51
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Ruan L, Wang GL, Chen Y, Yi H, Tang CE, Zhang PF, Li MY, Li C, Peng F, Li JL, Chen ZC, Xiao ZQ. Identification of tyrosine phosphoproteins in signaling pathway triggered TGF-a by using functional proteomics technology. Med Oncol 2010; 27:1407-14. [DOI: 10.1007/s12032-009-9394-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 12/14/2009] [Indexed: 01/03/2023]
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52
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Kim KM, Lee SG, Cho YA, Song YG, Song JY, Kang HL, Lee WK, Cho MJ, Rhee KH, Baik SC. Identification ofHelicobacter pyloriStrain 51 Major Outer Membrane Proteins by Quadrupole Time of Flight Mass Spectrometry. ACTA ACUST UNITED AC 2010. [DOI: 10.4167/jbv.2010.40.3.103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Kyung-Mi Kim
- Department of Microbiology, Gyeongsang National University, Jinju, Korea
| | - Seung-Gyu Lee
- National Institute of Animal Science, Rural Development Administration, Suwon, Korea
| | - Young-A Cho
- Department of Microbiology, Gyeongsang National University, Jinju, Korea
| | - Yun-Gyu Song
- Department of Microbiology, Gyeongsang National University, Jinju, Korea
| | - Jea-Young Song
- Department of Microbiology, Gyeongsang National University, Jinju, Korea
| | - Hyung-Lyun Kang
- Department of Microbiology, Gyeongsang National University, Jinju, Korea
- Research Institute of Life Science, Gyeongsang Nationa University, Jinju, Korea
| | - Woo-Kon Lee
- Department of Microbiology, Gyeongsang National University, Jinju, Korea
- Research Institute of Life Science, Gyeongsang Nationa University, Jinju, Korea
| | - Myung-Je Cho
- Department of Microbiology, Gyeongsang National University, Jinju, Korea
- Research Institute of Life Science, Gyeongsang Nationa University, Jinju, Korea
| | - Kwang-Ho Rhee
- Department of Microbiology, Gyeongsang National University, Jinju, Korea
- Research Institute of Life Science, Gyeongsang Nationa University, Jinju, Korea
| | - Seung-Chul Baik
- Department of Microbiology, Gyeongsang National University, Jinju, Korea
- Research Institute of Life Science, Gyeongsang Nationa University, Jinju, Korea
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53
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Tucker KL, Kaiser WJ, Bergeron AL, Hu H, Dong JF, Tan TH, Gibbins JM. Proteomic analysis of resting and thrombin-stimulated platelets reveals the translocation and functional relevance of HIP-55 in platelets. Proteomics 2009; 9:4340-54. [PMID: 19725075 DOI: 10.1002/pmic.200900024] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The platelet surface is a dynamic interface that changes rapidly in response to stimuli to co-ordinate the formation of thrombi at sites of vascular injury. Tight control is essential as loss of organisation may result in the inappropriate formation of thrombi (thrombosis) or excessive bleeding. In this paper we describe the comparative analysis of resting and thrombin-stimulated platelet membrane proteomes and associated proteins to identify proteins important to platelet function. Surface proteins were labelled using a biotin tag and isolated by NeurtrAvidin affinity chromatography. Liquid phase IEF and SDS-PAGE were used to separate proteins, and bands of increased intensity in the stimulated platelet fractions were digested and identified by FT-ICR mass spectrometry. Novel proteins were identified along with proteins known to be translocated to the platelet surface. Furthermore, many platelet proteins revealed changes in location associated with function, including G6B and Hip-55. HIP-55 is an SH3-binding protein important in T-cell receptor signalling. Further analysis of HIP-55 revealed that this adaptor protein becomes increasingly associated with both Syk and integrin beta3 upon platelet activation. Analysis of HIP-55 deficient platelets revealed reduced fibrinogen binding upon thrombin stimulation, suggesting HIP-55 to be an important regulator of platelet function.
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Affiliation(s)
- Katherine L Tucker
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, The University of Reading, Whiteknights, Reading, UK.
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54
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Steele BM, Harper MT, Macaulay IC, Morrell CN, Perez-Tamayo A, Foy M, Habas R, Poole AW, Fitzgerald DJ, Maguire PB. Canonical Wnt signaling negatively regulates platelet function. Proc Natl Acad Sci U S A 2009; 106:19836-41. [PMID: 19901330 PMCID: PMC2785253 DOI: 10.1073/pnas.0906268106] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Indexed: 12/20/2022] Open
Abstract
Wnts regulate important intracellular signaling events, and dysregulation of the Wnt pathway has been linked to human disease. Here, we uncover numerous Wnt canonical effectors in human platelets where Wnts, their receptors, and downstream signaling components have not been previously described. We demonstrate that the Wnt3a ligand inhibits platelet adhesion, activation, dense granule secretion, and aggregation. Wnt3a also altered platelet shape change and inhibited the activation of the small GTPase RhoA. In addition, we found the Wnt-beta-catenin signaling pathway to be functional in platelets. Finally, disruption of the Wnt Frizzled 6 receptor in the mouse resulted in a hyperactivatory platelet phenotype and a reduced sensitivity to Wnt3a. Taken together our studies reveal a novel functional role for Wnt signaling in regulating anucleate platelet function and may provide a tractable target for future antiplatelet therapy.
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Affiliation(s)
- Brian M. Steele
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Matthew T. Harper
- Department of Physiology and Pharmacology, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Iain C. Macaulay
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Craig N. Morrell
- Department of Molecular and Comparative Pathobiology, John Hopkins University School of Medicine, Baltimore, MD 21205; and
| | - Alita Perez-Tamayo
- Department of Molecular and Comparative Pathobiology, John Hopkins University School of Medicine, Baltimore, MD 21205; and
| | - Martina Foy
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Raymond Habas
- Department of Biochemistry, Robert Wood Johnson School of Medicine, Piscataway, NJ 08854
| | - Alastair W. Poole
- Department of Physiology and Pharmacology, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Desmond J. Fitzgerald
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Patricia B. Maguire
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
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55
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Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling. PLoS One 2009; 4:e7627. [PMID: 19859549 PMCID: PMC2762604 DOI: 10.1371/journal.pone.0007627] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Accepted: 10/02/2009] [Indexed: 12/23/2022] Open
Abstract
During atherogenesis and vascular inflammation quiescent platelets are activated to increase the surface expression and ligand affinity of the integrin αIIbβ3 via inside-out signaling. Diverse signals such as thrombin, ADP and epinephrine transduce signals through their respective GPCRs to activate protein kinases that ultimately lead to the phosphorylation of the cytoplasmic tail of the integrin αIIbβ3 and augment its function. The signaling pathways that transmit signals from the GPCR to the cytosolic domain of the integrin are not well defined. In an effort to better understand these pathways, we employed a combination of proteomic profiling and computational analyses of isolated human platelets. We analyzed ten independent human samples and identified a total of 1507 unique proteins in platelets. This is the most comprehensive platelet proteome assembled to date and includes 190 membrane-associated and 262 phosphorylated proteins, which were identified via independent proteomic and phospho-proteomic profiling. We used this proteomic dataset to create a platelet protein-protein interaction (PPI) network and applied novel contextual information about the phosphorylation step to introduce limited directionality in the PPI graph. This newly developed contextual PPI network computationally recapitulated an integrin signaling pathway. Most importantly, our approach not only provided insights into the mechanism of integrin αIIbβ3 activation in resting platelets but also provides an improved model for analysis and discovery of PPI dynamics and signaling pathways in the future.
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56
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Senis YA, Antrobus R, Severin S, Parguiña AF, Rosa I, Zitzmann N, Watson SP, García A. Proteomic analysis of integrin alphaIIbbeta3 outside-in signaling reveals Src-kinase-independent phosphorylation of Dok-1 and Dok-3 leading to SHIP-1 interactions. J Thromb Haemost 2009; 7:1718-26. [PMID: 19682241 DOI: 10.1111/j.1538-7836.2009.03565.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND AND OBJECTIVES Outside-in integrin alphaIIbbeta3 signaling involves a series of tyrosine kinase reactions that culminate in platelet spreading on fibrinogen. The aim of this study was to identify novel tyrosine phosphorylated signaling proteins downstream of alphaIIbbeta3, and explore their role in platelet signaling. METHODS AND RESULTS Utilizing proteomics to search for novel platelet proteins that contribute to outside-in signaling by the integrin alphaIIbbeta3, we identified 27 proteins, 17 of which were not previously shown to be part of a tyrosine phosphorylation-based signaling complex downstream of alphaIIbbeta3. The proteins identified include the novel immunoreceptors G6f and G6b-B, and two members of the Dok family of adapters, Dok-1 and Dok-3, which underwent increased tyrosine phosphorylation following platelet spreading on fibrinogen. Dok-3 was also inducibly phosphorylated in response to the GPVI-specific agonist collagen-related peptide (CRP) and the PAR-1 and -4 agonist thrombin, independently of the integrin alphaIIbbeta3. Tyrosine phosphorylation of Dok-1 and Dok-3 was primarily Src kinase-independent downstream of the integrin, whereas it was Src kinase-dependent downstream of GPVI. Moreover, both proteins inducibly interacted with Grb-2 and SHIP-1 in fibrinogen-spread platelets. CONCLUSIONS This study provides new insights into the molecular mechanism regulating alphaIIbbeta3-mediated platelet spreading on fibrinogen. The novel platelet adapter Dok-3 and the structurally related Dok-1 are tyrosine phosphorylated in an Src kinase-independent manner downstream of alphaIIbbeta3 in human platelets, leading to an interaction with Grb2 and SHIP-1.
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Affiliation(s)
- Y A Senis
- Centre for Cardiovascular Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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Rex S, Beaulieu LM, Perlman DH, Vitseva O, Blair PS, McComb ME, Costello CE, Freedman JE. Immune versus thrombotic stimulation of platelets differentially regulates signalling pathways, intracellular protein-protein interactions, and alpha-granule release. Thromb Haemost 2009; 102:97-110. [PMID: 19572074 DOI: 10.1160/th08-08-0513] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In addition to haemostasis, platelets mediate inflammation and clearance of bacteria from the bloodstream. As with platelet-platelet interactions, platelet-bacteria interactions involve cytoskeletal rearrangements and release of granular content. Stimulation of the immune Toll-like receptor 2 (TLR2) on the platelet surface, activates phosphoinositide-3-kinase (PI3K) and causes platelet activation and platelet-dependent thrombosis. It remains unknown if platelet activation by immune versus thrombotic pathways leads to the differential regulation of signal transduction, protein-protein interactions, and alpha-granule release, and the physiological relevance of these potential differences. We investigated these processes after immune versus thrombotic platelet stimulation. We examined selected signalling pathways and found that phosphorylation kinetics of Akt, ERK1/2 and p38 differed dramatically between agonists. Next, we investigated platelet protein-protein interactions by mass spectrometry (MS)-based proteomics specifically targeting cytosolic factor XIIIa (FXIIIa) because of its function as a cytoskeleton-crosslinking protein whose binding partners have limited characterisation. Four FXIIIa-binding proteins were identified, two of which are novel interactions: FXIIIa-focal adhesion kinase (FAK) and FXIIIa-gelsolin. The binding of FAK to FXIIIa was found to be altered differentially by immune versus thrombotic stimulation. Lastly, we studied the effect of thrombin versus Pam(3)CSK(4) stimulation on alpha-granule release and observed differential release patterns for selected granule proteins and decreased fibrin clot formation compared with thrombin. The inhibition of PI3K caused a decrease in protein release after Pam(3)CSK(4)- but not after thrombin-stimulation. In summary, stimulation of platelets by either thrombotic or immune receptors leads to markedly different signalling responses and granular protein release consistent with differential contribution to coagulation and thrombosis.
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Affiliation(s)
- Sybille Rex
- Whitaker Cardiovascular Institute, Department of Medicine, Boston University School of Medicine, Boston, 02118 MA, USA
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Abstract
The main purpose of this article is to provide an overview of the currently available evidence of antiplatelet properties of resveratrol (3,4('),5-trihydroxystilbene). Resveratrol, a phenolic compound found naturally in fruits, nuts, flowers, seeds and bark of different plants is integral part of human diet. It exhibits a wide range of biological effects, including antiplatelet, anti-inflammatory, anticancer, antimutagenic and antifungal properties. It is also a potent antioxidant, reactive oxygen species scavenger and metal chelators. Resveratrol reduces lipid peroxidation, oxidation and nitration of platelet and plasma proteins. This review article describes the chemical structure of resveratrol, its biological activity, the effects on blood platelet functions and the mechanisms involved in its action on blood platelets, the cells which play an important role not only in the haemostatic process, but also in pathogenesis of cardiovascular diseases.
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Affiliation(s)
- Beata Olas
- Department of General Biochemistry, Institute of Biochemistry, University of Łodź, Poland
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59
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Blood-related proteomics. J Proteomics 2009; 73:483-507. [PMID: 19567275 DOI: 10.1016/j.jprot.2009.06.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 06/17/2009] [Accepted: 06/20/2009] [Indexed: 12/12/2022]
Abstract
Blood-related proteomics is an emerging field, recently gaining momentum. Indeed, a wealth of data is now available and a plethora of groups has contributed to add pieces to the jigsaw puzzle of protein complexity within plasma and blood cells. In this review article we purported to sail across the mare magnum of the actual knowledge in this research endeavour. The main strides in proteomic investigations on red blood cells, platelets, plasma and white blood cells are hereby presented in a chronological order. Moreover, a glance is given at prospective studies which promise to shift the focus of attention from the end product to its provider, the donor, in a sort of Kantian "Copernican revolution". A well-rounded portrait of the usefulness of proteomics in blood-related research is accurately given. In particular, proteomic tools could be adopted to follow the main steps of the blood-banking production processes (a comparison of collection methods, pathogen inactivation techniques, storage protocols). Thus proteomics has been recently transformed from a mere basic-research extremely-expensive toy into a dramatically-sensitive and efficient eye-lens to either delve into the depths of the molecular mechanisms of blood and blood components or to establish quality parameters in the blood-banking production chain totally anew.
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Condina MR, Guthridge MA, McColl SR, Hoffmann P. A sensitive magnetic bead method for the detection and identification of tyrosine phosphorylation in proteins by MALDI-TOF/TOF MS. Proteomics 2009; 9:3047-57. [DOI: 10.1002/pmic.200701179] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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61
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Proteomic analysis of membrane microdomain-associated proteins in the dorsolateral prefrontal cortex in schizophrenia and bipolar disorder reveals alterations in LAMP, STXBP1 and BASP1 protein expression. Mol Psychiatry 2009; 14:601-13. [PMID: 18268500 DOI: 10.1038/mp.2008.7] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The dorsolateral prefrontal cortex (dlpfc) is strongly implicated in the pathogenesis of schizophrenia (SCZ) and bipolar disorder (BPD) and, within this region, abnormalities in glutamatergic neurotransmission and synaptic function have been described. Proteins associated with these functions are enriched in membrane microdomains (MM). In the current study, we used two complementary proteomic methods, two-dimensional difference gel electrophoresis and one-dimensional sodium dodecyl sulphate polyacrylamide gel electrophoresis followed by reverse phase-liquid chromatography-tandem mass spectrometry (RP-LC-MS/MS) (gel separation liquid chromatography-tandem mass spectrometry (GeLC-MS/MS)) to assess protein expression in MM in pooled samples of dlpfc from SCZ, BPD and control cases (n=10 per group) from the Stanley Foundation Brain series. We identified 16 proteins altered in one/both disorders using proteomic methods. We selected three proteins with roles in synaptic function (syntaxin-binding protein 1 (STXBP1), brain abundant membrane-attached signal protein 1 (BASP1) and limbic system-associated membrane protein (LAMP)) for validation by western blotting. This revealed significantly increased expression of these proteins in SCZ (STXBP1 (24% difference; P<0.001), BASP1 (40% difference; P<0.05) and LAMP (22% difference; P<0.01)) and BPD (STXBP1 (31% difference; P<0.001), BASP1 (23% difference; P<0.01) and LAMP (20% difference; P<0.01)) in the Stanley brain series (n=20 per group). Further validation in dlpfc from the Harvard brain subseries (n=10 per group) confirmed increased protein expression in SCZ of STXBP1 (18% difference; P<0.0001), BASP1 (14% difference; P<0.0001) but not LAMP (20% difference; P=0.14). No significant differences in STXBP1, BASP1 or LAMP protein expression in BPD dlpfc were observed. This study, through proteomic assessments of MM in dlpfc and validation in two brain series, strongly implicates LAMP, STXBP1 and BASP1 in SCZ and supports the view of a neuritic and synaptic dysfunction in the neuropathology of SCZ.
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Lukas TJ, Wang AL, Yuan M, Neufeld AH. Early cellular signaling responses to axonal injury. Cell Commun Signal 2009; 7:5. [PMID: 19284657 PMCID: PMC2661080 DOI: 10.1186/1478-811x-7-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 03/13/2009] [Indexed: 12/20/2022] Open
Abstract
Background We have used optic nerve injury as a model to study early signaling events in neuronal tissue following axonal injury. Optic nerve injury results in the selective death of retinal ganglion cells (RGCs). The time course of cell death takes place over a period of days with the earliest detection of RGC death at about 48 hr post injury. We hypothesized that in the period immediately following axonal injury, there are changes in the soma that signal surrounding glia and neurons and that start programmed cell death. In the current study, we investigated early changes in cellular signaling and gene expression that occur within the first 6 hrs post optic nerve injury. Results We found evidence of cell to cell signaling within 30 min of axonal injury. We detected differences in phosphoproteins and gene expression within the 6 hrs time period. Activation of TNFα and glutamate receptors, two pathways that can initiate cell death, begins in RGCs within 6 hrs following axonal injury. Differential gene expression at 6 hrs post injury included genes involved in cytokine, neurotrophic factor signaling (Socs3) and apoptosis (Bax). Conclusion We interpret our studies to indicate that both neurons and glia in the retina have been signaled within 30 min after optic nerve injury. The signals are probably initiated by the RGC soma. In addition, signals activating cellular death pathways occur within 6 hrs of injury, which likely lead to RGC degeneration.
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Affiliation(s)
- Thomas J Lukas
- Forsythe Laboratory for the Investigation of the Aging Retina, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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Gevaert K, Vandekerckhove J. Reverse-phase diagonal chromatography for phosphoproteome research. Methods Mol Biol 2009; 527:219-ix. [PMID: 19241016 DOI: 10.1007/978-1-60327-834-8_16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We present a gel-free proteomics procedure for the specific isolation of phosphorylated peptides from whole proteome digests. Central is the use of diagonal, reverse-phase chromatography which consists of two consecutive reverse-phase peptide separations with a modification step in between. The latter alters the column retention of affected peptides, thereby allowing their specific isolation from the bulk of nonaffected peptides. To isolate phosphopeptides from complex mixtures, this modification step is a dephosphorylation reaction using a cocktail of broad-spectrum phosphatases. Upon dephosphorylation, peptides undergo a hydrophobic shift and are thereby sorted from in vivo nonphosphorylated peptides. To increase the overall yield of phosphopeptides, a pre-enrichment step was found necessary and to further distinguish true ex-phosphorylated peptides from nonphosphorylated peptides sorted artificially, differential isotope labeling was introduced. The complete COFRADIC sorting procedure is described here.
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Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research, Ghent University, Ghent, Belgium
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Thon JN, Schubert P, Devine DV. Platelet storage lesion: a new understanding from a proteomic perspective. Transfus Med Rev 2008; 22:268-79. [PMID: 18848154 DOI: 10.1016/j.tmrv.2008.05.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Platelet storage and availability for the purposes of transfusion are currently restricted by a markedly short shelf life of 5 to 7 days owing to an increased risk of bacterial growth and storage-related deterioration called the platelet storage lesion. Because most bacteria grow to confluence within 5 days during storage at room temperature, there is little increased risk of bacterial overgrowth with testing in place, and the only remaining issue is the quality of platelets during the extended storage. Although the manifestations of the storage lesion have been well studied using a variety of in vitro measures, the precise biochemical pathways involved in the initiation and progression of this process have yet to be identified. Proteomics has emerged as a powerful tool to identify and monitor changes during platelet storage and, in combination with biochemical and physiologic studies, facilitates the development of a sophisticated mechanistic view. In this review, we summarize recent experimental work that has led to a detailed overview of protein changes linked to platelet functions and signaling pathways, providing potential targets for inhibitors to ameliorate the storage lesion.
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65
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Proteomic analysis of the porcine platelet proteome and alterations induced by thrombin activation. J Proteomics 2008; 71:547-60. [DOI: 10.1016/j.jprot.2008.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 08/26/2008] [Accepted: 08/28/2008] [Indexed: 12/25/2022]
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Howes JM, 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 2008; 5:205-12. [PMID: 18777494 DOI: 10.3132/dvdr.2008.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Thrombus formation underpins the development of cardiovascular diseases, including acute coronary syndromes and ischaemic stroke. A number of well-characterised cardiovascular risk factors which contribute to the development of the majority of cardiovascular events have been identified, including dyslipidaemia, hypertension and diabetes. Individuals with type 2 diabetes mellitus (T2DM) have a 3- to 5-fold increased risk for development of cardiovascular disease (CVD). They may have a cluster of haemostatic abnormalities, including elevated levels of plasminogen activator inhibitor-1 (PAI-1) and fibrinogen, which contribute to acute thrombotic events. It is clear that additional unidentified risk factors contribute to the pathogenesis of cardiovascular events, and so the search for novel biomarkers and effectors, particularly in individuals with T2DM, remains a major challenge of cardiovascular medicine. Plasma and cellular proteins which contribute to thrombus formation have the potential to confer a pro-thrombotic state and represent a link between genotype, environment and disease phenotype. The comprehensive analysis of these proteins is now increasingly facilitated through the continued development of proteomic technologies which provide multifaceted approaches to the identification of novel biomarkers and/or effectors of thrombus formation and on which future anticoagulant and thrombolytic therapies may be based. This review provides an overview of current proteomic technologies. It focuses on the recent studies in which these technologies have been applied in the search for novel proteins that may confer increased risk of acute cardiovascular diseases and therefore that may influence disease progression and therapy.
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Affiliation(s)
- Joanna-Marie Howes
- Division of Cardiovascular & Diabetes Research, The LIGHT Laboratories, University of Leeds, LS2 9JT, UK
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Liumbruno G, D'Amici GM, Grazzini G, Zolla L. Transfusion medicine in the era of proteomics. J Proteomics 2008; 71:34-45. [DOI: 10.1016/j.jprot.2008.02.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 02/18/2008] [Accepted: 02/18/2008] [Indexed: 12/21/2022]
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69
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Liumbruno GM. Proteomics: applications in transfusion medicine. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2008; 6:70-85. [PMID: 18946951 PMCID: PMC2626841 DOI: 10.2450/2008.0038-07] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Accepted: 12/20/2007] [Indexed: 12/30/2022]
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Vivanco F, Padial L, Darde V, de la Cuesta F, Alvarez-Llamas G, Diaz-Prieto N, Barderas M. Proteomic Biomarkers of Atherosclerosis. Biomark Insights 2008; 3:101-113. [PMID: 19578499 PMCID: PMC2688368 DOI: 10.4137/bmi.s488] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
SUMMARY: Biomarkers provide a powerful approach to understanding the spectrum of cardiovascular diseases. They have application in screening, diagnostic, prognostication, prediction of recurrences and monitoring of therapy. The "omics" tool are becoming very useful in the development of new biomarkers in cardiovascular diseases. Among them, proteomics is especially fitted to look for new proteins in health and disease and is playing a significant role in the development of new diagnostic tools in cardiovascular diagnosis and prognosis. This review provides an overview of progress in applying proteomics to atherosclerosis. First, we describe novel proteins identified analysing atherosclerotic plaques directly. Careful analysis of proteins within the atherosclerotic vascular tissue can provide a repertoire of proteins involved in vascular remodelling and atherogenesis. Second, we discuss recent data concerning proteins secreted by atherosclerotic plaques. The definition of the atheroma plaque secretome resides in that proteins secreted by arteries can be very good candidates of novel biomarkers. Finally we describe proteins that have been differentially expressed (versus controls) by individual cells which constitute atheroma plaques (endothelial cells, vascular smooth muscle cells, macrophages and foam cells) as well as by circulating cells (monocytes, platelets) or novel biomarkers present in plasma.
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Affiliation(s)
- F. Vivanco
- Department of Immunology. Fundación Jiménez Díaz, Madrid, Spain
- Department of Biochemistry and Molecular Biology I, Universidad Complutense, Proteomic Unit, Madrid, Spain
| | - L.R. Padial
- Department of Cardiology. Hospital Virgen de la Salud, SESCAM, Toledo, Spain
| | - V.M. Darde
- Department of Immunology. Fundación Jiménez Díaz, Madrid, Spain
| | - F. de la Cuesta
- Department of Immunology. Fundación Jiménez Díaz, Madrid, Spain
| | | | - Natacha Diaz-Prieto
- Department of Vascular Pathophysiology. Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
| | - M.G. Barderas
- Department of Immunology. Fundación Jiménez Díaz, Madrid, Spain
- Department of Vascular Pathophysiology. Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
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71
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Thon JN, Schubert P, Duguay M, Serrano K, Lin S, Kast J, Devine D. Comprehensive proteomic analysis of protein changes during platelet storage requires complementary proteomic approaches. Transfusion 2008; 48:425-35. [DOI: 10.1111/j.1537-2995.2007.01546.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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72
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Li Y, Qi D, Deng C, Yang P, Zhang X. Cerium Ion-Chelated Magnetic Silica Microspheres for Enrichment and Direct Determination of Phosphopeptides by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. J Proteome Res 2008; 7:1767-77. [DOI: 10.1021/pr070385l] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yan Li
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Dawei Qi
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xiangmin Zhang
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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73
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Schuchardt S, Borlak J. Quantitative mass spectrometry to investigate epidermal growth factor receptor phosphorylation dynamics. MASS SPECTROMETRY REVIEWS 2008; 27:51-65. [PMID: 18023079 DOI: 10.1002/mas.20155] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Identifying proteins of signaling networks has received much attention, because an array of biological processes are entirely dependent on protein cross-talk and protein-protein interactions. Protein posttranslational modifications (PTM) add an additional layer of complexity, resulting in complex signaling networks. Of particular interest to our working group are the signaling networks of epidermal growth factor (EGF) receptor, a transmembrane receptor tyrosine kinase involved in various cellular processes, including cell proliferation, differentiation, and survival. Ligand binding to the N-terminal residue of the extracellular domain of EGF receptor induces conformational changes, dimerization, and (auto)-phosphorylation of intracellular tyrosine residues. In addition, activated EGF receptor may positively affect survival pathways, and thus determines the pathways for tumor growth and progression. Notably, in many human malignancies exaggerated EGF receptor activities are commonly observed. An understanding of the mechanism that results in aberrant phosphorylation of EGF receptor tyrosine residues and derived signaling cascades is crucial for an understanding of molecular mechanisms in cancer development. Here, we summarize recent labeling methods and discuss the difficulties in quantitative MS-based phosphorylation assays to probe for receptor tyrosine kinase (RTK) activity. We also review recent advances in sample preparation to investigate membrane-bound RTKs, MS-based detection of phosphopeptides, and the diligent use of different quantitative methods for protein labeling.
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Affiliation(s)
- Sven Schuchardt
- Department of Drug Research and Medical Biotechnology, Fraunhofer Institute of Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs-Strasse 1, Hannover, Germany
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74
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Birschmann I, Mietner S, Dittrich M, Pfrang J, Dandekar T, Walter U. Use of functional highly purified human platelets for the identification of new proteins of the IPP signaling pathway. Thromb Res 2008; 122:59-68. [DOI: 10.1016/j.thromres.2007.08.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Revised: 08/27/2007] [Accepted: 08/30/2007] [Indexed: 01/05/2023]
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75
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Gevaert K, Van Damme P, Ghesquière B, Impens F, Martens L, Helsens K, Vandekerckhove J. A la carte proteomics with an emphasis on gel-free techniques. Proteomics 2007; 7:2698-718. [PMID: 17640001 DOI: 10.1002/pmic.200700114] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Since the introduction of the proteome term somewhat more than a decade ago the field of proteomics witnessed a rapid growth mainly fueled by instrumental analytical improvements. Of particular notice is the advent of a diverse set of gel-free proteomics techniques. In this review, we discuss several of these gel-free techniques both for monitoring protein concentration changes and protein modifications, in particular protein phosphorylation, glycosylation, and protein processing. Furthermore, different approaches for (multiplexed) gel-free proteome analysis are discussed.
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Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.
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76
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Winkler W, Zellner M, Diestinger M, Babeluk R, Marchetti M, Goll A, Zehetmayer S, Bauer P, Rappold E, Miller I, Roth E, Allmaier G, Oehler R. Biological variation of the platelet proteome in the elderly population and its implication for biomarker research. Mol Cell Proteomics 2007; 7:193-203. [PMID: 17962630 DOI: 10.1074/mcp.m700137-mcp200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Knowledge about the extent of total variation experienced between samples from different individuals is of great importance for the design of not only proteomics but every clinical study. This variation defines the smallest statistically significant detectable signal difference when comparing two groups of individuals. We isolated platelets from 20 healthy human volunteers aged 56-100 years because this age group is most commonly encountered in the clinics. We determined the technical and total variation experienced in a proteome analysis using two-dimensional DIGE with IPGs in the pI ranges 4-7 and 6-9. Only spots that were reproducibly detectable in at least 90% of all gels (n = 908) were included in the study. All spots had a similar technical variation with a median coefficient of variation (cv) of about 7%. In contrast, spots showed a more diverse total variation between individuals with a surprisingly low median cv of only 18%. Because most known biomarkers show an effect size in a 1-2-fold range of their cv, any future clinical proteomics study with platelets will require an analytical method that is able to detect such small quantitative differences. In addition, we calculated the minimal number of samples (sample size) needed to detect given protein expression differences with statistical significance.
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Affiliation(s)
- Wolfgang Winkler
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, A-1060 Vienna, Austria
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77
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Abstract
Deciphering the cellular and molecular interactions that drive disease within the tissue microenvironment holds promise for discovering drug targets of the future. In order to recapitulate the in vivo interactions through molecular analysis, one must be able to analyze specific cell populations within the context of their heterogeneous tissue microecology. Laser capture microdissection is a method to procure subpopulations of tissue cells under direct microscopic visualization. Laser capture microdissection technology can harvest the cells of interest directly or can isolate specific cells by cutting away unwanted cells to give histologically pure enriched cell populations. A variety of downstream applications exist: DNA genotyping and loss-of-heterozygosity analysis, RNA transcript profiling, cDNA library generation, mass spectrometry proteomics discovery and signal pathway profiling.
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Affiliation(s)
- Virginia Espina
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA 20110, USA.
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78
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Behan ÁT, Foy M, Wynne K, Clarke M, Sullivan M, Cotter DR, Maguire PB. Analysis of membrane microdomain-associated proteins in the insular cortex of post-mortem human brain. Proteomics Clin Appl 2007; 1:1324-31. [DOI: 10.1002/prca.200700047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Indexed: 12/26/2022]
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79
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Vivanco F, Mas S, Darde VM, De la Cuesta F, Alvarez-Llamas G, Barderas MG. Vascular proteomics. Proteomics Clin Appl 2007; 1:1102-22. [DOI: 10.1002/prca.200700190] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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80
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Kim YM, Seo J, Kim YH, Jeong J, Joo HJ, Lee DH, Koh GY, Lee KJ. Systemic Analysis of Tyrosine Phosphorylated Proteins in Angiopoietin-1 Induced Signaling Pathway of Endothelial Cells. J Proteome Res 2007; 6:3278-90. [PMID: 17595127 DOI: 10.1021/pr070168k] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Angiogenesis is an essential process in physiological and pathological processes and is well-regulated to maintain the cellular homeostasis by balancing the endothelial cells in proliferation and apoptosis. Angiopoietin-1 (Ang1) regulates angiogenesis as a ligand of Tie 2 receptor tyrosine kinase. However, the regulation pathways are not well-understood. To date, only a few of the signaling molecules involved in the Tie 2 receptor tyrosine kinase-mediated angiogenesis have been identified. In this study, we systematically identified tyrosine-phosphorylated proteins in Ang1-induced signaling cascade in human umbilical vein endothelial cells (HUVECs), employing proteomic analyses combining two-dimensional gel electrophoresis, Western analysis using phosphotyrosine antibody and mass spectrometry (MALDI-TOF MS and nanoLC-ESI-q-TOF tandem MS). We report here the identification, semiquantitative analysis, and kinetic changes of tyrosine-phosphorylated proteins in response to Ang1 in HUVECs and identified 66 proteins among 69 protein spots showing significant changes. Of these, p54nrb was validated as a molecule involved in cell migration. These results suggest that Ang1 induces stabilization of neo-vessel network by regulating the phosphorylations of metabolic and structural proteins.
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Affiliation(s)
- Young Mee Kim
- Center for Cell Signaling & Drug Discovery Research, College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Korea
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81
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Wang WY, Hsieh PW, Wu YC, Wu CC. Synthesis and pharmacological evaluation of novel beta-nitrostyrene derivatives as tyrosine kinase inhibitors with potent antiplatelet activity. Biochem Pharmacol 2007; 74:601-11. [PMID: 17601492 DOI: 10.1016/j.bcp.2007.06.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 03/28/2007] [Accepted: 05/30/2007] [Indexed: 11/23/2022]
Abstract
Protein tyrosine kinases have been known to be involved in regulation of platelet aggregation, suggesting a potential target for antiplatelet therapy. Our previous study showed that 3,4-methylenedioxy-beta-nitrostyrene (MNS) prevented platelet aggregation caused by various stimulators, and this action was accompanied by inhibition of tyrosine kinases. In the present study, in order to examine the structural determinants required for the actions of MNS and to develop more potent tyrosine kinase inhibitors and antiplatelet agents, a new series of beta-nitrostyrene derivatives were synthesized and pharmacologically characterized. The beta-nitrostyrene derivatives inhibited thrombin- or collagen-induced human platelet aggregation, ATP secretion, GPIIb/IIIa activation and protein tyrosine phosphorylation. In recombinant enzyme assay, some beta-nitrostyrene derivatives also demonstrated potent inhibition of Src and/or Syk kinase activity. Furthermore, there was a good correlation between the inhibitory potency of these compounds on tyrosine kinases and on platelet activation/aggregation. Among them, a benzoyl ester derivative (compound 10) possess up to 8-fold greater potency than MNS and over two orders of magnitude greater potency than genistein or tyrphostin A47 in inhibiting platelet responses to thrombin. Our data suggest that beta-nitrostyrenes may represent a new class of tyrosine kinase inhibitors with potent antiplatelet activity.
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Affiliation(s)
- Wei-Ya Wang
- Graduate Institute of Natural Products, Kaohsiung Medical University, 100 Shih-Chuan 1st Rd., Kaohsiung City, Taiwan
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82
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Coppinger JA, O'Connor R, Wynne K, Flanagan M, Sullivan M, Maguire PB, Fitzgerald DJ, Cagney G. Moderation of the platelet releasate response by aspirin. Blood 2007; 109:4786-92. [PMID: 17303692 DOI: 10.1182/blood-2006-07-038539] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Modulation of the proteins released during activation is one mechanism whereby aspirin may influence platelet-mediated human disease. We investigated the effect of aspirin on the platelet releasate using mass spectrometry and found that different agonists evoked different releasate profiles, with aspirin having a general moderating effect on the amount of protein released regardless of the agonist. These observations were confirmed for several cytokines using an antibody array approach.
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Affiliation(s)
- Judith A Coppinger
- Department of Cell Biology, Scripps Research Institute, La Jolla, CA, USA
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83
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84
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Abstract
Blood-based therapeutics are cellular or plasma components derived from human blood. Their production requires appropriate selection and treatment of the donor and processing of cells or plasma proteins. In contrast to clearly defined, chemically synthesized drugs, blood-derived therapeutics are highly complex mixtures of plasma proteins or even more complex cells. Pathogen transmission by the product as well as changes in the integrity of blood constituents resulting in loss of function or immune modulation are currently important issues in transfusion medicine. Protein modifications can occur during various steps of the production process, such as acquisition, enrichment of separate components (e.g. coagulation factors, cell populations), virus inactivation, conservation, and storage. Contemporary proteomic strategies allow a comprehensive assessment of protein modifications with high coverage, offer capabilities for qualitative and even quantitative analysis, and for high-throughput protein identification. Traditionally, proteomics approaches predominantly relied on two-dimensional gel electrophoresis (2-DE). Even if 2-DE is still state of the art, it has inherent limitations that are mainly based on the physicochemical properties of the proteins analyzed; for example, proteins with extremes in molecular mass and hydrophobicity (most membrane proteins) are difficult to assess by 2-DE. These limitations have fostered the development of mass spectrometry centered on non-gel-based separation approaches, which have proven to be highly successful and are thus complementing and even partially replacing 2-DE-based approaches. Although blood constituents have been extensively analyzed by proteomics, this technology has not been widely applied to assess or even improve blood-derived therapeutics, or to monitor the production processes. As proteomic technologies have the capacity to provide comprehensive information about changes occurring during processing and storage of blood products, proteomics can potentially guide improvement of pathogen inactivation procedures and engineering of stem cells, and may also allow a better understanding of factors influencing the immunogenicity of blood-derived therapeutics. An important development in proteomics is the reduction of inter-assay variability. This now allows the screening of samples taken from the same product over time or before and after processing. Optimized preparation procedures and storage conditions will reduce the risk of protein alterations, which in turn may contribute to better recovery, reduced exposure to allogeneic proteins, and increased transfusion safety.
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Affiliation(s)
- Thomas Thiele
- Institute of Immunology and Transfusion Medicine, Ernst-Moritz-Arndt University, Greifswald, Germany
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85
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Senis YA, Tomlinson MG, García A, Dumon S, Heath VL, Herbert J, Cobbold SP, Spalton JC, Ayman S, Antrobus R, Zitzmann N, Bicknell R, Frampton J, Authi KS, Martin A, Wakelam MJO, Watson SP. 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 2006; 6:548-64. [PMID: 17186946 PMCID: PMC1860054 DOI: 10.1074/mcp.d600007-mcp200] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The platelet surface is poorly characterized due to the low abundance of many membrane proteins and the lack of specialist tools for their investigation. In this study we identified novel human platelet and mouse megakaryocyte membrane proteins using specialist proteomics and genomics approaches. Three separate methods were used to enrich platelet surface proteins prior to identification by liquid chromatography and tandem mass spectrometry: lectin affinity chromatography, biotin/NeutrAvidin affinity chromatography, and free flow electrophoresis. Many known, abundant platelet surface transmembrane proteins and several novel proteins were identified using each receptor enrichment strategy. In total, two or more unique peptides were identified for 46, 68, and 22 surface membrane, intracellular membrane, and membrane proteins of unknown subcellular localization, respectively. The majority of these were single transmembrane proteins. To complement the proteomics studies, we analyzed the transcriptome of a highly purified preparation of mature primary mouse megakaryocytes using serial analysis of gene expression in view of the increasing importance of mutant mouse models in establishing protein function in platelets. This approach identified all of the major classes of platelet transmembrane receptors, including multitransmembrane proteins. Strikingly 17 of the 25 most megakaryocyte-specific genes (relative to 30 other serial analysis of gene expression libraries) were transmembrane proteins, illustrating the unique nature of the megakaryocyte/platelet surface. The list of novel plasma membrane proteins identified using proteomics includes the immunoglobulin superfamily member G6b, which undergoes extensive alternate splicing. Specific antibodies were used to demonstrate expression of the G6b-B isoform, which contains an immunoreceptor tyrosine-based inhibition motif. G6b-B undergoes tyrosine phosphorylation and association with the SH2 domain-containing phosphatase, SHP-1, in stimulated platelets suggesting that it may play a novel role in limiting platelet activation.
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Affiliation(s)
- Yotis A Senis
- Centre for Cardiovascular Sciences, Institute of Biomedical Research, University of Birmingham, Wolfson Drive, Edgbaston, Birmingham B15 2TT, United Kingdom.
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86
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Queloz PA, Thadikkaran L, Crettaz D, Rossier JS, Barelli S, Tissot JD. Proteomics and transfusion medicine: Future perspectives. Proteomics 2006; 6:5605-14. [PMID: 16972297 DOI: 10.1002/pmic.200600179] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Limited number of important discoveries have greatly contributed to the progresses achieved in the blood transfusion; ABO histo-blood groups, citrate as anticoagulant, fractionation of plasma proteins, plastic bags and apheresis machines. Three major types of blood products are transfused to patients: red cell concentrates, platelet concentrates and fresh frozen plasma. Several parameters of these products change during storage process and they have been well studied over the years. However, several aspects have completely been ignored; in particular those related to peptide and protein changes. This review presents what has been done using proteomic tools and the potentials of proteomics for transfusion medicine.
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87
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Zahedi RP, Begonja AJ, Gambaryan S, Sickmann A. Phosphoproteomics of human platelets: A quest for novel activation pathways. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1963-76. [PMID: 17049321 DOI: 10.1016/j.bbapap.2006.08.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 07/28/2006] [Accepted: 08/21/2006] [Indexed: 01/05/2023]
Abstract
Besides their role in hemostasis, platelets are also highly involved in the pathogenesis and progression of cardiovascular diseases. Since important and initial steps of platelet activation and aggregation are regulated by phosphorylation events, a comprehensive study aimed at the characterization of phosphorylation-driven signaling cascades might lead to the identification of new target proteins for clinical research. However, it becomes increasingly evident that only a comprehensive phosphoproteomic approach may help to characterize functional protein networks and their dynamic alteration during physiological and pathophysiological processes in platelets. In this review, we discuss current methodologies in phosphoproteome research including their potentials as well as limitations, from sample preparation to classical approaches like radiolabeling and state-of-the-art mass spectrometry techniques.
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Affiliation(s)
- René P Zahedi
- Protein Mass Spectrometry and Functional Proteomics Group, Rudolf-Virchow-Center for Experimental Biomedicine, University of Wuerzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany
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88
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Weihofen WA, Berger M, Chen H, Saenger W, Hinderlich S. Structures of human N-Acetylglucosamine kinase in two complexes with N-Acetylglucosamine and with ADP/glucose: insights into substrate specificity and regulation. J Mol Biol 2006; 364:388-99. [PMID: 17010375 DOI: 10.1016/j.jmb.2006.08.085] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 08/29/2006] [Accepted: 08/30/2006] [Indexed: 11/15/2022]
Abstract
N-Acetylglucosamine (GlcNAc), a major component of complex carbohydrates, is synthesized de novo or salvaged from lysosomally degraded glycoconjugates and from nutritional sources. The salvage pathway requires that GlcNAc kinase converts GlcNAc to GlcNAc-6-phosphate, a component utilized in UDP-GlcNAc biosynthesis or energy metabolism. GlcNAc kinase belongs to the sugar kinase/Hsp70/actin superfamily that catalyze phosphoryl transfer from ATP to their respective substrates, and in most cases catalysis is associated with a large conformational change in which the N-terminal small and C-terminal large domains enclose the substrates. Here we report two crystal structures of homodimeric human GlcNAc kinase, one in complex with GlcNAc and the other in complex with ADP and glucose. The active site of GlcNAc kinase is located in a deep cleft between the two domains of the V-shaped monomer. The enzyme adopts a "closed" configuration in the GlcNAc-bound complex and GlcNAc interacts with residues of both domains. In addition, the N-acetyl methyl group contacts residues of the other monomer in the homodimer, a unique feature compared to other members of the sugar kinase/Hsp70/actin superfamily. This contrasts an "open" configuration in the ADP/glucose-bound structure, where glucose cannot form these interactions, explaining its low binding affinity for GlcNAc kinase. Our results support functional implications derived from apo crystal structures of GlcNAc kinases from Chromobacter violaceum and Porphyromonas gingivalis and show that Tyr205, which is phosphorylated in thrombin-activated platelets, lines the GlcNAc binding pocket. This suggests that phosphorylation of Tyr205 may modulate GlcNAc kinase activity and/or specificity.
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Affiliation(s)
- Wilhelm A Weihofen
- Freie Universität Berlin, Institut für Chemie und Biochemie-Kristallographie, Takustrasse 6, 14195 Berlin-Dahlem, Germany
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89
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Schubert P, Hoffman MD, Sniatynski MJ, Kast J. Advances in the analysis of dynamic protein complexes by proteomics and data processing. Anal Bioanal Chem 2006; 386:482-93. [PMID: 16933131 DOI: 10.1007/s00216-006-0609-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 06/05/2006] [Accepted: 06/08/2006] [Indexed: 01/12/2023]
Abstract
Signal transduction governs virtually every cellular function of multicellular organisms, and its deregulation leads to a variety of diseases. This intricate network of molecular interactions is mediated by proteins that are assembled into complexes within individual signaling pathways, and their composition and function is often regulated by different post-translational modifications. Proteomic approaches are commonly used to analyze biological complexes and networks, but often lack the specificity to address the dynamic and hence transient nature of the interactions and the influence of the multiple post-translational modifications that govern these processes. Here we review recent developments in proteomic research to address these limitations, and discuss several technologies that have been developed for this purpose. The synergy between these proteomic and computational tools, when applied together with global methods to the analysis of individual proteins, complexes and pathways, may allow researchers to unravel the underlying mechanisms of signaling networks in greater detail than previously possible.
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Affiliation(s)
- Peter Schubert
- The Biomedical Research Centre, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
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90
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Abstract
Platelets play critical roles in diverse hemostatic and pathologic disorders and are broadly implicated in various biological processes that include inflammation, wound healing, and thrombosis. Recent progress in high-throughput mRNA and protein profiling techniques has advanced our understanding of the biological functions of platelets. Platelet proteomics has been adopted to decode the complex processes that underlie platelet function by identifying novel platelet-expressed proteins, dissecting mechanisms of signal or metabolic pathways, and analyzing functional changes of the platelet proteome in normal and pathologic states. The integration of transcriptomics and proteomics, coupled with progress in bioinformatics, provides novel tools for dissecting platelet biology. In this review, we focus on current advances in platelet proteomic studies, with emphasis on the importance of parallel transcriptomic studies to optimally dissect platelet function. Applications of these global profiling approaches to investigate platelet genetic diseases and platelet-related disorders are also addressed.
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Affiliation(s)
- Dmitri V Gnatenko
- Department of Medicine, Program in Genetics, Division of Hematology, State University of New York, Stony Brook, NY 11794-8151, USA.
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91
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Luo F, Liu X, Wang S, Chen H. Effect of homocysteine on platelet activation induced by collagen. Nutrition 2006; 22:69-75. [PMID: 16455445 DOI: 10.1016/j.nut.2005.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Accepted: 04/19/2005] [Indexed: 02/05/2023]
Abstract
OBJECTIVE The present study investigated the effects of homocysteine on platelet activation induced by collagen and the downstream signaling pathways potentially involved in these effects. METHODS Washed human platelets were incubated with homocysteine and collagen type I. The effects of homocysteine on platelet aggregation and adhesion and the tyrosine phosphorylation of total platelet proteins, Src kinase, and phospholipase-Cgamma2 (PLCgamma2) were studied. RESULTS Homocysteine (10 to 100 microM) increased collagen-induced aggregation of washed platelets. Upon homocysteine (50 to 100 microM) treatment, platelet deposition to collagen-coated surface was significantly augmented under the low shear rate model (100/s) but not under the high shear rate model (1600/s). Collagen-stimulated total protein tyrosine phosphorylation in platelets was further enhanced by incubation with homocysteine. This effect was almost abrogated by genistein. Homocysteine potentiated collagen-stimulated tyrosine phosphorylation of the Src kinase and PLCgamma2, which was partly decreased by integrin beta1 blocking antibody. CONCLUSION Homocysteine (at 10 to 100 microM) potentiates collagen type I induced-platelet activation through signaling components of glycoprotein VI and integrin alpha2beta1 pathway. Our results suggested that upregulation of tyrosine phosphorylation of proteins such as Src and PLCgamma2 is involved in the downstream signaling events of homocysteine stimulation in human platelets.
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Affiliation(s)
- Fengming Luo
- Laboratory of Cardiovascular Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan, Peoples Republic of China
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92
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Moebius J, Zahedi RP, Sickmann A. Platelet Proteomics: Essentials for Understanding and Application. Transfus Med Hemother 2006. [DOI: 10.1159/000091372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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93
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94
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Pluder F, Mörl K, Beck-Sickinger AG. Proteome analysis to study signal transduction of G protein-coupled receptors. Pharmacol Ther 2006; 112:1-11. [PMID: 16644018 DOI: 10.1016/j.pharmthera.2006.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Accepted: 03/01/2006] [Indexed: 12/28/2022]
Abstract
G protein-coupled receptors (GPCR) play an important role in drug development. Although many classical signal transduction pathways have been elucidated, more and more cross-talk to other cascades, e.g. MAP-kinase have been reported. In order to identify the overall function of receptor stimulation in a specific cell type or under certain conditions proteome analysis has been shown to be a very successful and powerful approach. Here, we will summarize the current state of the art of proteome analysis applied to GPCR.
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Affiliation(s)
- Franka Pluder
- Institute of Biochemistry, University of Leipzig, Brüderstrasse 34, D-04103, Leipzig, Germany
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95
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Wang J, Zhang Y, Jiang H, Cai Y, Qian X. Phosphopeptide detection using automated online IMAC-capillary LC-ESI-MS/MS. Proteomics 2006; 6:404-11. [PMID: 16342239 DOI: 10.1002/pmic.200500223] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
IMAC has become a commonly used technique in phosphoprotein analysis because of its affinity for phosphopeptides. However, the commonly used strategy combining offline IMAC enrichment with desalting procedures prior to MS/MS makes this method laborious. Here we report the development of a robust and automatic IMAC-capillary RP HPLC-ESI MS/MS technology platform, by which all procedures needed in phosphopeptide analysis including IMAC enrichment, RP HPLC separation and nanospray MS/MS can be done automatically controlled by the MassLynx program. The platform was optimized by analyzing standard phosphopeptide, and was then applied to the identification of phosphorylation sites of recombinant human telomeric repeat binding factor 1 treated with kinase in vitro, and two phosphorylation sites are defined.
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Affiliation(s)
- Jinglan Wang
- The Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, PR China
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96
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García A. Proteome analysis of signaling cascades in human platelets. Blood Cells Mol Dis 2006; 36:152-6. [PMID: 16487730 DOI: 10.1016/j.bcmd.2005.12.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Accepted: 12/07/2005] [Indexed: 11/24/2022]
Abstract
During the last 15 years, advances in mass spectrometry (MS) instrumentation and techniques have revolutionized the emerging field of proteomics. Proteomics technology allows a comprehensive and efficient analysis of the protein content (i.e., the proteome) of any cell, tissue or biological fluid and has become an indispensable tool in biomedical research, complementing the powerful field of genomics. Proteomics is based on the huge analytical power offered by mass spectrometry in combination with several separation techniques, such as two-dimensional gel electrophoresis (2-DE) or multidimensional liquid chromatography. The technology is particularly suitable for platelets because of the absence of a nucleus. In the recent years, there has been success in mapping the proteome of the platelet in a basal state. Furthermore, a handful of research groups have also applied this technology to the study of signaling cascades in human platelets, allowing the identification of novel platelet signaling proteins and phosphorylation events. Those studies provide new insights into the mechanisms of platelet activation and build the basis for the development of therapeutic agents for thrombotic disease. This article focus on the application of 2-DE-based proteomics to the study of signaling cascades in human platelets.
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Affiliation(s)
- Angel García
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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97
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Lam L, Lind J, Semsarian C. Application of proteomics in cardiovascular medicine. Int J Cardiol 2006; 108:12-9. [PMID: 16466817 DOI: 10.1016/j.ijcard.2006.01.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 12/21/2005] [Accepted: 01/12/2006] [Indexed: 11/13/2022]
Abstract
Proteomics is an emerging field that has the potential to uncover new therapeutic targets for the treatment and prevention of cardiovascular disease, as well as new diagnostic biomarkers for early disease detection. The basic strategy when carrying out proteomic analysis of cardiovascular disease is to compare the protein complements of diseased hearts or sera with controls. Any proteins that have altered expression between the two groups can be studied further for their involvement in disease pathogenesis. A number of steps need to be taken to identify changes in protein expression, including sample preparation, protein separation, imaging, and protein identification. Such studies are already underway in some cardiovascular conditions including dilated cardiomyopathy and atrial fibrillation. This review provides a summary of the techniques used in proteomic analysis and their application to cardiovascular research.
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Affiliation(s)
- Lien Lam
- Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, Sydney, Australia
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98
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Macaulay IC, Carr P, Gusnanto A, Ouwehand WH, Fitzgerald D, Watkins NA. Platelet genomics and proteomics in human health and disease. J Clin Invest 2006; 115:3370-7. [PMID: 16322782 PMCID: PMC1297260 DOI: 10.1172/jci26885] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Proteomic and genomic technologies provide powerful tools for characterizing the multitude of events that occur in the anucleate platelet. These technologies are beginning to define the complete platelet transcriptome and proteome as well as the protein-protein interactions critical for platelet function. The integration of these results provides the opportunity to identify those proteins involved in discrete facets of platelet function. Here we summarize the findings of platelet proteome and transcriptome studies and their application to diseases of platelet function.
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Affiliation(s)
- Iain C Macaulay
- Department of Haematology, University of Cambridge, Cambridge, UK
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99
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García A, Watson SP, Dwek RA, Zitzmann N. Applying proteomics technology to platelet research. MASS SPECTROMETRY REVIEWS 2005; 24:918-930. [PMID: 15599945 DOI: 10.1002/mas.20047] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Platelets are small enucleated cells that circulate in the blood, where they play a key role in hemostasis and contribute to the formation of vascular plugs. Pathologically, they are involved in thrombosis and heart disease. Because platelets do not have a nucleus, proteomics offers a powerful way to approach their biology. Proteomics technology is based on the huge analytical power offered by mass spectrometry in combination with several separation techniques, such as two-dimensional gel electrophoresis (2DGE) or multidimensional liquid chromatography. Proteomics provides information about the complete set of proteins present in platelets, the platelet proteome, including post-translational variants. Over the last years, several research groups have applied proteomics to platelet research. A detailed analysis of the general proteome and signaling cascades in human platelets will improve our knowledge of platelet function, and thereby aid the development of new therapeutic agents to treat thrombotic diseases. This review presents the major advances in mass spectrometry-based proteomics techniques and their application to platelet research, and analyzes in detail the most relevant contributions to the field.
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Affiliation(s)
- Angel García
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
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100
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Kelly P, Maguire PB, Bennett M, Fitzgerald DJ, Edwards RJ, Thiede B, Treumann A, Collins JK, O'Sullivan GC, Shanahan F, Dunne C. Correlation of probioticLactobacillus salivariusgrowth phase with its cell wall-associated proteome. FEMS Microbiol Lett 2005; 252:153-9. [PMID: 16214296 DOI: 10.1016/j.femsle.2005.08.051] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 08/13/2005] [Accepted: 08/29/2005] [Indexed: 01/04/2023] Open
Abstract
Lactobacillus salivarius subsp. salivarius UCC118 is a probiotic bacterium that was originally isolated from human intestinal tissues and was subsequently shown in a pilot study to alleviate symptoms associated with mild-moderate Crohn's disease. Strain UCC118 can adhere to animal and human intestinal tissue, and to both healthy and inflamed ulcerative colitis mucosa, irrespective of location in the gut. In this study, an enzymatic technique has been combined with proteomic analysis to correlate bacterial growth phase with the presence of factors present in the cell wall of the bacterium. Using PAGE electrophoresis, it was determined that progression from lag to log to stationary growth phases in vitro correlated with increasing prominence of an 84kD protein associated with in vitro adherence ability. Isolated proteins from the 84kD band region were further separated by two-dimensional electrophoresis, resolving this band into 20 individual protein spots at differing isoelectric points. The protein moieties were excised, trypsin digested and subjected to tandem mass spectrometry. The observed proteins are analogous to those reported to be associated with the Listeria monocytogenes cell-wall proteome, and include DnaK, Ef-Ts and pyruvate kinase. These data suggest that at least some of the beneficial attributes of probiotic lactobacilli, and in particular this strain, may be due to nonpathogenic mimicry of pathogens and potentially be mediated through a form of attenuated virulence.
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Affiliation(s)
- Peter Kelly
- Department of Medicine, Cork Cancer Research Centre and Alimentary Pharmabiotic Centre at the National University of Ireland, Cork, Ireland
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