platelets are genes with and to their and to and genes with the genes with as are also in platelets are genes with the and its of and involved in protein synthesis in the Molecular and are not to expression in platelets than other tissues. tissues a expression of genes in categories as factor and regulator genes with an expression the cell with the as well as in the to on the cell are highly expressed in platelets as a these ontology results that platelets have a of receptor and signal while they are in messages for involved in the of protein The platelet transcriptome is and analysis of platelet RNA much platelet Our results are in with data on the platelet transcriptome obtained using oligonucleotide arrays (14Gnatenko D.V. Dunn J.J. McCorkle S.R. Weissmann D. Perrotta P.L. Bahou W.F. Transcript profiling of human platelets using microarray and serial analysis of gene expression..Blood. 2003; 101: 2285-2293Google Scholar). The the platelet transcriptome and proteome the of platelet RNA as a to platelet 69% of secreted platelet proteins identified by are detectable at the RNA in platelets, that platelet messages the platelet protein profile. results were obtained with two platelet proteomic is a high of that proteomic are than of mRNA D. R. of mRNA expression and protein for the of the of in the of proteins and 2002; Scholar). in the and and translation of mRNA and protein that individual and protein not D. R. of mRNA expression and protein for the of the of in the of proteins and 2002; Scholar, S.P. Y. R. protein and mRNA in Cell Biol. 1999; Scholar, Y. D. N. S.M. and proteomic analysis of the analysis of gene expression in the cell 2002; Scholar). gene in platelets, and translation is we well the transcriptome reflected the proteome in platelets. The from in other the platelet proteomic are and the to a of In and protein is and the is on a D. R. of mRNA expression and protein for the of the of in the of proteins and 2002; Scholar, K. K. Y. S. R. N. T. Y. transcriptome and proteome analysis as a to genes in Res. 2001; Scholar, C. C. of the by proteome and transcriptome 2002; Scholar, U. C. K. R. and proteome analysis of gene expression by 2002; Scholar, expression in Scholar, D. C. K. protein and mRNA expression on a Biol. 2003; Scholar). In more are identified than proteins, to the detection of protein and a of was in a of human proteins J. A of mRNA and protein in human Scholar), while in cells a was reported J.M. S.M. protein and mRNA expression in 2002; Scholar). In the protein were not and a with other studies protein and mRNA is not However, we compared whether a protein in of the proteomic studies an of with on the platelet mRNA the was among the in have an protein and as gene expression S.P. Y. R. protein and mRNA in Cell Biol. 1999; Scholar). in the proteins in more proteome studies are the in a proteome with mRNA platelet is is with a of for mRNA and protein in a cell et al. of proteins to present on an of Y. D. N. S.M. and proteomic analysis of the analysis of gene expression in the cell 2002; Scholar). While their analysis is the in the are of 82 secreted proteins present for et al. 82 of proteins and for et al. of proteins The we proteome and transcriptome in platelets is of the the protein synthesis the and RNA However, messages for of proteins were not being on the RNA protein synthesis in the in the in proteins for which In some platelet proteins as and are from plasma and not have in the platelet. However, the of proteins detected at the by and et as well as the of that of RNA not in platelets. an of the transcriptional and proteomic In of 2,928 distinct platelet messages have identified by proteomic and was a of in the proteins identified in the proteomic with proteins being detected and in studies However, the proteomic are distinct of the platelet We identified proteins secreted from activated platelets, et al. their to proteins in the (12O’Neill E.E. Brock C.J. von Kriegsheim A.F. Pearce A.C. Dwek R.A. Watson S.P. Hebestreit H.F. Towards complete analysis of the platelet proteome..Proteomics. 2002; 2: 288-305Google Scholar), while et al. their analysis to proteins K. Immler D. Sternberger J. Meyer H.E. 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. 2000; 21: 2622-2636Google Scholar). a major the proteome studies is not to We that as more platelet proteomic studies are the of the platelet transcriptome to at the protein of the mRNAs is is but proteins are in platelets and messages are with in platelets (7Lindemann S. Tolley N.D. Dixon D.A. McIntyre T.M. Prescott S.M. Zimmerman G.A. Weyrich A.S. Activated platelets mediate inflammatory signaling by regulated interleukin 1β synthesis..J. Cell Biol. 2001; 154: 485-490Google Scholar), that messages are to their translation into is not their that platelets are of translation of mRNA for two categories of proteins have detected in platelets: proteins that are including major receptors as and and as protein kinase C isoforms (3Chang J.D. Xu Y. Raychowdhury M.K. Ware J.A. 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. 1993; 268: 14208-14214Google and inflammatory proteins from RNA in activated platelets and as Bcl-3 and IL-1β (7Lindemann S. Tolley N.D. Dixon D.A. McIntyre T.M. Prescott S.M. Zimmerman G.A. Weyrich A.S. Activated platelets mediate inflammatory signaling by regulated interleukin 1β synthesis..J. Cell Biol. 2001; 154: 485-490Google Scholar). These two messages are not abundant in platelets, the of the platelet messages While is the of to determine their we that reported in human of mRNA was S.R. S. to as a with in 2003; 13: Scholar). and are among the most abundant platelet messages that that activated platelets at of a of proteins, release of protein of the secreted platelet also present in the transcriptome, are also in J.A. S. T. O. J.P. A. of the proteins from activated platelets to of novel platelet proteins in human Scholar). We that the most platelet-specific messages include platelet proteins, as well as signaling Ontological analysis these The categories of cell and signal are more highly in platelets than a of other cell of these are also highly expressed in platelets, including categories of receptors and ion channels, the to and to a of and including a of and and and The some coagulation reported in platelets at the RNA as well as receptors involved in as and The cytokine and categories are also highly expressed in platelets. of the platelet messages (4Power C.A. Clemetson J.M. Clemetson K.J. Wells T.N. Chemokine and chemokine receptor mRNA expression in human platelets..Cytokine. 1995; 7: 479-482Google Scholar), and are chemokines in other tissues is much than that in platelets. The platelet long known to to inflammatory the release of as A. A. C. human platelets release two that Scholar), and of and with J. 1995; Scholar). Indeed, IL-1β from activated platelets in cell S. activation of for the of 2001; Scholar, R. K. J.A. C.A. Activated platelets of in vitro an 1993; Scholar, interleukin human expression and cytokine Scholar). have also reported to regulate the inflammatory in N. C. platelets protein receptors and regulate cell 2002; Scholar). While some of these proteins are the of regulated IL-1β translation in platelets (7Lindemann S. Tolley N.D. Dixon D.A. McIntyre T.M. Prescott S.M. Zimmerman G.A. Weyrich A.S. Activated platelets mediate inflammatory signaling by regulated interleukin 1β synthesis..J. Cell Biol. 2001; 154: 485-490Google Scholar) other In the the platelet transcriptome and proteomic studies the of both datasets. of the proteins in the have not reported at the mRNA in platelets, and as the protein and protein identified in the platelet have not previously reported in platelets Some of these, as protein are in the transcriptional to analysis using than Affymetrix and represent an of the platelet transcriptome that previously transcriptional analysis of platelets in to other tissues for proteins expressed megakaryocyte function and platelet as as well as messages in platelet function in and The transcriptome in platelets the profile of protein expression and may provide novel insights to the of platelet disorders. with