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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; 22:1689-1703. [PMID: 38521192 DOI: 10.1016/j.jtha.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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2
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Shibeko AM, Ilin IS, Podoplelova NA, Sulimov VB, Panteleev MA. Chemical Adjustment of Fibrinolysis. Pharmaceuticals (Basel) 2024; 17:92. [PMID: 38256925 PMCID: PMC10819531 DOI: 10.3390/ph17010092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Fibrinolysis is the process of the fibrin-platelet clot dissolution initiated after bleeding has been stopped. It is regulated by a cascade of proteolytic enzymes with plasmin at its core. In pathological cases, the balance of normal clot formation and dissolution is replaced by a too rapid lysis, leading to bleeding, or an insufficient one, leading to an increased thrombotic risk. The only approved therapy for emergency thrombus lysis in ischemic stroke is recombinant tissue plasminogen activator, though streptokinase or urokinase-type plasminogen activators could be used for other conditions. Low molecular weight compounds are of great interest for long-term correction of fibrinolysis dysfunctions. Their areas of application might go beyond the hematology field because the regulation of fibrinolysis could be important in many conditions, such as fibrosis. They enhance or weaken fibrinolysis without significant effects on other components of hemostasis. Here we will describe and discuss the main classes of these substances and their mechanisms of action. We will also explore avenues of research for the development of new drugs, with a focus on the use of computational models in this field.
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Affiliation(s)
- Alexey M. Shibeko
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 109029 Moscow, Russia; (A.M.S.); (M.A.P.)
- National Medical Research Center of Pediatric Hematology, Oncology and Immunology Named after Dmitry Rogachev, 117197 Moscow, Russia
| | - Ivan S. Ilin
- Research Computing Center, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.S.I.); (V.B.S.)
- Dimonta, Ltd., 117186 Moscow, Russia
| | - Nadezhda A. Podoplelova
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 109029 Moscow, Russia; (A.M.S.); (M.A.P.)
- National Medical Research Center of Pediatric Hematology, Oncology and Immunology Named after Dmitry Rogachev, 117197 Moscow, Russia
| | - Vladimir B. Sulimov
- Research Computing Center, Lomonosov Moscow State University, 119991 Moscow, Russia; (I.S.I.); (V.B.S.)
- Dimonta, Ltd., 117186 Moscow, Russia
| | - Mikhail A. Panteleev
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 109029 Moscow, Russia; (A.M.S.); (M.A.P.)
- National Medical Research Center of Pediatric Hematology, Oncology and Immunology Named after Dmitry Rogachev, 117197 Moscow, Russia
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3
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A Review of Quantitative Systems Pharmacology Models of the Coagulation Cascade: Opportunities for Improved Usability. Pharmaceutics 2023; 15:pharmaceutics15030918. [PMID: 36986779 PMCID: PMC10054658 DOI: 10.3390/pharmaceutics15030918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
Despite the numerous therapeutic options to treat bleeding or thrombosis, a comprehensive quantitative mechanistic understanding of the effects of these and potential novel therapies is lacking. Recently, the quality of quantitative systems pharmacology (QSP) models of the coagulation cascade has improved, simulating the interactions between proteases, cofactors, regulators, fibrin, and therapeutic responses under different clinical scenarios. We aim to review the literature on QSP models to assess the unique capabilities and reusability of these models. We systematically searched the literature and BioModels database reviewing systems biology (SB) and QSP models. The purpose and scope of most of these models are redundant with only two SB models serving as the basis for QSP models. Primarily three QSP models have a comprehensive scope and are systematically linked between SB and more recent QSP models. The biological scope of recent QSP models has expanded to enable simulations of previously unexplainable clotting events and the drug effects for treating bleeding or thrombosis. Overall, the field of coagulation appears to suffer from unclear connections between models and irreproducible code as previously reported. The reusability of future QSP models can improve by adopting model equations from validated QSP models, clearly documenting the purpose and modifications, and sharing reproducible code. The capabilities of future QSP models can improve from more rigorous validation by capturing a broader range of responses to therapies from individual patient measurements and integrating blood flow and platelet dynamics to closely represent in vivo bleeding or thrombosis risk.
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4
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Kholmukhamedov A. Procoagulant Platelets. Platelets 2020. [DOI: 10.5772/intechopen.92638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
There are two well-known subpopulations of activated platelets: pro-aggregatory and procoagulant. Procoagulant platelets represent a subpopulation of activated platelets, which are morphologically and functionally distinct from pro-aggregatory ones. Although various names have been used to describe these platelets in the literature (CoaT, CoaTed, highly activated, ballooned, capped, etc.), there is a consensus on their phenotypic features including exposure of high levels of phosphatidylserine (PSer) on the surface; decreased aggregatory and adhesive properties; support of active tenase and prothrombinase complexes; maximal generation by co-stimulation of glycoprotein VI (GPVI) and protease-activated receptors (PAR). In this chapter, morphologic and functional features of procoagulant platelets, as well as the mechanisms of their formation, will be discussed.
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5
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Nechipurenko DY, Shibeko AM, Sveshnikova AN, Panteleev MA. In Silico Hemostasis Modeling and Prediction. Hamostaseologie 2020; 40:524-535. [PMID: 32916753 DOI: 10.1055/a-1213-2117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Computational physiology, i.e., reproduction of physiological (and, by extension, pathophysiological) processes in silico, could be considered one of the major goals in computational biology. One might use computers to simulate molecular interactions, enzyme kinetics, gene expression, or whole networks of biochemical reactions, but it is (patho)physiological meaning that is usually the meaningful goal of the research even when a single enzyme is its subject. Although exponential rise in the use of computational and mathematical models in the field of hemostasis and thrombosis began in the 1980s (first for blood coagulation, then for platelet adhesion, and finally for platelet signal transduction), the majority of their successful applications are still focused on simulating the elements of the hemostatic system rather than the total (patho)physiological response in situ. Here we discuss the state of the art, the state of the progress toward the efficient "virtual thrombus formation," and what one can already get from the existing models.
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Affiliation(s)
- Dmitry Y Nechipurenko
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia.,Center for Theoretical Problems of Physicochemical Pharmacology of the Russian Academy of Sciences, Moscow, Russia.,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Aleksey M Shibeko
- Center for Theoretical Problems of Physicochemical Pharmacology of the Russian Academy of Sciences, Moscow, Russia.,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anastasia N Sveshnikova
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia.,Center for Theoretical Problems of Physicochemical Pharmacology of the Russian Academy of Sciences, Moscow, Russia.,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Mikhail A Panteleev
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia.,Center for Theoretical Problems of Physicochemical Pharmacology of the Russian Academy of Sciences, Moscow, Russia.,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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Shibeko AM, Chopard B, Hoekstra AG, Panteleev MA. Redistribution of TPA Fluxes in the Presence of PAI-1 Regulates Spatial Thrombolysis. Biophys J 2020; 119:638-651. [PMID: 32653051 DOI: 10.1016/j.bpj.2020.06.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 12/18/2022] Open
Abstract
The fibrin clot is gelatinous matter formed upon injury to stop blood loss and is later destroyed by fibrinolysis, an enzymatic cascade with feedback. Pharmacological fibrinolysis stimulation is also used to destroy pathological, life-threatening clots and thrombi (thrombolysis). The regulation of the nonlinear spatially nonuniform fibrinolytic process in thrombolysis is not currently well understood. We developed a reaction-diffusion-advection model of thrombolysis by tissue plasminogen activator (TPA) in an occluded vessel with a pressure gradient. Sensitivity-analysis-based model reduction was used to reveal the critical processes controlling different steps of thrombolysis. The propagation of thrombolysis in the system without flow was predominantly controlled by TPA diffusion, whereas transport of other active components was rendered nonessential either by their high fibrin-binding parameters and short lifetimes or their initial uniform distribution. The concentration of the main TPA inhibitor plasminogen activator inhibitor 1 (PAI-1) controlled both the extent of lysis propagation and the shape of fibrin spatial distribution during lysis. Interestingly, PAI-1 remained important even when its concentration was an order of magnitude below that of TPA because of its role at the edge of the diffusing TPA front. The system was robust to reaction rate constant perturbations. Using these data, a reduced model of thrombolysis was proposed. In the presence of flow, convection of TPA was the critical controlling process; although the role of PAI-1 concentration was much less in the presence of flow, its influence became greater in the presence of collateral bypassing vessels, which sufficiently reduced TPA flux through the thrombus. Flow bypass through the collateral vessel caused a decrease in TPA flux in the clotted vessel, which increased the PAI-1/TPA ratio, thus making PAI-1-induced inhibition relevant for the regulation of spatial lysis up to its arrest.
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Affiliation(s)
- Alexey M Shibeko
- 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
| | - Bastien Chopard
- Computer Science Department, University of Geneva, Carouge, Switzerland
| | - Alfons G Hoekstra
- Computational Science Lab, Institute for Informatics, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - 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.
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7
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Panteleev MA, Andreeva AA, Lobanov AI. Differential Drug Target Selection in Blood Coagulation: What can we get from Computational Systems Biology Models? Curr Pharm Des 2020; 26:2109-2115. [DOI: 10.2174/1381612826666200406091807] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/01/2020] [Indexed: 12/19/2022]
Abstract
Discovery and selection of the potential targets are some of the important issues in pharmacology.
Even when all the reactions and the proteins in a biological network are known, how does one choose the optimal
target? Here, we review and discuss the application of the computational methods to address this problem using
the blood coagulation cascade as an example. The problem of correct antithrombotic targeting is critical for this
system because, although several anticoagulants are currently available, all of them are associated with bleeding
risks. The advantages and the drawbacks of different sensitivity analysis strategies are considered, focusing on the
approaches that emphasize: 1) the functional modularity and the multi-tasking nature of this biological network;
and 2) the need to normalize hemostasis during the anticoagulation therapy rather than completely suppress it. To
illustrate this effect, we show the possibility of the differential regulation of lag time and endogenous thrombin
potential in the thrombin generation. These methods allow to identify the elements in the blood coagulation cascade
that may serve as the targets for the differential regulation of this system.
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Affiliation(s)
| | - Anna A. Andreeva
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Alexey I. Lobanov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
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8
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Ratto N, Tokarev A, Chelle P, Tardy-Poncet B, Volpert V. Clustering of Thrombin Generation Test Data Using a Reduced Mathematical Model of Blood Coagulation. Acta Biotheor 2020; 68:21-43. [PMID: 31853681 DOI: 10.1007/s10441-019-09372-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 12/04/2019] [Indexed: 11/28/2022]
Abstract
Correct interpretation of the data from integral laboratory tests, including Thrombin Generation Test (TGT), requires biochemistry-based mathematical models of blood coagulation. The purpose of this study is to describe the experimental TGT data from healthy donors and hemophilia A (HA) and B (HB) patients. We derive a simplified ODE model and apply it to analyze the TGT data from healthy donors and HA/HB patients with in vitro added tissue factor pathway inhibitor (TFPI) antibody. This model allows the characterization of hemophilia patients in the space of three most important model parameters. The proposed approach may provide a new quantitative tool for the analysis of experimental TGT. Also, it gives a reduced model of coagulation verified against clinical data to be used in future theoretical large-scale modeling of thrombosis in flow.
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Affiliation(s)
- N Ratto
- Institute Camille Jordan, UMR 5208 CNRS, University Lyon 1, 69622, Villeurbanne, France.
| | - A Tokarev
- Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russian Federation
| | - P Chelle
- Center for Health Engineering, UMR 5307, Ecole Nationale Supérieure des Mines de Saint-Etienne, 42023, Saint-Etienne, France
- Unite Inserm Sainbiose U1059, Université Jean Monnet, 42023, Saint-Etienne, France
| | - B Tardy-Poncet
- Unite Inserm Sainbiose U1059, Université Jean Monnet, 42023, Saint-Etienne, France
- Inserm CIC1408, CHU de Saint-Etienne, 42023, Saint-Etienne, France
- CRC Hémophilie CHU St Etienne, 42023, Saint-Etienne, France
| | - V Volpert
- Institute Camille Jordan, UMR 5208 CNRS, University Lyon 1, 69622, Villeurbanne, France
- Institute Camille Jordan, INRIA, Université de Lyon, Université Lyon 1, 69200, Villeurbanne, France
- Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russian Federation
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9
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Chen J, Diamond SL. Reduced model to predict thrombin and fibrin during thrombosis on collagen/tissue factor under venous flow: Roles of γ'-fibrin and factor XIa. PLoS Comput Biol 2019; 15:e1007266. [PMID: 31381558 PMCID: PMC6695209 DOI: 10.1371/journal.pcbi.1007266] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/15/2019] [Accepted: 07/08/2019] [Indexed: 01/29/2023] Open
Abstract
During thrombosis, thrombin generates fibrin, however fibrin reversibly binds thrombin with low affinity E-domain sites (KD = 2.8 μM) and high affinity γ’-fibrin sites (KD = 0.1 μM). For blood clotting on collagen/tissue factor (1 TF-molecule/μm2) at 200 s-1 wall shear rate, high μM-levels of intraclot thrombin suggest robust prothrombin penetration into clots. Setting intraclot zymogen concentrations to plasma levels (and neglecting cofactor rate limitations) allowed the linearization of 7 Michaelis-Menton reactions between 6 species to simulate intraclot generation of: Factors FXa (via TF/VIIa or FIXa), FIXa (via TF/FVIIa or FXIa), thrombin, fibrin, and FXIa. This reduced model [7 rates, 2 KD’s, enzyme half-lives~1 min] predicted the measured clot elution rate of thrombin-antithrombin (TAT) and fragment F1.2 in the presence and absence of the fibrin inhibitor Gly-Pro-Arg-Pro. To predict intraclot fibrin reaching 30 mg/mL by 15 min, the model required fibrinogen penetration into the clot to be strongly diffusion-limited (actual rate/ideal rate = 0.05). The model required free thrombin in the clot (~100 nM) to have an elution half-life of ~2 sec, consistent with measured albumin elution, with most thrombin (>99%) being fibrin-bound. Thrombin-feedback activation of FXIa became prominent and reached 5 pM FXIa at >500 sec in the simulation, consistent with anti-FXIa experiments. In predicting intrathrombus thrombin and fibrin during 15-min microfluidic experiments, the model revealed “cascade amplification” from 30 pM levels of intrinsic tenase to 15 nM prothrombinase to 15 μM thrombin to 90 μM fibrin. Especially useful for multiscale simulation, this reduced model predicts thrombin and fibrin co-regulation during thrombosis under flow. During blood clotting events, a complex series of reaction are involved. Simulation gives insights to the concentration of different enzymes which are at too low of concentration to be detected. However, the models are often large and difficult to solve for clotting under flow conditions. With a thin film approximation, we were able to simplify clotting under flow with parameters from literature, with only 3 adjusted in order to fit the experimental data. This model gave insights into the dynamics of the species involved, and the roles of γ’-fibrin and thrombin feedback activation. This reduced model may be useful in further multiscale simulations.
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Affiliation(s)
- Jason Chen
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Scott L. Diamond
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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10
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Rat liver folate metabolism can provide an independent functioning of associated metabolic pathways. Sci Rep 2019; 9:7657. [PMID: 31113966 PMCID: PMC6529478 DOI: 10.1038/s41598-019-44009-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/30/2019] [Indexed: 11/27/2022] Open
Abstract
Folate metabolism in mammalian cells is essential for multiple vital processes, including purine and pyrimidine synthesis, histidine catabolism, methionine recycling, and utilization of formic acid. It remains unknown, however, whether these processes affect each other via folate metabolism or can function independently based on cellular needs. We addressed this question using a quantitative mathematical model of folate metabolism in rat liver cytoplasm. Variation in the rates of metabolic processes associated with folate metabolism (i.e., purine and pyrimidine synthesis, histidine catabolism, and influxes of formate and methionine) in the model revealed that folate metabolism is organized in a striking manner that enables activation or inhibition of each individual process independently of the metabolic fluxes in others. In mechanistic terms, this independence is based on the high activities of a group of enzymes involved in folate metabolism, which efficiently maintain close-to-equilibrium ratios between substrates and products of enzymatic reactions.
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Kuprash AD, Shibeko AM, Vijay R, Nair SC, Srivastava A, Ataullakhanov FI, Panteleev MA, Balandina AN. Sensitivity and Robustness of Spatially Dependent Thrombin Generation and Fibrin Clot Propagation. Biophys J 2018; 115:2461-2473. [PMID: 30514632 DOI: 10.1016/j.bpj.2018.11.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 10/25/2018] [Accepted: 11/05/2018] [Indexed: 11/25/2022] Open
Abstract
Blood coagulation is a delicately regulated space- and time-dependent process that leads to the formation of fibrin clots preventing blood loss upon vascular injury. The sensitivity of the coagulation network was previously investigated without accounting for transport processes. To investigate its sensitivity to coagulation factor deficiencies in a spatial reaction-diffusion system, we combined an in vitro experimental design with a computational systems biology model. Clot formation in platelet-free plasma supplemented with phospholipids was activated with identical amounts of tissue factor (TF) either homogeneously distributed (concentration 5 pM, homogeneous model) or immobilized on the surface (surface density 100 pmole/m2, spatially heterogeneous model). Fibrin clot growth and thrombin concentration dynamic in space were observed using video microscopy in plasma of healthy donors or patients with deficiencies in factors (F) II, FV, FVII, FVIII, FIX, FX, or FXI. In the spatially heterogeneous model, near-activator thrombin generation was decreased in FV-, FVII-, and FX-deficient plasma. In the homogeneous model, clotting was not registered in these samples. The simulation and experiment data showed that the coagulation threshold depended on the TF concentration. Our data indicate that the velocity of spatial clot propagation correlates linearly with the concentration of thrombin at the clot wave front but not with the overall thrombin wave amplitude. Spatial clot growth in normal plasma at early stages was neither reaction nor diffusion limited but became diffusion limited later. In contrast, clot growth was always diffusion limited in FV-, FVII-, and FX-deficient plasma and reaction limited in FVIII-, FIX-, and FXI-deficient plasma. We conclude that robustness of the spatially heterogeneous coagulation system was achieved because of the combination of 1) a local high TF surface density that overcomes activation thresholds, 2) diffusion control being shared between different active factors, and 3) an early saturated stimulus-response dependence of fibrin clot formation by thrombin.
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Affiliation(s)
- Anna D Kuprash
- Center for Theoretical Problems of Physicochemical Pharmacology RAS, Moscow, Russia; Department of Biophysics and Systems Biology, National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexey M Shibeko
- Center for Theoretical Problems of Physicochemical Pharmacology RAS, Moscow, Russia; Department of Biophysics and Systems Biology, National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Ramya Vijay
- Department of Haematology, Christian Medical College, Vellore, India
| | - Sukesh C Nair
- Department of Haematology, Christian Medical College, Vellore, India
| | - Alok Srivastava
- Department of Haematology, Christian Medical College, Vellore, India
| | - Fazoil I Ataullakhanov
- Center for Theoretical Problems of Physicochemical Pharmacology RAS, Moscow, Russia; Department of Biophysics and Systems Biology, National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia; Department of Physics, Lomonosov Moscow State University, Moscow, Russia; Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mikhail A Panteleev
- Center for Theoretical Problems of Physicochemical Pharmacology RAS, Moscow, Russia; Department of Biophysics and Systems Biology, National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia; Department of Physics, Lomonosov Moscow State University, Moscow, Russia; Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - Anna N Balandina
- Center for Theoretical Problems of Physicochemical Pharmacology RAS, Moscow, Russia; Department of Biophysics and Systems Biology, National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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12
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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] [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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Evaluation and Calibration of In Silico Models of Thrombin Generation Using Experimental Data from Healthy and Haemophilic Subjects. Bull Math Biol 2018; 80:1989-2025. [DOI: 10.1007/s11538-018-0440-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 04/20/2018] [Indexed: 01/17/2023]
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14
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Modeling thrombosis in silico: Frontiers, challenges, unresolved problems and milestones. Phys Life Rev 2018; 26-27:57-95. [PMID: 29550179 DOI: 10.1016/j.plrev.2018.02.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/21/2018] [Accepted: 02/24/2018] [Indexed: 12/24/2022]
Abstract
Hemostasis is a complex physiological mechanism that functions to maintain vascular integrity under any conditions. Its primary components are blood platelets and a coagulation network that interact to form the hemostatic plug, a combination of cell aggregate and gelatinous fibrin clot that stops bleeding upon vascular injury. Disorders of hemostasis result in bleeding or thrombosis, and are the major immediate cause of mortality and morbidity in the world. Regulation of hemostasis and thrombosis is immensely complex, as it depends on blood cell adhesion and mechanics, hydrodynamics and mass transport of various species, huge signal transduction networks in platelets, as well as spatiotemporal regulation of the blood coagulation network. Mathematical and computational modeling has been increasingly used to gain insight into this complexity over the last 30 years, but the limitations of the existing models remain profound. Here we review state-of-the-art-methods for computational modeling of thrombosis with the specific focus on the analysis of unresolved challenges. They include: a) fundamental issues related to physics of platelet aggregates and fibrin gels; b) computational challenges and limitations for solution of the models that combine cell adhesion, hydrodynamics and chemistry; c) biological mysteries and unknown parameters of processes; d) biophysical complexities of the spatiotemporal networks' regulation. Both relatively classical approaches and innovative computational techniques for their solution are considered; the subjects discussed with relation to thrombosis modeling include coarse-graining, continuum versus particle-based modeling, multiscale models, hybrid models, parameter estimation and others. Fundamental understanding gained from theoretical models are highlighted and a description of future prospects in the field and the nearest possible aims are given.
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Zhalyalov AS, Panteleev MA, Gracheva MA, Ataullakhanov FI, Shibeko AM. Co-ordinated spatial propagation of blood plasma clotting and fibrinolytic fronts. PLoS One 2017; 12:e0180668. [PMID: 28686711 PMCID: PMC5501595 DOI: 10.1371/journal.pone.0180668] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/19/2017] [Indexed: 11/20/2022] Open
Abstract
Fibrinolysis is a cascade of proteolytic reactions occurring in blood and soft tissues, which functions to disintegrate fibrin clots when they are no more needed. In order to elucidate its regulation in space and time, fibrinolysis was investigated using an in vitro reaction-diffusion experimental model of blood clot formation and dissolution. Clotting was activated by a surface with immobilized tissue factor in a thin layer of recalcified blood plasma supplemented with tissue plasminogen activator (TPA), urokinase plasminogen activator or streptokinase. Formation and dissolution of fibrin clot was monitored by videomicroscopy. Computer systems biology model of clot formation and lysis was developed for data analysis and experimental planning. Fibrin clot front propagated in space from tissue factor, followed by a front of clot dissolution propagating from the same source. Velocity of lysis front propagation linearly depended on the velocity clotting front propagation (correlation r2 = 0.91). Computer model revealed that fibrin formation was indeed the rate-limiting step in the fibrinolysis front propagation. The phenomenon of two fronts which switched the state of blood plasma from liquid to solid and then back to liquid did not depend on the fibrinolysis activator. Interestingly, TPA at high concentrations began to increase lysis onset time and to decrease lysis propagation velocity, presumably due to plasminogen depletion. Spatially non-uniform lysis occurred simultaneously with clot formation and detached the clot from the procoagulant surface. These patterns of spatial fibrinolysis provide insights into its regulation and might explain clinical phenomena associated with thrombolytic therapy.
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Affiliation(s)
- Ansar S. Zhalyalov
- Center for Theoretical Problems of Physicochemical Pharmacology RAS, Moscow, Russia
| | - Mikhail A. Panteleev
- Center for Theoretical Problems of Physicochemical Pharmacology RAS, Moscow, Russia
- National Scientific and Practical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Department of Physics, Moscow State University, Moscow, Russia
- Faculty of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Marina A. Gracheva
- National Scientific and Practical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Fazoil I. Ataullakhanov
- Center for Theoretical Problems of Physicochemical Pharmacology RAS, Moscow, Russia
- National Scientific and Practical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Department of Physics, Moscow State University, Moscow, Russia
- Faculty of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey M. Shibeko
- Center for Theoretical Problems of Physicochemical Pharmacology RAS, Moscow, Russia
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Podoplelova NA, Sveshnikova AN, Kurasawa JH, Sarafanov AG, Chambost H, Vasil'ev SA, Demina IA, Ataullakhanov FI, Alessi MC, Panteleev MA. Hysteresis-like binding of coagulation factors X/Xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1216-27. [DOI: 10.1016/j.bbamem.2016.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 01/20/2016] [Accepted: 02/09/2016] [Indexed: 10/22/2022]
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The effect of continuous elimination methods on the hemostatic profile of a cardiac surgery patient monitored using thromboelastography. Int J Artif Organs 2016; 39:106-13. [PMID: 27102694 DOI: 10.5301/ijao.5000490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2016] [Indexed: 11/20/2022]
Abstract
INTRODUCTION This work is focused on mapping issues of hemostasis in patients during continuous renal replacement therapy, or the possible impact of the use of anticoagulants. METHODS The study included 30 consecutive patients requiring continuous renal replacement therapy following cardiac surgery in the period of 2009 to 2012. Patients were placed into 2 branches according to the selected method of anticoagulation (regional citrate anticoagulation-RCA, unfractionated heparin UFH). According to the given scheme (t1-t7) thromboelastography and laboratory testing related to the testing of blood clotting during continuous renal replacement therapy were performed. RESULTS The average lifespan of a hemofilter during continuous renal replacement is 58.13 ± 9.968 hours. During continuous renal replacement therapy there are significant changes in the initiation of coagulation according to thromboelastographic parameters (R, K, alpha angle) in both branches of anticoagulation. The maximum image changes in hemostasis occur around 24 hours (t4) from the start of the procedure. The nature of the changes is the procoagulant activity in these parameters. In the branch of regional citrate anticoagulation a higher value of functional fibrinogen is apparent. There was no significant difference in the activation of native blood between UFH and RCA. CONCLUSIONS During continuous renal replacement therapy significant changes occur in the thromboelastographic image and the laboratory parameters in blood clotting. The nature of the change is the procoagulant activity. The question remains about the complexity of the changes that TEG is not able to detect, especially in the cellular area.
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Identification and Management of Pump Thrombus in the HeartWare Left Ventricular Assist Device System: A Novel Approach Using Log File Analysis. JACC-HEART FAILURE 2015; 3:849-56. [PMID: 26454842 DOI: 10.1016/j.jchf.2015.06.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/29/2015] [Accepted: 06/03/2015] [Indexed: 11/20/2022]
Abstract
OBJECTIVES The study sought to characterize patterns in the HeartWare (HeartWare Inc., Framingham, Massachusetts) ventricular assist device (HVAD) log files associated with successful medical treatment of device thrombosis. BACKGROUND Device thrombosis is a serious adverse event for mechanical circulatory support devices and is often preceded by increased power consumption. Log files of the pump power are easily accessible on the bedside monitor of HVAD patients and may allow early diagnosis of device thrombosis. Furthermore, analysis of the log files may be able to predict the success rate of thrombolysis or the need for pump exchange. METHODS The log files of 15 ADVANCE trial patients (algorithm derivation cohort) with 16 pump thrombus events treated with tissue plasminogen activator (tPA) were assessed for changes in the absolute and rate of increase in power consumption. Successful thrombolysis was defined as a clinical resolution of pump thrombus including normalization of power consumption and improvement in biochemical markers of hemolysis. Significant differences in log file patterns between successful and unsuccessful thrombolysis treatments were verified in 43 patients with 53 pump thrombus events implanted outside of clinical trials (validation cohort). RESULTS The overall success rate of tPA therapy was 57%. Successful treatments had significantly lower measures of percent of expected power (130.9% vs. 196.1%, p = 0.016) and rate of increase in power (0.61 vs. 2.87, p < 0.0001). Medical therapy was successful in 77.7% of the algorithm development cohort and 81.3% of the validation cohort when the rate of power increase and percent of expected power values were <1.25% and 200%, respectively. CONCLUSIONS Log file parameters can potentially predict the likelihood of successful tPA treatments and if validated prospectively, could substantially alter the approach to thrombus management.
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Panteleev MA, Dashkevich NM, Ataullakhanov FI. Hemostasis and thrombosis beyond biochemistry: roles of geometry, flow and diffusion. Thromb Res 2015; 136:699-711. [DOI: 10.1016/j.thromres.2015.07.025] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/22/2015] [Accepted: 07/26/2015] [Indexed: 11/16/2022]
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Shibeko AM, Panteleev MA. Untangling the complexity of blood coagulation network: use of computational modelling in pharmacology and diagnostics. Brief Bioinform 2015; 17:429-39. [DOI: 10.1093/bib/bbv040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 01/22/2023] Open
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Monteiro JP, Wise C, Morine MJ, Teitel C, Pence L, Williams A, McCabe-Sellers B, Champagne C, Turner J, Shelby B, Ning B, Oguntimein J, Taylor L, Toennessen T, Priami C, Beger RD, Bogle M, Kaput J. Methylation potential associated with diet, genotype, protein, and metabolite levels in the Delta Obesity Vitamin Study. GENES & NUTRITION 2014; 9:403. [PMID: 24760553 PMCID: PMC4026438 DOI: 10.1007/s12263-014-0403-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 04/06/2014] [Indexed: 12/28/2022]
Abstract
Micronutrient research typically focuses on analyzing the effects of single or a few nutrients on health by analyzing a limited number of biomarkers. The observational study described here analyzed micronutrients, plasma proteins, dietary intakes, and genotype using a systems approach. Participants attended a community-based summer day program for 6-14 year old in 2 years. Genetic makeup, blood metabolite and protein levels, and dietary differences were measured in each individual. Twenty-four-hour dietary intakes, eight micronutrients (vitamins A, D, E, thiamin, folic acid, riboflavin, pyridoxal, and pyridoxine) and 3 one-carbon metabolites [homocysteine (Hcy), S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH)], and 1,129 plasma proteins were analyzed as a function of diet at metabolite level, plasma protein level, age, and sex. Cluster analysis identified two groups differing in SAM/SAH and differing in dietary intake patterns indicating that SAM/SAH was a potential marker of nutritional status. The approach used to analyze genetic association with the SAM/SAH metabolites is called middle-out: SNPs in 275 genes involved in the one-carbon pathway (folate, pyridoxal/pyridoxine, thiamin) or were correlated with SAM/SAH (vitamin A, E, Hcy) were analyzed instead of the entire 1M SNP data set. This procedure identified 46 SNPs in 25 genes associated with SAM/SAH demonstrating a genetic contribution to the methylation potential. Individual plasma metabolites correlated with 99 plasma proteins. Fourteen proteins correlated with body mass index, 49 with group age, and 30 with sex. The analytical strategy described here identified subgroups for targeted nutritional interventions.
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Affiliation(s)
- Jacqueline Pontes Monteiro
- />Department of Pediatrics, Faculty of Medicine, Faculty of Nutrition and Metabolism, University of São Paulo, Ribeirão Prêto, SP Brazil
| | - Carolyn Wise
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Melissa J. Morine
- />Department of Mathematics, University of Trento, Trento, Italy
- />The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Candee Teitel
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Lisa Pence
- />Division of Systems Biology, NCTR/FDA, Jefferson, AR USA
| | - Anna Williams
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Beverly McCabe-Sellers
- />Delta Obesity Prevention Research Unit, United States Department of Agriculture, Agricultural Research Service, Little Rock, AR USA
| | - Catherine Champagne
- />Dietary Assessment and Nutrition Counseling, Pennington Biomedical Research Center, Baton Rouge, LA USA
| | - Jerome Turner
- />Boys, Girls, Adults Community Development Center & The Phillips County Community Partners, Marvell, AR USA
| | - Beatrice Shelby
- />Boys, Girls, Adults Community Development Center & The Phillips County Community Partners, Marvell, AR USA
| | - Baitang Ning
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Joan Oguntimein
- />Shepherd Program for the Interdisciplinary Study of Poverty and Human Capability, Washington and Lee University, Lexington, VA USA
- />Medical School, Drexel University, Philadelphia, PA USA
| | - Lauren Taylor
- />Shepherd Program for the Interdisciplinary Study of Poverty and Human Capability, Washington and Lee University, Lexington, VA USA
- />Emory School of Public Health, Atlanta, GA USA
| | - Terri Toennessen
- />Division of Personalized Nutrition and Medicine, National Center for Toxicological Research (NCTR), Food and Drug Administration (FDA), Jefferson, AR USA
| | - Corrado Priami
- />Department of Mathematics, University of Trento, Trento, Italy
- />The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | | | - Margaret Bogle
- />Delta Obesity Prevention Research Unit, United States Department of Agriculture, Agricultural Research Service, Little Rock, AR USA
| | - Jim Kaput
- />Systems Nutrition and Health Unit, Nestle Institute of Health Sciences, Innovation Square, EPFL Campus, 1015 Lausanne, Switzerland
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Pogorelova EA, Lobanov AI. Influence of enzymatic reactions on blood coagulation autowave. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350914010151] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Lipets E, Vlasova O, Urnova E, Margolin O, Soloveva A, Ostapushchenko O, Andersen J, Ataullakhanov F, Panteleev M. Circulating contact-pathway-activating microparticles together with factors IXa and XIa induce spontaneous clotting in plasma of hematology and cardiologic patients. PLoS One 2014; 9:e87692. [PMID: 24498168 PMCID: PMC3909194 DOI: 10.1371/journal.pone.0087692] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 01/02/2014] [Indexed: 11/19/2022] Open
Abstract
Background and Objective Using an in vitro experimental model of immobilized tissue factor-initiated clot growth in platelet-free plasma (thrombodynamics), we observed formation of activator-independent isolated spontaneous clots (SC) throughout the plasma volume in patients with cardiac infarction, acute leukemia, hemolytic anemia, and some other disorders. The aim of this work was to characterize this phenomenon and to identify the mechanisms of SC formation. Methods and Results Tissue factor inhibitor (VIIai) prevented SC in only 2 out of 23 patient plasma samples. Specific inhibitors of factors IXa and XIa were efficient in all 8 cases that we tested. Also, only factors IXa and XIa added to normal donors’ plasma induced SC formations from isolated centers, in a pattern similar to that in patients’ plasma. In contrast, factors VIIa, Va, tissue factor induced uniform plasma clotting. SC disappeared after high-speed centrifugation. However, phospholipid supplementation of centrifuged plasma returned them at least partially in 5 out of 22 patients’ plasmas, indicating some other role of microparticles than providing phospholipid surface. Circulating procoagulant microparticles isolated from plasma directly activated factor XII in buffer and in diluted plasma. Flow cytometry revealed an increase in procoagulant microparticles in patients’ plasmas with SC. Conclusion Our data suggest that combination of circulating active factors (specifically, factors IXa and XIa) with circulating procoagulant and contact-pathway-activating microparticles is the predominant mechanism causing spontaneous clotting in patient plasma.
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Affiliation(s)
- Elena Lipets
- Federal Research and Clinical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- HemaCore LLC, Moscow, Russia
| | - Olga Vlasova
- Lomonosov Moscow State University, Moscow, Russia
| | - Evdokiya Urnova
- National Research Center for Hematology, Health Ministry RF, Moscow, Russia
| | - Oleg Margolin
- National Research Center for Hematology, Health Ministry RF, Moscow, Russia
| | - Anna Soloveva
- National Research Center for Hematology, Health Ministry RF, Moscow, Russia
| | | | - John Andersen
- National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Fazoil Ataullakhanov
- Federal Research and Clinical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- HemaCore LLC, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
- National Research Center for Hematology, Health Ministry RF, Moscow, Russia
- Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Panteleev
- Federal Research and Clinical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- HemaCore LLC, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
- National Research Center for Hematology, Health Ministry RF, Moscow, Russia
- Center for Theoretical Problems of Physico-Chemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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Parunov LA, Soshitova NP, Fadeeva OA, Balandina AN, Kopylov KG, Kumskova MA, Gilbert JC, Schaub RG, McGinness KE, Ataullakhanov FI, Panteleev MA. Drug-drug interaction of the anti-TFPI aptamer BAX499 and factor VIII: studies of spatial dynamics of fibrin clot formation in hemophilia A. Thromb Res 2013; 133:112-9. [PMID: 24263002 DOI: 10.1016/j.thromres.2013.10.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND In recent years, a number of tissue factor pathway inhibitor (TFPI) antagonists have been developed to serve as bypassing agents to improve hemostasis in hemophilia A. Since TFPI antagonists and FVIII concentrates are procoagulants, their combined effect on spatial clot formation could be potentially pro-thrombotic. OBJECTIVE To investigate the cooperative effect of TFPI inhibition and supplementation of FVIII in hemophilia A in a spatial, reaction-diffusion experiment in vitro. METHODS Plasma was collected at different time points from hemophilia A patients undergoing prophylaxis and was supplemented in vitro with TFPI inhibitor BAX499 (formerly ARC19499) at concentrations from 0 up to 600nM. Clotting propagation in recalcified plasma activated by a surface with immobilized tissue factor (TF) was monitored by videomicroscopy. RESULTS Increasing concentration of BAX499 improved coagulation for all hemophilia A plasma samples activated with TF at 1.6pmole/m(2) by shortening lag time and increasing initial clot growth velocity and clot size. In contrast, plasma concentration of FVIII had little effect on lag time, but increased spatial clot growth velocity. There was a decrease in the BAX499 efficiency as FVIII concentration increased (lag time shortened by 50% if FVIII:C<5%, but the effect was only 25% if FVIII:C>30%). CONCLUSIONS The results indicate that BAX499 has an effect on clotting in hemophilia A plasma at low FVIII concentrations, however has little effect at high FVIII concentrations.
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Affiliation(s)
- Leonid A Parunov
- Center for Theoretical Problems of Physicochemical Pharmacology, 4 Kosygina Street, Moscow 119991, Russia.
| | - Natalia P Soshitova
- National Research Center for Hematology, 4 Novyi Zykovskii Passage, Moscow 125167, Russia
| | - Olga A Fadeeva
- National Research Center for Hematology, 4 Novyi Zykovskii Passage, Moscow 125167, Russia
| | - Anna N Balandina
- Center for Theoretical Problems of Physicochemical Pharmacology, 4 Kosygina Street, Moscow 119991, Russia; National Research Center for Hematology, 4 Novyi Zykovskii Passage, Moscow 125167, Russia; Center of Pediatric Hematology, Oncology and Immunology, 1 Samora Mashely, Moscow , Russia
| | - Konstantin G Kopylov
- National Research Center for Hematology, 4 Novyi Zykovskii Passage, Moscow 125167, Russia; Center of Pediatric Hematology, Oncology and Immunology, 1 Samora Mashely, Moscow , Russia
| | - Maria A Kumskova
- National Research Center for Hematology, 4 Novyi Zykovskii Passage, Moscow 125167, Russia; Center of Pediatric Hematology, Oncology and Immunology, 1 Samora Mashely, Moscow , Russia
| | | | | | | | - Fazoil I Ataullakhanov
- Center for Theoretical Problems of Physicochemical Pharmacology, 4 Kosygina Street, Moscow 119991, Russia; National Research Center for Hematology, 4 Novyi Zykovskii Passage, Moscow 125167, Russia; Center of Pediatric Hematology, Oncology and Immunology, 1 Samora Mashely, Moscow , Russia; Department of Physics, Moscow State University, 1 Vorobyevy Gory, Moscow 119991, Russia
| | - Mikhail A Panteleev
- Center for Theoretical Problems of Physicochemical Pharmacology, 4 Kosygina Street, Moscow 119991, Russia; National Research Center for Hematology, 4 Novyi Zykovskii Passage, Moscow 125167, Russia; Center of Pediatric Hematology, Oncology and Immunology, 1 Samora Mashely, Moscow , Russia; Department of Physics, Moscow State University, 1 Vorobyevy Gory, Moscow 119991, Russia
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Modelling of thrombus growth in flow with a DPD-PDE method. J Theor Biol 2013; 337:30-41. [DOI: 10.1016/j.jtbi.2013.07.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 05/24/2013] [Accepted: 07/22/2013] [Indexed: 11/22/2022]
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Ataullakhanov FI, Melnik KS, Butylin AA. Molecular self-organization and multiple equilibrium systems. Biophysics (Nagoya-shi) 2013. [DOI: 10.1134/s0006350913010028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Stern MD. Coagulation makes waves. Biophys J 2012. [PMID: 23200038 DOI: 10.1016/j.bpj.2012.09.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Michael D Stern
- National Institute on Aging, Gerontology Research Center, National Institutes of Health, Baltimore, MD, USA.
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Abstract
Injury-induced bleeding is stopped by a hemostatic plug formation that is controlled by a complex nonlinear and spatially heterogeneous biochemical network of proteolytic enzymes called blood coagulation. We studied spatial dynamics of thrombin, the central enzyme of this network, by developing a fluorogenic substrate-based method for time- and space-resolved imaging of thrombin enzymatic activity. Clotting stimulation by immobilized tissue factor induced localized thrombin activity impulse that propagated in space and possessed all characteristic traits of a traveling excitation wave: constant spatial velocity, constant amplitude, and insensitivity to the initial stimulation once it exceeded activation threshold. The parameters of this traveling wave were controlled by the availability of phospholipids or platelets, and the wave did not form in plasmas from hemophilia A or C patients who lack factors VIII and XI, which are mediators of the two principal positive feedbacks of coagulation. Stimulation of the negative feedback of the protein C pathway with thrombomodulin produced nonstationary patterns of wave formation followed by deceleration and annihilation. This indicates that blood can function as an excitable medium that conducts traveling waves of coagulation.
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Hemker HC, Kerdelo S, Kremers RMW. Is there value in kinetic modeling of thrombin generation? No (unless…). J Thromb Haemost 2012; 10:1470-7. [PMID: 22650179 DOI: 10.1111/j.1538-7836.2012.04802.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- H C Hemker
- Synapse BV, Cardiovascular Research Institute, Maastricht University, Maastricht, the Netherlands.
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Positive feedback loops for factor V and factor VII activation supply sensitivity to local surface tissue factor density during blood coagulation. Biophys J 2012; 101:1816-24. [PMID: 22004734 DOI: 10.1016/j.bpj.2011.08.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Revised: 07/12/2011] [Accepted: 08/09/2011] [Indexed: 11/22/2022] Open
Abstract
Blood coagulation is triggered not only by surface tissue factor (TF) density but also by surface TF distribution. We investigated recognition of surface TF distribution patterns during blood coagulation and identified the underlying molecular mechanisms. For these investigations, we employed 1), an in vitro reaction-diffusion experimental model of coagulation; and 2), numerical simulations using a mathematical model of coagulation in a three-dimensional space. When TF was uniformly immobilized over the activating surface, the clotting initiation time in normal plasma increased from 4 min to >120 min, with a decrease in TF density from 100 to 0.7 pmol/m(2). In contrast, surface-immobilized fibroblasts initiated clotting within 3-7 min, independently of fibroblast quantity and despite a change in average surface TF density from 0.5 to 130 pmol/m(2). Experiments using factor V-, VII-, and VIII-deficient plasma and computer simulations demonstrated that different responses to these two TF distributions are caused by two positive feedback loops in the blood coagulation network: activation of the TF-VII complex by factor Xa, and activation of factor V by thrombin. This finding suggests a new role for these reactions: to supply sensitivity to local TF density during blood coagulation.
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Topalov NN, Kotova YN, Vasil’ev SA, Panteleev MA. Identification of signal transduction pathways involved in the formation of platelet subpopulations upon activation. Br J Haematol 2012; 157:105-15. [DOI: 10.1111/j.1365-2141.2011.09021.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Parunov LA, Fadeeva OA, Balandina AN, Soshitova NP, Kopylov KG, Kumskova MA, Gilbert JC, Schaub RG, McGinness KE, Ataullakhanov FI, Panteleev MA. Improvement of spatial fibrin formation by the anti-TFPI aptamer BAX499: changing clot size by targeting extrinsic pathway initiation. J Thromb Haemost 2011; 9:1825-34. [PMID: 21696535 DOI: 10.1111/j.1538-7836.2011.04412.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Tissue factor pathway inhibitor (TFPI) is a major regulator of clotting initiation and a promising target for pro- and anticoagulation therapy. The aptamer BAX499 (formerly ARC19499) is a high-affinity specific TFPI antagonist designed to improve hemostasis. However, it is not clear how stimulation of coagulation onset by inactivating TFPI will affect spatial and temporal clot propagation. OBJECTIVE To examine the BAX499 effect on clotting in a spatial, reaction-diffusion experimental system in comparison with that of recombinant activated factor VII (rVIIa). METHODS Clotting in plasma activated by immobilized tissue factor (TF) was monitored by videomicroscopy. RESULTS BAX499 dose-dependently improved coagulation in normal and hemophilia A plasma activated with TF at 2 pmole m(-2) by shortening lag time and increasing clot size by up to ~2-fold. The effect was TFPI specific as confirmed by experiments in TFPI-depleted plasma with or without TFPI supplementation. Clotting improvement was half-maximal at 0.7 nm of BAX499 and reached a plateau at 10 nm, remaining there at concentrations up to 1000 nm. The BAX499 effect decreased with TF surface density increase. RVIIa improved clotting in hemophilia A plasma activated with TF at 2 or 20 pmole m(-2) , both by shortening lag time and increasing spatial velocity of clot propagation; its effects were strongly concentration dependent. CONCLUSIONS BAX499 significantly improves spatial coagulation by inhibiting TFPI in a spatially localized manner that is different to that observed with rVIIa.
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Affiliation(s)
- L A Parunov
- Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
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