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Rees PA, Lowy RJ. Optimizing reduction of western blotting analytical variations: Use of replicate test samples, multiple normalization methods, and sample loading positions. Anal Biochem 2023:115198. [PMID: 37302777 DOI: 10.1016/j.ab.2023.115198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/13/2023]
Abstract
Western blot (WB) analysis is widely used, but obtaining consistent results can be problematic, especially when using multiple gels. This study examines WB performance by explicitly applying a method commonly used to test analytical instrumentation. Test samples were lysates from RAW 264.7 murine macrophages treated with LPS to activate MAPK and NF-kB signaling targets. Samples from the pooled cell lysates placed in every lane on multiple gels were analyzed by WBs for levels of p-ERK, ERK, IkBβ and non-target protein. Different normalization methods and sample groupings were applied to the density values and the resulting coefficients of variation (CV) and ratios of maximal to minimal values (Max/Min) were compared. Ideally with identical sample replicates the CVs would be 0 and the Max/Min 1; deviation indicating introduction of variability by the WB process. Common normalizations to reduce analytical variance, total lane protein, % Control, and p-ERK/ERK ratios, did not have the lowest CVs or Max/Min values. Normalization using the sum of target protein values combined with analytical replication most effectively reduced variability, resulting CV and Max/Min values as low as 5-10% and 1.1. These methods should allow reliable interpretation of complex experiments that require samples to be placed on multiple gels.
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Affiliation(s)
- Phyllis A Rees
- Scientific Research Department, Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - R Joel Lowy
- Scientific Research Department, Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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2
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Zharkova O, Salamah MF, Babak MV, Rajan E, Lim LHK, Andrade F, Gil CD, Oliani SM, Moraes LA, Vaiyapuri S. Deletion of Annexin A1 in Mice Upregulates the Expression of Its Receptor, Fpr2/3, and Reactivity to the AnxA1 Mimetic Peptide in Platelets. Int J Mol Sci 2023; 24:ijms24043424. [PMID: 36834844 PMCID: PMC9962723 DOI: 10.3390/ijms24043424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Annexin A1 (ANXA1) is an endogenous protein, which plays a central function in the modulation of inflammation. While the functions of ANXA1 and its exogenous peptidomimetics, N-Acetyl 2-26 ANXA1-derived peptide (ANXA1Ac2-26), in the modulation of immunological responses of neutrophils and monocytes have been investigated in detail, their effects on the modulation of platelet reactivity, haemostasis, thrombosis, and platelet-mediated inflammation remain largely unknown. Here, we demonstrate that the deletion of Anxa1 in mice upregulates the expression of its receptor, formyl peptide receptor 2/3 (Fpr2/3, orthologue of human FPR2/ALX). As a result, the addition of ANXA1Ac2-26 to platelets exerts an activatory role in platelets, as characterised by its ability to increase the levels of fibrinogen binding and the exposure of P-selectin on the surface. Moreover, ANXA1Ac2-26 increased the development of platelet-leukocyte aggregates in whole blood. The experiments carried out using a pharmacological inhibitor (WRW4) for FPR2/ALX, and platelets isolated from Fpr2/3-deficient mice ascertained that the actions of ANXA1Ac2-26 are largely mediated through Fpr2/3 in platelets. Together, this study demonstrates that in addition to its ability to modulate inflammatory responses via leukocytes, ANXA1 modulates platelet function, which may influence thrombosis, haemostasis, and platelet-mediated inflammation under various pathophysiological settings.
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Affiliation(s)
- Olga Zharkova
- Immunology Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | | | - Maria V. Babak
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | | | - Lina H. K. Lim
- Immunology Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Frans Andrade
- Department of Morphology and Genetics, Federal University of São Paulo (UNIFESP), São Paulo 04023-900, Brazil
| | - Cristiane D. Gil
- Department of Morphology and Genetics, Federal University of São Paulo (UNIFESP), São Paulo 04023-900, Brazil
| | - Sonia M. Oliani
- Department of Morphology and Genetics, Federal University of São Paulo (UNIFESP), São Paulo 04023-900, Brazil
- Department of Biology, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), São Paulo State University (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Leonardo A. Moraes
- Immunology Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- School of Pharmacy, University of Reading, Reading RG6 6UB, UK
| | - Sakthivel Vaiyapuri
- School of Pharmacy, University of Reading, Reading RG6 6UB, UK
- Correspondence:
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Saumell-Esnaola M, Elejaga-Jimeno A, Echeazarra L, Borrega-Román L, Barrondo S, López de Jesús M, González-Burguera I, Gómez-Caballero A, Goicolea MA, Sallés J, García del Caño G. Design and validation of recombinant protein standards for quantitative Western blot analysis of cannabinoid CB1 receptor density in cell membranes: an alternative to radioligand binding methods. Microb Cell Fact 2022; 21:192. [PMID: 36109736 PMCID: PMC9479267 DOI: 10.1186/s12934-022-01914-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Background Replacement of radioligand binding assays with antibody-antigen interaction-based approaches for quantitative analysis of G protein-coupled receptor (GPCR) levels requires the use of purified protein standards containing the antigen. GPCRs in general and cannabinoid CB1 receptor in particular show a progressive tendency to aggregate and precipitate in aqueous solution outside of their biological context due to the low solubility that the hydrophobic nature imprinted by their seven transmembrane domains. This renders full-length recombinant GPCRs useless for analytical purposes, a problem that can be overcome by engineering soluble recombinant fragments of the receptor containing the antigen. Results Here we generated highly soluble and stable recombinant protein constructs GST-CB1414–472 and GST-CB1414-442 containing much of the human CB1 receptor C-terminal tail for use as standard and negative control, respectively, in quantitative Western blot analysis of CB1 receptor expression on crude synaptosomes of the adult rat brain cortex. To this end we used three different antibodies, all raised against a peptide comprising the C-terminal residues 443–473 of the mouse CB1 receptor that corresponds to residues 442–472 in the human homolog. Estimated values of CB1 receptor density obtained by quantitative Western blot were of the same order of magnitude but slightly higher than values obtained by the radioligand saturation binding assay. Conclusions Collectively, here we provide a suitable Western blot-based design as a simple, cost-effective and radioactivity-free alternative for the quantitative analysis of CB1 receptor expression, and potentially of any GPCR, in a variety of biological samples. The discrepancies between the results obtained by quantitative Western blot and radioligand saturation binding techniques are discussed in the context of their particular theoretical bases and methodological constraints. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01914-1.
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Štefl M, Herbst K, Rübsam M, Benda A, Knop M. Single-Color Fluorescence Lifetime Cross-Correlation Spectroscopy In Vivo. Biophys J 2020; 119:1359-1370. [PMID: 32919495 DOI: 10.1016/j.bpj.2020.06.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 01/18/2023] Open
Abstract
The ability to quantify protein concentrations and to measure protein interactions in vivo is key information needed for the understanding of complex processes inside cells, but the acquisition of such information from living cells is still demanding. Fluorescence-based methods like two-color fluorescence cross-correlation spectroscopy can provide this information, but measurement precision is hampered by various sources of errors caused by instrumental or optical limitations such as imperfect overlap of detection volumes or detector cross talk. Furthermore, the nature and properties of used fluorescent proteins or fluorescent dyes, such as labeling efficiency, fluorescent protein maturation, photostability, bleaching, and fluorescence brightness can have an impact. Here, we take advantage of previously published fluorescence lifetime correlation spectroscopy which relies on lifetime differences as a mean to discriminate fluorescent proteins with similar spectral properties and to use them for single-color fluorescence lifetime cross-correlation spectroscopy (sc-FLCCS). By using only one excitation and one detection wavelength, this setup avoids all sources of errors resulting from chromatic aberrations and detector cross talk. To establish sc-FLCCS, we first engineered and tested multiple green fluorescent protein (GFP)-like fluorescent proteins for their suitability. This identified a novel, to our knowledge, GFP variant termed short-lifetime monomeric GFP with the so-far shortest lifetime. Monte-Carlo simulations were employed to explore the suitability of different combinations of GFP variants. Two GFPs, Envy and short-lifetime monomeric GFP, were predicted to constitute the best performing couple for sc-FLCCS measurements. We demonstrated application of this GFP pair for measuring protein interactions between the proteasome and interacting proteins and for measuring protein interactions between three partners when combined with a red florescent protein. Together, our findings establish sc-FLCCS as a valid alternative for conventional dual-color fluorescence cross-correlation spectroscopy measurements.
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Affiliation(s)
- Martin Štefl
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany; J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Prague, Czech Republic.
| | - Konrad Herbst
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Marc Rübsam
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Aleš Benda
- IMCF at BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.
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Arvin NE, Dawod M, Lamb DT, Anderson JP, Furtaw MD, Kennedy RT. Fast Immunoassay for Microfluidic Western Blotting by Direct Deposition of Reagents onto Capture Membrane. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:1606-1616. [PMID: 32661464 PMCID: PMC7357712 DOI: 10.1039/d0ay00207k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Western blotting is a widely used protein assay platform, but the technique requires long analysis times and multiple manual steps. Microfluidic systems are currently being explored for increased automation and reduction of analysis times, sample volumes, and reagent consumption for western blots. Previous work has demonstrated that proteins separated by microchip electrophoresis can be captured on membranes by dragging the microchip outlet across the membrane. This process reduces the separation and transfer time of a western blot to a few minutes. To further improve the speed and miniaturization of a complete western blot, a microscale immunoassay with direct deposition of immunoassay reagents has been developed. Flow deposition of antibodies is used to overcome diffusion limited binding kinetics so that the entire immunoassay can be completed in 1 h with detection sensitivity comparable to incubation steps requiring 20 h. The use of low microliter/min flow rates with antibody reagents applied directly and locally to the membrane where the target proteins have been captured, reduced antibody consumption ~30-fold. The complete western blot was applied to the detection of GAPDH and β-Tubulin from A431 cell lysate.
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Affiliation(s)
- Natalie E. Arvin
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Mohamed Dawod
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
- Vaccine Analytical R&D, Merck Research Laboratories, 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Don T. Lamb
- LI-COR Biosciences, 4647 Superior St., Lincoln, Nebraska 68504, United States
| | - Jon P. Anderson
- LI-COR Biosciences, 4647 Superior St., Lincoln, Nebraska 68504, United States
| | - Michael D. Furtaw
- LI-COR Biosciences, 4647 Superior St., Lincoln, Nebraska 68504, United States
| | - Robert T. Kennedy
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
- Department of Pharmacology, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, Michigan 48109, United States
- Corresponding author: Robert T. Kennedy, , Tel: 734-615-4363, Fax: 745-615-6462
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Dunster JL, Unsworth AJ, Bye AP, Haining EJ, Sowa MA, Di Y, Sage T, Pallini C, Pike JA, Hardy AT, Nieswandt B, García Á, Watson SP, Poulter NS, Gibbins JM, Pollitt AY. Interspecies differences in protein expression do not impact the spatiotemporal regulation of glycoprotein VI mediated activation. J Thromb Haemost 2020; 18:485-496. [PMID: 31680418 PMCID: PMC7027541 DOI: 10.1111/jth.14673] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Accurate protein quantification is a vital prerequisite for generating meaningful predictions when using systems biology approaches, a method that is increasingly being used to unravel the complexities of subcellular interactions and as part of the drug discovery process. Quantitative proteomics, flow cytometry, and western blotting have been extensively used to define human platelet protein copy numbers, yet for mouse platelets, a model widely used for platelet research, evidence is largely limited to a single proteomic dataset in which the total amount of proteins was generally comparatively higher than those found in human platelets. OBJECTIVES To investigate the functional implications of discrepancies between levels of mouse and human proteins in the glycoprotein VI (GPVI) signalling pathway using a systems pharmacology model of GPVI. METHODS The protein copy number of mouse platelet receptors was determined using flow cytometry. The Virtual Platelet, a mathematical model of GPVI signalling, was used to determine the consequences of protein copy number differences observed between human and mouse platelets. RESULTS AND CONCLUSION Despite the small size of mouse platelets compared to human platelets they possessed a greater density of surface receptors alongside a higher concentration of intracellular signalling proteins. Surprisingly the predicted temporal profile of Syk activity was similar in both species with predictions supported experimentally. Super resolution microscopy demonstrates that the spatial distribution of Syk is similar between species, suggesting that the spatial distribution of receptors and signalling molecules in activated platelets, rather than their copy number, is important for signalling pathway regulation.
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Affiliation(s)
- Joanne L. Dunster
- Institute for Cardiovascular and Metabolic Research (ICMR)School of Biological SciencesUniversity of ReadingReadingUK
| | - Amanda J. Unsworth
- Institute for Cardiovascular and Metabolic Research (ICMR)School of Biological SciencesUniversity of ReadingReadingUK
- Department of Life SciencesSchool of Science and EngineeringManchester Metropolitan UniversityManchesterUK
| | - Alexander P. Bye
- Institute for Cardiovascular and Metabolic Research (ICMR)School of Biological SciencesUniversity of ReadingReadingUK
| | - Elizabeth J. Haining
- Institute of Cardiovascular Sciences (ICVS)College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| | - Marcin A. Sowa
- Institute for Cardiovascular and Metabolic Research (ICMR)School of Biological SciencesUniversity of ReadingReadingUK
- Platelet Proteomics GroupCenter for Research in Molecular Medicine and Chronic Diseases (CIMUS)Universidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Ying Di
- Institute of Cardiovascular Sciences (ICVS)College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| | - Tanya Sage
- Institute for Cardiovascular and Metabolic Research (ICMR)School of Biological SciencesUniversity of ReadingReadingUK
| | - Chiara Pallini
- Institute of Cardiovascular Sciences (ICVS)College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| | - Jeremy A. Pike
- Centre of Membrane Proteins and Receptors (COMPARE)Universities of Birmingham and NottinghamMidlandsBirminghamUK
| | - Alexander T. Hardy
- Institute of Cardiovascular Sciences (ICVS)College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
| | - Bernhard Nieswandt
- Department of Experimental BiomedicineUniversity HospitalUniversity of WürzburgWürzburgGermany
| | - Ángel García
- Platelet Proteomics GroupCenter for Research in Molecular Medicine and Chronic Diseases (CIMUS)Universidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Steve P. Watson
- Institute of Cardiovascular Sciences (ICVS)College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
- Centre of Membrane Proteins and Receptors (COMPARE)Universities of Birmingham and NottinghamMidlandsBirminghamUK
| | - Natalie S. Poulter
- Institute of Cardiovascular Sciences (ICVS)College of Medical and Dental SciencesUniversity of BirminghamBirminghamUK
- Centre of Membrane Proteins and Receptors (COMPARE)Universities of Birmingham and NottinghamMidlandsBirminghamUK
| | - Jonathan M. Gibbins
- Institute for Cardiovascular and Metabolic Research (ICMR)School of Biological SciencesUniversity of ReadingReadingUK
| | - Alice Y. Pollitt
- Institute for Cardiovascular and Metabolic Research (ICMR)School of Biological SciencesUniversity of ReadingReadingUK
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Critical roles for the phosphatidylinositide 3-kinase isoforms p110β and p110γ in thrombopoietin-mediated priming of platelet function. Sci Rep 2019; 9:1468. [PMID: 30728366 PMCID: PMC6365529 DOI: 10.1038/s41598-018-37012-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/27/2018] [Indexed: 12/17/2022] Open
Abstract
Thrombopoietin (TPO) enhances platelet activation through activation of the tyrosine kinase; JAK2 and the lipid kinase phosphatidylinositide 3-kinase (PI3K). The aim of our study was to identify the PI3K isoforms involved in mediating the effect of TPO on platelet function and elucidate the underlying mechanism. We found that p110β plays an essential role in TPO-mediated (i) priming of protease-activated receptor (PAR)-mediated integrin αIIbβ3 activation and α-granule secretion, (ii) synergistic enhancement of PAR-mediated activation of the small GTPase RAP1, a regulator of integrin activation and (iii) phosphorylation of the PI3K effector Akt. More importantly, the synergistic effect of TPO on phosphorylation of extracellular-regulated kinase (ERK1/2) and thromboxane (TxA2) synthesis was dependent on both p110β and p110γ. p110β inhibition/deletion, or inhibition of p110γ, resulted in a partial reduction, whereas inhibiting both p110β and p110γ completely prevented the synergistic effect of TPO on ERK1/2 phosphorylation and TxA2 synthesis. The latter was ablated by inhibition of MEK, but not p38, confirming a role for ERK1/2 in regulating TPO-mediated increases in TxA2 synthesis. In conclusion, the synergistic effect of TPO on RAP1 and integrin activation is largely mediated by p110β, whereas p110β and p110γ contribute to the effect of TPO on ERK1/2 phosphorylation and TxA2 formation.
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Díaz Galicia ME, Aldehaiman A, Hong S, Arold ST, Grünberg R. Methods for the recombinant expression of active tyrosine kinase domains: Guidelines and pitfalls. Methods Enzymol 2019; 621:131-152. [DOI: 10.1016/bs.mie.2019.02.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Precise Quantification of Platelet Proteins and Their Phosphorylation States. Methods Mol Biol 2018. [PMID: 30171575 DOI: 10.1007/978-1-4939-8585-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Systems biology and modeling approaches require quantitative data-rich temporal experiments to better understand the dynamics and regulation of the components of the signaling pathways that governs cell biology and physiology. Here we present a modified Western blotting method to rapidly analyze and accurately quantify protein copy number, and their respective phosphorylation states at specific sites over detailed time courses.
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Regulation of Early Steps of GPVI Signal Transduction by Phosphatases: A Systems Biology Approach. PLoS Comput Biol 2015; 11:e1004589. [PMID: 26584182 PMCID: PMC4652868 DOI: 10.1371/journal.pcbi.1004589] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/06/2015] [Indexed: 11/19/2022] Open
Abstract
We present a data-driven mathematical model of a key initiating step in platelet activation, a central process in the prevention of bleeding following Injury. In vascular disease, this process is activated inappropriately and causes thrombosis, heart attacks and stroke. The collagen receptor GPVI is the primary trigger for platelet activation at sites of injury. Understanding the complex molecular mechanisms initiated by this receptor is important for development of more effective antithrombotic medicines. In this work we developed a series of nonlinear ordinary differential equation models that are direct representations of biological hypotheses surrounding the initial steps in GPVI-stimulated signal transduction. At each stage model simulations were compared to our own quantitative, high-temporal experimental data that guides further experimental design, data collection and model refinement. Much is known about the linear forward reactions within platelet signalling pathways but knowledge of the roles of putative reverse reactions are poorly understood. An initial model, that includes a simple constitutively active phosphatase, was unable to explain experimental data. Model revisions, incorporating a complex pathway of interactions (and specifically the phosphatase TULA-2), provided a good description of the experimental data both based on observations of phosphorylation in samples from one donor and in those of a wider population. Our model was used to investigate the levels of proteins involved in regulating the pathway and the effect of low GPVI levels that have been associated with disease. Results indicate a clear separation in healthy and GPVI deficient states in respect of the signalling cascade dynamics associated with Syk tyrosine phosphorylation and activation. Our approach reveals the central importance of this negative feedback pathway that results in the temporal regulation of a specific class of protein tyrosine phosphatases in controlling the rate, and therefore extent, of GPVI-stimulated platelet activation.
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