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Almansour S, Dunster JL, Crofts JJ, Nelson MR. A systematic evaluation of the influence of macrophage phenotype descriptions on inflammatory dynamics. Math Med Biol 2024:dqae004. [PMID: 38604176 DOI: 10.1093/imammb/dqae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/18/2024] [Accepted: 03/28/2024] [Indexed: 04/13/2024]
Abstract
Macrophages play a wide range of roles in resolving the inflammatory damage that underlies many medical conditions, and have the ability to adopt different phenotypes in response to different environmental stimuli. Categorising macrophage phenotypes exactly is a difficult task, and there is disparity in the literature around the optimal nomenclature to describe these phenotypes; however, what is clear is that macrophages can exhibit both pro- and anti-inflammatory behaviours dependent upon their phenotype, rendering mathematical models of the inflammatory response potentially sensitive to their description of the macrophage populations that they incorporate. Many previous models of inflammation include a single macrophage population with both pro- and anti-inflammatory functions. Here, we build upon these existing models to include explicit descriptions of distinct macrophage phenotypes and examine the extent to which this influences the inflammatory dynamics that the models emit. We analyse our models via numerical simulation in Matlab and dynamical systems analysis in XPPAUT, and show that models that account for distinct macrophage phenotypes separately can offer more realistic steady state solutions than precursor models do (better capturing the anti-inflammatory activity of tissue resident macrophages), as well as oscillatory dynamics not previously observed. Finally, we reflect on the conclusions of our analysis in the context of the ongoing hunt for potential new therapies for inflammatory conditions, highlighting manipulation of macrophage polarisation states as a potential therapeutic target.
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Affiliation(s)
- Suliman Almansour
- School of Science & Technology, Nottingham Trent University, Nottingham, NG11 8NS, United Kingdom
| | - Joanne L Dunster
- Institute for Cardiovascular and Metabolic Research, University of Reading, Reading, RG6 6AS, United Kingdom
| | - Jonathan J Crofts
- School of Science & Technology, Nottingham Trent University, Nottingham, NG11 8NS, United Kingdom
| | - Martin R Nelson
- School of Science & Technology, Nottingham Trent University, Nottingham, NG11 8NS, United Kingdom
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2
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Owen MJ, Wright JR, Tuddenham EGD, King JR, Goodall AH, Dunster JL. Mathematical models of coagulation-are we there yet? J Thromb Haemost 2024:S1538-7836(24)00167-3. [PMID: 38521192 DOI: 10.1016/j.jtha.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/24/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Mathematical models of coagulation have been developed to mirror thrombin generation in plasma, with the aim of investigating how variation in coagulation factor levels regulates hemostasis. However, current models vary in the reactions they capture and the reaction rates used, and their validation is restricted by a lack of large coherent datasets, resulting in questioning of their utility. OBJECTIVES To address this debate, we systematically assessed current models against a large dataset, using plasma coagulation factor levels from 348 individuals with normal hemostasis to identify the causes of these variations. METHODS We compared model predictions with measured thrombin generation, quantifying and comparing the ability of each model to predict thrombin generation, the contributions of the individual reactions, and their dependence on reaction rates. RESULTS We found that no current model predicted the hemostatic response across the whole cohort and all produced thrombin generation curves that did not resemble those obtained experimentally. Our analysis has identified the key reactions that lead to differential model predictions, where experimental uncertainty leads to variability in predictions, and we determined reactions that have a high influence on measured thrombin generation, such as the contribution of factor XI. CONCLUSION This systematic assessment of models of coagulation, using large dataset inputs, points to ways in which these models can be improved. A model that accurately reflects the effects of the multiple subtle variations in an individual's hemostatic profile could be used for assessing antithrombotics or as a tool for precision medicine.
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Affiliation(s)
- Matt J Owen
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom. https://twitter.com/MattJOwen_
| | - Joy R Wright
- Department of Cardiovascular Sciences, University of Leicester, Clinical Sciences Wing, Glenfield Hospital, Leicester, United Kingdom; National Institute for Healthcare Research, Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Edward G D Tuddenham
- Royal Free Hospital Haemophilia Centre, University College London, London, United Kingdom
| | - John R King
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Alison H Goodall
- Department of Cardiovascular Sciences, University of Leicester, Clinical Sciences Wing, Glenfield Hospital, Leicester, United Kingdom; National Institute for Healthcare Research, Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Joanne L Dunster
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, University of Reading, Reading, United Kingdom.
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3
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Mitchell JL, Dunster JL, Kriek N, Unsworth AJ, Sage T, Mohammed YMM, De Simone I, Taylor KA, Bye AP, Ólafsson G, Brunton M, Mark S, Dymott LD, Whyte A, Ruparelia N, Mckenna C, Gibbins JM, Jones CI. The rate of platelet activation determines thrombus size and structure at arterial shear. J Thromb Haemost 2023:S1538-7836(23)00333-1. [PMID: 37085037 DOI: 10.1016/j.jtha.2023.03.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/02/2023] [Accepted: 03/28/2023] [Indexed: 04/23/2023]
Abstract
BACKGROUND The response of platelets to activating stimuli and pharmaceutical agents varies greatly within the normal population. Current platelet function tests measure endpoint levels of platelet activation without taking the speed at which platelets activate into account, potentially missing vital metrics to characterise platelet reactivity. OBJECTIVES To identify variability, to agonist and between individuals, in platelet activation kinetics and assess the impact of this on thrombus formation. METHODS We have developed a bespoke real-time flow cytometry assay and analysis package that measures the rate of platelet activation over time using two parameters of platelet activation, fibrinogen binding and P-selectin exposure. RESULTS The rate of platelet activation varied considerably within the normal population but did not correlate with maximal platelet activation, demonstrating that platelet activation rate is a separate and novel metric to describe platelet reactivity. The relative rate of platelet response between agonists was strongly correlated, suggesting a central control mechanism regulates the rate of platelet response to all agonists. CONCLUSIONS For the first time, we have shown that platelet response rate corresponds to thrombus size and structure, where faster responders form larger, more densely packed thrombi at arterial, but crucially not venous shear. We have demonstrated that the rate of platelet activation is an important metric in stratifying individual platelet responses and will provide a novel focus for the design and development of anti-platelet therapy, targeting high shear thrombosis without exacerbating bleeding at low shear.
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Affiliation(s)
- Joanne L Mitchell
- School of Biological Sciences, University of Reading, UK; Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, UK
| | | | - Neline Kriek
- School of Biological Sciences, University of Reading, UK
| | | | - Tanya Sage
- School of Biological Sciences, University of Reading, UK
| | | | | | - Kirk A Taylor
- School of Biological Sciences, University of Reading, UK
| | - Alexander P Bye
- Molecular and Clinical Sciences Research Institute, St George's University, Cranmer Terrace, London, UK
| | - Geir Ólafsson
- Bristol Composites Institute, Faculty of Civil, Aerospace and Mechanical Engineering, University of Bristol, UK
| | - Mark Brunton
- University Department of Cardiology, Royal Berkshire Hospital, UK
| | - Sharon Mark
- University Department of Cardiology, Royal Berkshire Hospital, UK
| | - Leanne D Dymott
- University Department of Cardiology, Royal Berkshire Hospital, UK
| | - Abigail Whyte
- University Department of Cardiology, Royal Berkshire Hospital, UK
| | - Neil Ruparelia
- School of Biological Sciences, University of Reading, UK; University Department of Cardiology, Royal Berkshire Hospital, UK
| | - Charlie Mckenna
- University Department of Cardiology, Royal Berkshire Hospital, UK
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Dunster JL, Gibbins JM, Nelson MR. Exploring the constituent mechanisms of hepatitis: a dynamical systems approach. Math Med Biol 2023; 40:24-48. [PMID: 36197900 PMCID: PMC10009886 DOI: 10.1093/imammb/dqac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/07/2022]
Abstract
Hepatitis is the term used to describe inflammation in the liver. It is associated with a high rate of mortality, but the underlying disease mechanisms are not completely understood and treatment options are limited. We present a mathematical model of hepatitis that captures the complex interactions between hepatocytes (liver cells), hepatic stellate cells (cells in the liver that produce hepatitis-associated fibrosis) and the immune components that mediate inflammation. The model is in the form of a system of ordinary differential equations. We use numerical techniques and bifurcation analysis to characterize and elucidate the physiological mechanisms that dominate liver injury and its outcome to a healthy or unhealthy, chronic state. This study reveals the complex interactions between the multiple cell types and mediators involved in this complex disease and highlights potential problems in targeting inflammation in the liver therapeutically.
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Affiliation(s)
| | - Jonathan M Gibbins
- Institute for Cardiovascular and Metabolic Research, University of Reading, Reading, RG6 6AS, UK
| | - Martin R Nelson
- School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
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5
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Tantiwong C, Dunster JL, Cavill R, Tomlinson MG, Wierling C, Heemskerk JWM, Gibbins JM. An agent-based approach for modelling and simulation of glycoprotein VI receptor diffusion, localisation and dimerisation in platelet lipid rafts. Sci Rep 2023; 13:3906. [PMID: 36890261 PMCID: PMC9994409 DOI: 10.1038/s41598-023-30884-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/02/2023] [Indexed: 03/10/2023] Open
Abstract
Receptor diffusion plays an essential role in cellular signalling via the plasma membrane microenvironment and receptor interactions, but the regulation is not well understood. To aid in understanding of the key determinants of receptor diffusion and signalling, we developed agent-based models (ABMs) to explore the extent of dimerisation of the platelet- and megakaryocyte-specific receptor for collagen glycoprotein VI (GPVI). This approach assessed the importance of glycolipid enriched raft-like domains within the plasma membrane that lower receptor diffusivity. Our model simulations demonstrated that GPVI dimers preferentially concentrate in confined domains and, if diffusivity within domains is decreased relative to outside of domains, dimerisation rates are increased. While an increased amount of confined domains resulted in further dimerisation, merging of domains, which may occur upon membrane rearrangements, was without effect. Modelling of the proportion of the cell membrane which constitutes lipid rafts indicated that dimerisation levels could not be explained by these alone. Crowding of receptors by other membrane proteins was also an important determinant of GPVI dimerisation. Together, these results demonstrate the value of ABM approaches in exploring the interactions on a cell surface, guiding the experimentation for new therapeutic avenues.
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Affiliation(s)
- Chukiat Tantiwong
- School of Biological Sciences, University of Reading, Reading, UK.,Department of Biochemistry, CARIM, Maastricht University, Maastricht, The Netherlands
| | - Joanne L Dunster
- School of Biological Sciences, University of Reading, Reading, UK
| | - Rachel Cavill
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | | | | | - Johan W M Heemskerk
- Department of Biochemistry, CARIM, Maastricht University, Maastricht, The Netherlands.,Synapse Research Institute, Maastricht, The Netherlands
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Dunster JL, Wright JR, Samani NJ, Goodall AH. A System-Wide Investigation and Stratification of the Hemostatic Proteome in Premature Myocardial Infarction. Front Cardiovasc Med 2022; 9:919394. [PMID: 35845083 PMCID: PMC9281867 DOI: 10.3389/fcvm.2022.919394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction Advancing understanding of key factors that determine the magnitude of the hemostatic response may facilitate the identification of individuals at risk of generating an occlusive thrombus as a result of an atherothrombotic event such as an acute Myocardial Infarction (MI). While fibrinogen levels are a recognized risk factor for MI, the association of thrombotic risk with other coagulation proteins is inconsistent. This is likely due to the complex balance of pro- and anticoagulant factors in any individual. Methods We compared measured levels of pro- and anticoagulant proteins in plasma from 162 patients who suffered an MI at an early age (MI <50 y) and 186 age- and gender-matched healthy controls with no history of CAD. We then used the measurements from these individuals as inputs for an established mathematical model to investigate how small variations in hemostatic factors affect the overall amplitude of the hemostatic response and to identify differential key drivers of the hemostatic response in male and female patients and controls. Results Plasma from the MI patients contained significantly higher levels of Tissue Factor (P = 0.007), the components of the tenase (FIX and FVIII; P < 0.0001 for both) and the prothrombinase complexes (FX; P = 0.003), and lower levels of Tissue Factor Pathway Inhibitor (TFPI; P = 0.033) than controls. The mathematical model, which generates time-dependent predictions describing the depletion, activation, and interaction of the main procoagulant factors and inhibitors, identified different patterns of hemostatic response between MI patients and controls, and additionally, between males and females. Whereas, in males, TF, FVIII, FIX, and the inhibitor TFPI contribute to the differences seen between case and controls, and in females, FII, FVIII, and FIX had the greatest influence on the generation of thrombin. We additionally show that further donor stratification may be possible according to the predicted donor response to anticoagulant therapy. Conclusions We suggest that modeling could be of value in enhancing our prediction of risk of premature MI, recurrent risk, and therapeutic efficacy.
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Affiliation(s)
- Joanne L. Dunster
- School of Biological Sciences, Institute for Cardiovascular and Metabolic Research, Reading, United Kingdom
| | - Joy R. Wright
- Department of Cardiovascular Sciences, University of Leicester & NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester & NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Alison H. Goodall
- Department of Cardiovascular Sciences, University of Leicester & NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
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7
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Fernández DI, Provenzale I, Cheung HY, van Groningen J, Tullemans BM, Veninga A, Dunster JL, Honarnejad S, van den Hurk H, Kuijpers MJ, Heemskerk JW. Ultra-high-throughput Ca 2+ assay in platelets to distinguish ITAM-linked and G-protein-coupled receptor activation. iScience 2022; 25:103718. [PMID: 35072010 PMCID: PMC8762394 DOI: 10.1016/j.isci.2021.103718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/12/2021] [Accepted: 12/29/2021] [Indexed: 12/30/2022] Open
Abstract
Antiplatelet drugs targeting G-protein-coupled receptors (GPCRs), used for the secondary prevention of arterial thrombosis, coincide with an increased bleeding risk. Targeting ITAM-linked receptors, such as the collagen receptor glycoprotein VI (GPVI), is expected to provide a better antithrombotic-hemostatic profile. Here, we developed and characterized an ultra-high-throughput (UHT) method based on intracellular [Ca2+]i increases to differentiate GPVI and GPCR effects on platelets. In 96-, 384-, or 1,536-well formats, Calcium-6-loaded human platelets displayed a slow-prolonged or fast-transient [Ca2+]i increase when stimulated with the GPVI agonist collagen-related peptide or with thrombin and other GPCR agonists, respectively. Semi-automated curve fitting revealed five parameters describing the Ca2+ responses. Verification of the UHT assay was done with a robustness compound library and clinically relevant platelet inhibitors. Taken together, these results present proof of principle of distinct receptor-type-dependent Ca2+ signaling curves in platelets, which allow identification of new inhibitors in a UHT way.
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Affiliation(s)
- Delia I. Fernández
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
- Platelet Proteomics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Isabella Provenzale
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
- Institute for Cardiovascular and Metabolic Research, University of Reading, RG6 6AX Reading, UK
| | - Hilaire Y.F. Cheung
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
- ISASLeibniz-Institut fur Analytische Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany
- Institute of Cardiovascular Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Bibian M.E. Tullemans
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Alicia Veninga
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Joanne L. Dunster
- Institute for Cardiovascular and Metabolic Research, University of Reading, RG6 6AX Reading, UK
| | | | | | - Marijke J.E. Kuijpers
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
- Thrombosis Expertise Centre, Heart and Vascular Centre, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Johan W.M. Heemskerk
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
- Synapse Research Institute, Kon. Emmaplein 7, 6214 AC, Maastricht, the Netherlands
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Dunster JL, Mitchell JL, Mohammed YMM, Taylor KA, Gibbins JM, Jones CI. Kinetx: A Combined Flow Cytometry Assay and Analysis Software Framework to Quantitatively Measure and Categorize Platelet Activation in Real-time. J Vis Exp 2021. [PMID: 34694288 DOI: 10.3791/62947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Platelets react rapidly to vascular injury and undergo activation in response to a range of stimuli to limit blood loss. Many platelet function tests measure endpoint responses after a defined time period and not the rate of platelet activation. However, the rate at which platelets convert extracellular stimuli into a functional response is an essential factor in determining how efficiently they can respond to injury, bind to a forming thrombus, and signal to recruit other platelets. This paper describes a flow cytometry-based platelet function assay that enables simultaneous data acquisition and sample stimulation and utilizes newly developed bespoke open-source software (Kinetx) to enable quantitative kinetic measurements of platelet granule release, fibrinogen binding, and intracellular calcium flux. Kinetix was developed in R so that users can alter parameters such as degree of smoothing, identification of outlying data points, or time scales. To aid users unfamiliar with the R environment, Kinetix analysis of data can be performed by a single command. Together, this allows real-time platelet activation metrics, such as rate, acceleration, time to peak-rate, time to peak-calcium, and qualitative shape changes, to be accurately and reproducibly measured and categorized. Kinetic measurements of platelet activation give a unique insight into platelets' behavior during the first stages of activation and may provide a method of predicting the recruitment of platelets into a forming thrombus.
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Affiliation(s)
| | - Jo L Mitchell
- ICMR, School of Biological Sciences, University of Reading; Institute of Cardiovascular Sciences, University of Birmingham
| | | | - Kirk A Taylor
- ICMR, School of Biological Sciences, University of Reading
| | | | - Chris I Jones
- ICMR, School of Biological Sciences, University of Reading;
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9
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Kaneva VN, Dunster JL, Volpert V, Ataullahanov F, Panteleev MA, Nechipurenko DY. Modeling Thrombus Shell: Linking Adhesion Receptor Properties and Macroscopic Dynamics. Biophys J 2021; 120:334-351. [PMID: 33472026 DOI: 10.1016/j.bpj.2020.10.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 09/10/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
Damage to arterial vessel walls leads to the formation of platelet aggregate, which acts as a physical obstacle for bleeding. An arterial thrombus is heterogeneous; it has a dense inner part (core) and an unstable outer part (shell). The thrombus shell is very dynamic, being composed of loosely connected discoid platelets. The mechanisms underlying the observed mobility of the shell and its (patho)physiological implications are unclear. To investigate arterial thrombus mechanics, we developed a novel, to our knowledge, two-dimensional particle-based computational model of microvessel thrombosis. The model considers two types of interplatelet interactions: primary reversible (glycoprotein Ib (GPIb)-mediated) and stronger integrin-mediated interaction, which intensifies with platelet activation. At high shear rates, the former interaction leads to adhesion, and the latter is primarily responsible for stable platelet aggregation. Using a stochastic model of GPIb-mediated interaction, we initially reproduced experimental curves that characterize individual platelet interactions with a von Willebrand factor-coated surface. The addition of the second stabilizing interaction results in thrombus formation. The comparison of thrombus dynamics with experimental data allowed us to estimate the magnitude of critical interplatelet forces in the thrombus shell and the characteristic time of platelet activation. The model predicts moderate dependence of maximal thrombus height on the injury size in the absence of thrombin activity. We demonstrate that the developed stochastic model reproduces the observed highly dynamic behavior of the thrombus shell. The presence of primary stochastic interaction between platelets leads to the properties of thrombus consistent with in vivo findings; it does not grow upstream of the injury site and covers the whole injury from the first seconds of the formation. А simplified model, in which GPIb-mediated interaction is deterministic, does not reproduce these features. Thus, the stochasticity of platelet interactions is critical for thrombus plasticity, suggesting that interaction via a small number of bonds drives the dynamics of arterial thrombus shell.
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Affiliation(s)
- Valeriia N Kaneva
- Center for Theoretical Problems of Physico-chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Joanne L Dunster
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, University of Reading, Whiteknights, Reading, United Kingdom
| | - Vitaly Volpert
- Institut Camille Jordan, UMR 5208 CNRS, University Lyon 1, Villeurbanne, France; INRIA Team Dracula, INRIA Lyon La Doua, Villeurbanne, France; Peoples Friendship University of Russia (RUDN University), Moscow, Russian Federation
| | - Fazoil Ataullahanov
- Center for Theoretical Problems of Physico-chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia; Dmitry Rogachev National Medical Research Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia; Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia; Faculty of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
| | - Mikhail A Panteleev
- Center for Theoretical Problems of Physico-chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia; Dmitry Rogachev National Medical Research Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia; Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia; Faculty of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
| | - Dmitry Yu Nechipurenko
- Center for Theoretical Problems of Physico-chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia; Dmitry Rogachev National Medical Research Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia; Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia.
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10
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Bayani A, Dunster JL, Crofts JJ, Nelson MR. Spatial considerations in the resolution of inflammation: Elucidating leukocyte interactions via an experimentally-calibrated agent-based model. PLoS Comput Biol 2020; 16:e1008413. [PMID: 33137107 PMCID: PMC7660912 DOI: 10.1371/journal.pcbi.1008413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 11/12/2020] [Accepted: 10/01/2020] [Indexed: 01/13/2023] Open
Abstract
Many common medical conditions (such as cancer, arthritis, chronic obstructive pulmonary disease (COPD), and others) are associated with inflammation, and even more so when combined with the effects of ageing and multimorbidity. While the inflammatory response varies in different tissue types, under disease and in response to therapeutic interventions, it has common interactions that occur between immune cells and inflammatory mediators. Understanding these underlying inflammatory mechanisms is key in progressing treatments and therapies for numerous inflammatory conditions. It is now considered that constituent mechanisms of the inflammatory response can be actively manipulated in order to drive resolution of inflammatory damage; particularly, those mechanisms related to the pro-inflammatory role of neutrophils and the anti-inflammatory role of macrophages. In this article, we describe the assembly of a hybrid mathematical model in which the spatial spread of inflammatory mediators is described through partial differential equations, and immune cells (neutrophils and macrophages) are described individually via an agent-based modelling approach. We pay close attention to how immune cells chemotax toward pro-inflammatory mediators, presenting a model for cell chemotaxis that is calibrated against experimentally observed cell trajectories in healthy and COPD-affected scenarios. We illustrate how variations in key model parameters can drive the switch from resolution of inflammation to chronic outcomes, and show that aberrant neutrophil chemotaxis can move an otherwise healthy outcome to one of chronicity. Finally, we reflect on our results in the context of the on-going hunt for new therapeutic interventions. Inflammation is the body’s primary defence to harmful stimuli such as infections, toxins and tissue strain but also underlies a much broader range of conditions, including asthma, arthritis and cancer. The inflammatory response is key in resolving injury to facilitate recovery, and involves a range of interactions between immune cells (leukocytes, neutrophils and macrophages in particular) and inflammatory mediators. Immune cells are recruited from the blood stream in response to injury. Once in tissue, neutrophils release toxins to kill invading agents and resolve damage; however, if not carefully managed by other immune cells (mainly macrophages), their responses can increase inflammation instead of helping to resolve it. We model these interactions in response to damage using a spatial model, examining how a healthy response can prevent localised inflammation from spreading. We pay close attention to how cells migrate toward the damaged area, as many inflammatory conditions are associated with impairment of this process. We calibrate our model against experimentally-observed cell trajectories from healthy patients and patients with chronic obstructive pulmonary disease. We illustrate that a healthy outcome depends strongly upon efficient cell migration and a delicate balance between the pro- and anti-inflammatory effects of neutrophils and macrophages.
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Affiliation(s)
- Anahita Bayani
- Department of Physics & Mathematics, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS, United Kingdom
| | - Joanne L. Dunster
- Institute for Cardiovascular and Metabolic Research, University of Reading, Reading, RG6 6AS, United Kingdom
| | - Jonathan J. Crofts
- Department of Physics & Mathematics, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS, United Kingdom
| | - Martin R. Nelson
- Department of Physics & Mathematics, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS, United Kingdom
- * E-mail:
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11
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Martyanov AA, Balabin FA, Dunster JL, Panteleev MA, Gibbins JM, Sveshnikova AN. Control of Platelet CLEC-2-Mediated Activation by Receptor Clustering and Tyrosine Kinase Signaling. Biophys J 2020; 118:2641-2655. [PMID: 32396849 DOI: 10.1016/j.bpj.2020.04.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/06/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023] Open
Abstract
Platelets are blood cells responsible for vascular integrity preservation. The activation of platelet receptor C-type lectin-like receptor II-type (CLEC-2) could partially mediate the latter function. Although this receptor is considered to be of importance for hemostasis, the rate-limiting steps of CLEC-2-induced platelet activation are not clear. Here, we aimed to investigate CLEC-2-induced platelet signal transduction using computational modeling in combination with experimental approaches. We developed a stochastic multicompartmental computational model of CLEC-2 signaling. The model described platelet activation beginning with CLEC-2 receptor clustering, followed by Syk and Src family kinase phosphorylation, determined by the cluster size. Active Syk mediated linker adaptor for T cell protein phosphorylation and membrane signalosome formation, which resulted in the activation of Bruton's tyrosine kinase, phospholipase and phosphoinositide-3-kinase, calcium, and phosphoinositide signaling. The model parameters were assessed from published experimental data. Flow cytometry, total internal reflection fluorescence and confocal microscopy, and western blotting quantification of the protein phosphorylation were used for the assessment of the experimental dynamics of CLEC-2-induced platelet activation. Analysis of the model revealed that the CLEC-2 receptor clustering leading to the membrane-based signalosome formation is a critical element required for the accurate description of the experimental data. Both receptor clustering and signalosome formation are among the rate-limiting steps of CLEC-2-mediated platelet activation. In agreement with these predictions, the CLEC-2-induced platelet activation, but not activation mediated by G-protein-coupled receptors, was strongly dependent on temperature conditions and cholesterol depletion. Besides, the model predicted that CLEC-2-induced platelet activation results in cytosolic calcium spiking, which was confirmed by single-platelet total internal reflection fluorescence microscopy imaging. Our results suggest a refined picture of the platelet signal transduction network associated with CLEC-2. We show that tyrosine kinase activation is not the only rate-limiting step in CLEC-2-induced activation of platelets. Translocation of receptor-agonist complexes to the signaling region and linker adaptor for T cell signalosome formation in this region are limiting CLEC-2-induced activation as well.
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Affiliation(s)
- Alexey A Martyanov
- Center for Theoretical Problems of Physico-chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia; Dmitry Rogachev National Medical Research Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia; Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia; Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Fedor A Balabin
- Center for Theoretical Problems of Physico-chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia; Dmitry Rogachev National Medical Research Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Joanne L Dunster
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, Harborne Building, University of Reading, Whiteknights, Reading, United Kingdom
| | - Mikhail A Panteleev
- Center for Theoretical Problems of Physico-chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia; Dmitry Rogachev National Medical Research Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia; Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia; Faculty of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
| | - Jonathan M Gibbins
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, Harborne Building, University of Reading, Whiteknights, Reading, United Kingdom
| | - Anastasia N Sveshnikova
- Center for Theoretical Problems of Physico-chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia; Dmitry Rogachev National Medical Research Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia; Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia; Department of Normal Physiology, Sechenov First Moscow State Medical University, Moscow, Russia.
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12
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Bayani A, Dunster JL, Crofts JJ, Nelson MR. Mechanisms and Points of Control in the Spread of Inflammation: A Mathematical Investigation. Bull Math Biol 2020; 82:45. [PMID: 32222839 PMCID: PMC7103018 DOI: 10.1007/s11538-020-00709-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 02/14/2020] [Indexed: 02/07/2023]
Abstract
Understanding the mechanisms that control the body’s response to inflammation is of key importance, due to its involvement in myriad medical conditions, including cancer, arthritis, Alzheimer’s disease and asthma. While resolving inflammation has historically been considered a passive process, since the turn of the century the hunt for novel therapeutic interventions has begun to focus upon active manipulation of constituent mechanisms, particularly involving the roles of apoptosing neutrophils, phagocytosing macrophages and anti-inflammatory mediators. Moreover, there is growing interest in how inflammatory damage can spread spatially due to the motility of inflammatory mediators and immune cells. For example, impaired neutrophil chemotaxis is implicated in causing chronic inflammation under trauma and in ageing, while neutrophil migration is an attractive therapeutic target in ailments such as chronic obstructive pulmonary disease. We extend an existing homogeneous model that captures interactions between inflammatory mediators, neutrophils and macrophages to incorporate spatial behaviour. Through bifurcation analysis and numerical simulation, we show that spatially inhomogeneous outcomes can present close to the switch from bistability to guaranteed resolution in the corresponding homogeneous model. Finally, we show how aberrant spatial mechanisms can play a role in the failure of inflammation to resolve and discuss our results within the broader context of seeking novel inflammatory treatments.
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Affiliation(s)
- A Bayani
- Department of Physics and Mathematics, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS, UK
| | - J L Dunster
- Institute for Cardiovascular and Metabolic Research, University of Reading, Reading, RG6 6AS, UK
| | - J J Crofts
- Department of Physics and Mathematics, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS, UK
| | - M R Nelson
- Department of Physics and Mathematics, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS, UK.
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Beentjes CHL, Taylor-King JP, Bayani A, Davis CN, Dunster JL, Jabbari S, Mirams GR, Jenkinson C, Kilby MD, Hewison M, Tamblyn JA. Defining vitamin D status using multi-metabolite mathematical modelling: A pregnancy perspective. J Steroid Biochem Mol Biol 2019; 190:152-160. [PMID: 30926429 PMCID: PMC7614536 DOI: 10.1016/j.jsbmb.2019.03.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/11/2019] [Accepted: 03/25/2019] [Indexed: 11/21/2022]
Abstract
Vitamin D deficiency is linked to adverse pregnancy outcomes such as pre-eclampsia (PET) but remains defined by serum measurement of 25-hydroxyvitamin D3 (25(OH)D3) alone. To identify broader changes in vitamin D metabolism during normal and PET pregnancies we developed a relatively simple but fully parametrised mathematical model of the vitamin D metabolic pathway. The data used for parametrisation were serum vitamin D metabolites analysed for a cross-sectional group of women (n = 88); including normal pregnant women at 1 st (NP1, n = 25) and 3rd trimester (NP3, n = 21) and pregnant women with PET (n = 22), as well as non-pregnant female controls (n = 20). To account for the effects various metabolites have upon each other, data were analysed using an ordinary differential equation model of the vitamin D reaction network. Information obtained from the model was then also applied to serum vitamin D metabolome data (n = 50) obtained from a 2nd trimester pregnancy cohort, of which 25 prospectively developed PET. Statistical analysis of the data alone showed no significant difference between NP3 and PET for serum 25(OH)D3 and 24,25(OH)2D3 concentrations. Conversely, a statistical analysis informed by the reaction network model revealed that a better indicator of PET is the ratios of vitamin D metabolites in late pregnancy. Assessing the potential predicative value, no significant difference between NP3 and PET cases at 15 weeks gestation was found. Mathematical modelling offers a novel strategy for defining the impact of vitamin D metabolism on human health. This is particularly relevant within the context of pregnancy, where major changes in vitamin D metabolism occur across gestation, and dysregulated metabolism is evidenced in women with established PET.
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Affiliation(s)
- C H L Beentjes
- Mathematical Institute, University of Oxford, Oxford, UK
| | - J P Taylor-King
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 OAS, UK; Institute of Molecular Systems Biology, Department of Biology, ETHZ, CH-8093, Zurich, Switzerland
| | - A Bayani
- Department of Physics and Mathematics, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - C N Davis
- MathSys CDT, Mathematics Institute, University of Warwick, Coventry, UK
| | - J L Dunster
- Institute for Cardiovascular and Metabolic Research, University of Reading, UK
| | - S Jabbari
- School of Mathematics and Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - G R Mirams
- Centre for Mathematical Medicine & Biology, Mathematical Sciences, University of Nottingham, UK
| | - C Jenkinson
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - M D Kilby
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; Centre for Women's & Newborn Health, Birmingham Health Partners, Birmingham Women's & Children's Foundation Hospital, Edgbaston, Birmingham, UK; Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK; Fetal Medicine Centre, Birmingham Women's & Children's Foundation Trust, Edgbaston, Birmingham, UK
| | - M Hewison
- Centre for Women's & Newborn Health, Birmingham Health Partners, Birmingham Women's & Children's Foundation Hospital, Edgbaston, Birmingham, UK; Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
| | - J A Tamblyn
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; Centre for Women's & Newborn Health, Birmingham Health Partners, Birmingham Women's & Children's Foundation Hospital, Edgbaston, Birmingham, UK; Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK.
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15
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Belyaev AV, Dunster JL, Gibbins JM, Panteleev MA, Volpert V. Advancing research on blood coagulation and thrombosis: Reply to the comments on "Modeling thrombosis in silico: Frontiers, challenges, unresolved problems and milestones". Phys Life Rev 2018; 26-27:116-119. [PMID: 30297158 DOI: 10.1016/j.plrev.2018.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 11/17/2022]
Affiliation(s)
- A V Belyaev
- M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; RUDN University, ul. Miklukho-Maklaya 6, Moscow, 117198, Russia
| | - J L Dunster
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, University of Reading, Berkshire, RG6 6AX, United Kingdom
| | - J M Gibbins
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, University of Reading, Berkshire, RG6 6AX, United Kingdom
| | - M A Panteleev
- M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; National Medical Research Center of Pediatric Hematology, Oncology and Immunology named after Dmitry Rogachev, 117997 Moscow, Russia; Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, 119991, Moscow, Russia; Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - V Volpert
- Institut Camille Jordan, UMR 5208 CNRS, University Lyon 1, 69622 Villeurbanne, France; INRIA Team Dracula, INRIA Lyon La Doua, 69603 Villeurbanne, France; RUDN University, ul. Miklukho-Maklaya 6, Moscow, 117198, Russia.
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16
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Ward JP, Dunster JL, Derks G, Mistry P, Salazar JD. Predicting tyrosinaemia: a mathematical model of 4-hydroxyphenylpyruvate dioxygenase inhibition by nitisinone in rats. Math Med Biol 2017; 34:335-390. [PMID: 27305933 DOI: 10.1093/imammb/dqw006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 02/16/2016] [Indexed: 11/13/2022]
Abstract
Nitisinone or 2-(2-nitro-4-trifluoromethylbenzoyl)cyclohexane-1,3-dione is a reversible inhibitor of 4-hydroxyphenylpyruvate dioxygenase (HPPD), an enzyme important in tyrosine catabolism. Today, nitisinone is successfully used to treat Hereditary Tyrosinaemia type 1, although its original expected role was as a herbicide. In laboratory animals, treatment with nitisinone leads to the elevation of plasma tyrosine (tyrosinaemia). In rats and Beagle dogs, repeat low-dose exposure to nitisinone leads to corneal opacities whilst similar studies in the mouse and Rhesus monkey showed no comparable toxicities or other treatment related findings. The differences in toxicological sensitivities have been related to the upper limit of the concentration of tyrosine that accumulates in plasma, which is driven by the amount/activity of tyrosine aminotransferase. A physiologically based, pharmacodynamics ordinary differential equation model of HPPD inhibition to bolus exposure of nitisinone in vivo is presented. Going beyond traditional approaches, asymptotic analysis is used to separate the different timescales of events involved in HPPD inhibition and tyrosinaemia. This analysis elucidates, in terms of the model parameters, a critical inhibitor concentration (at which tyrosine concentration starts to rise) and highlights the contribution of in vitro measured parameters to events in an in vivo system. Furthermore, using parameter-fitting methods, a systematically derived reduced model is shown to fit well to rat data, making explicit how the parameters are informed by such data. This model in combination with in vitro descriptors has potential as a surrogate for animal experimentation to predict tyrosinaemia, and further development can extend its application to other related medical scenarios.
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Affiliation(s)
- John P Ward
- Department of Mathematical Sciences, Loughborough University, Loughborough LE11 3TU, UK
| | - Joanne L Dunster
- Department of Mathematics & Statistics, University of Reading, Reading RG6 6AX, UK
| | - Gianne Derks
- Department of Mathematics, University of Surrey, Guildford GU2 7XH, UK
| | - Pratibha Mistry
- Product Safety, Syngenta, Jealott's Hill International Research Centre, Bracknell RG42 6EY, UK
| | - José D Salazar
- Product Safety, Syngenta, Jealott's Hill International Research Centre, Bracknell RG42 6EY, UK
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17
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Mazet F, Dunster JL, Jones CI, Vaiyapuri S, Tindall MJ, Fry MJ, Gibbins JM. A high-density immunoblotting methodology for quantification of total protein levels and phosphorylation modifications. Sci Rep 2015; 5:16995. [PMID: 26592927 PMCID: PMC4655314 DOI: 10.1038/srep16995] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/22/2015] [Indexed: 01/04/2023] Open
Abstract
The components of many signaling pathways have been identified and there is now a need to conduct quantitative data-rich temporal experiments for systems biology and modeling approaches to better understand pathway dynamics and regulation. Here we present a modified Western blotting method that allows the rapid and reproducible quantification and analysis of hundreds of data points per day on proteins and their phosphorylation state at individual sites. The approach is of particular use where samples show a high degree of sample-to-sample variability such as primary cells from multiple donors. We present a case study on the analysis of >800 phosphorylation data points from three phosphorylation sites in three signaling proteins over multiple time points from platelets isolated from ten donors, demonstrating the technique's potential to determine kinetic and regulatory information from limited cell numbers and to investigate signaling variation within a population. We envisage the approach being of use in the analysis of many cellular processes such as signaling pathway dynamics to identify regulatory feedback loops and the investigation of potential drug/inhibitor responses, using primary cells and tissues, to generate information about how a cell's physiological state changes over time.
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Affiliation(s)
- F Mazet
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - J L Dunster
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - C I Jones
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - S Vaiyapuri
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - M J Tindall
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - M J Fry
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - J M Gibbins
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
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18
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Dunster JL. The macrophage and its role in inflammation and tissue repair: mathematical and systems biology approaches. Wiley Interdiscip Rev Syst Biol Med 2015; 8:87-99. [PMID: 26459225 DOI: 10.1002/wsbm.1320] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 08/25/2015] [Accepted: 08/28/2015] [Indexed: 02/05/2023]
Abstract
Macrophages are central to the inflammatory response and its ability to resolve effectively. They are complex cells that adopt a range of subtypes depending on the tissue type and stimulus that they find themselves under. This flexibility allows them to play multiple, sometimes opposing, roles in inflammation and tissue repair. Their central role in the inflammatory process is reflected in macrophage dysfunction being implicated in chronic inflammation and poorly healing wounds. In this study, we discuss recent attempts to model mathematically and computationally the macrophage and how it partakes in the complex processes of inflammation and tissue repair. There are increasing data describing the variety of macrophage phenotypes and their underlying transcriptional programs. Dynamic mathematical and computational models are an ideal way to test biological hypotheses against experimental data and could aid in understanding this multi-functional cell and its potential role as an attractive therapeutic target for inflammatory conditions and tissue repair.
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Affiliation(s)
- Joanne L Dunster
- Department of Mathematics and Statistics, University of Reading, Reading, UK.,Institute for Cardiovascular and Metabolic Research and School of Biological Sciences, University of Reading, Reading, UK
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19
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Dunster JL, Byrne HM, King JR. The resolution of inflammation: a mathematical model of neutrophil and macrophage interactions. Bull Math Biol 2014; 76:1953-80. [PMID: 25053556 DOI: 10.1007/s11538-014-9987-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 06/17/2014] [Indexed: 12/17/2022]
Abstract
There is growing interest in inflammation due to its involvement in many diverse medical conditions, including Alzheimer's disease, cancer, arthritis and asthma. The traditional view that resolution of inflammation is a passive process is now being superceded by an alternative hypothesis whereby its resolution is an active, anti-inflammatory process that can be manipulated therapeutically. This shift in mindset has stimulated a resurgence of interest in the biological mechanisms by which inflammation resolves. The anti-inflammatory processes central to the resolution of inflammation revolve around macrophages and are closely related to pro-inflammatory processes mediated by neutrophils and their ability to damage healthy tissue. We develop a spatially averaged model of inflammation centring on its resolution, accounting for populations of neutrophils and macrophages and incorporating both pro- and anti-inflammatory processes. Our ordinary differential equation model exhibits two outcomes that we relate to healthy and unhealthy states. We use bifurcation analysis to investigate how variation in the system parameters affects its outcome. We find that therapeutic manipulation of the rate of macrophage phagocytosis can aid in resolving inflammation but success is critically dependent on the rate of neutrophil apoptosis. Indeed our model predicts that an effective treatment protocol would take a dual approach, targeting macrophage phagocytosis alongside neutrophil apoptosis.
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Affiliation(s)
- J L Dunster
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, University of Reading, Reading, UK,
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