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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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Smith BT, Hashmi SM. In situ polymer gelation in confined flow controls intermittent dynamics. SOFT MATTER 2024; 20:1858-1868. [PMID: 38315155 DOI: 10.1039/d3sm01389h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Polymer flows through pores, nozzles and other small channels govern engineered and naturally occurring dynamics in many processes, from 3D printing to oil recovery in the earth's subsurface to a wide variety of biological flows. The crosslinking of polymers can change their material properties dramatically, and it is advantageous to know a priori whether or not crosslinking polymers will lead to clogged channels or cessation of flow. In this study, we investigate the flow of a common biopolymer, alginate, while it undergoes crosslinking by the addition of a crosslinker, calcium, driven through a microfluidic channel at constant flow rate. We map the boundaries defining complete clogging and flow as a function of flow rate, polymer concentration, and crosslinker concentration. Interestingly, the boundaries of the dynamic behavior qualitatively match the thermodynamic jamming phase diagram of attractive colloidal particles. That is, polymer clogging occurs in a region analogous to colloids in a jammed state, while the polymer flows in regions corresponding to colloids in a liquid phase. However, between the dynamic regimes of complete clogging and unrestricted flow, we observe a remarkable phenomenon in which the crosslinked polymer intermittently clogs the channel. This pattern of deposition and removal of a crosslinked gel is simultaneously highly reproducible, long-lasting, and controllable by system parameters. Higher concentrations of polymer and cross-linker result in more frequent ablation, while gels formed at lower component concentrations ablate less frequently. Upon ablation, the eluted gel maintains its shape, resulting in micro-rods several hundred microns long. Our results suggest both rich dynamics of intermittent flows in crosslinking polymers and the ability to control them.
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Affiliation(s)
- Barrett T Smith
- Department of Chemical Engineering, Northeastern University, USA.
| | - Sara M Hashmi
- Department of Chemical Engineering, Northeastern University, USA.
- Department of Mechanical & Industrial Engineering, Northeastern University, USA
- Department of Chemistry & Chemical Biology, Northeastern University, USA
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3
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Macleod Briongos I, Call ZD, Henry CS, Bark DL. Maximizing flow rate in single paper layer, rapid flow microfluidic paper-based analytical devices. MICROFLUIDICS AND NANOFLUIDICS 2023; 27:70. [PMID: 37719231 PMCID: PMC10499984 DOI: 10.1007/s10404-023-02679-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/26/2023] [Indexed: 09/19/2023]
Abstract
Small, single-layer microfluidic paper-based analytical devices (µPADs) offer potential for a range of point-of-care applications; however, they have been limited to low flow rates. Here, we investigate the role of laser cutting paper channels in maximizing flow rate in small profile devices with limited fluid volumes. We demonstrate that branching, laser-cut grooves can provide a 59.23-73.98% improvement in flow rate over a single cut, and a 435% increase over paper alone. These design considerations can be applied to more complex microfluidic devices with the aim of increasing the flow rate, and could be used in stand-alone channels for self-pumping. Supplementary Information The online version contains supplementary material available at 10.1007/s10404-023-02679-8.
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Affiliation(s)
- Iain Macleod Briongos
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523 USA
| | - Zachary D. Call
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523 USA
| | - Charles S. Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523 USA
| | - David L. Bark
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523 USA
- Division of Hematology and Oncology, Department of Pediatrics, Washington University in St. Louis, St. Louis, MO 63108 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA
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4
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Ranc A, Bru S, Mendez S, Giansily-Blaizot M, Nicoud F, Méndez Rojano R. Critical evaluation of kinetic schemes for coagulation. PLoS One 2023; 18:e0290531. [PMID: 37639392 PMCID: PMC10461854 DOI: 10.1371/journal.pone.0290531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/10/2023] [Indexed: 08/31/2023] Open
Abstract
Two well-established numerical representations of the coagulation cascade either initiated by the intrinsic system (Chatterjee et al., PLOS Computational Biology 2010) or the extrinsic system (Butenas et al., Journal of Biological Chemistry, 2004) were compared with thrombin generation assays under realistic pathological conditions. Biochemical modifications such as the omission of reactions not relevant to the case studied, the modification of reactions related to factor XI activation and auto-activation, the adaptation of initial conditions to the thrombin assay system, and the adjustment of some of the model parameters were necessary to align in vitro and in silico data. The modified models are able to reproduce thrombin generation for a range of factor XII, XI, and VIII deficiencies, with the coagulation cascade initiated either extrinsically or intrinsically. The results emphasize that when existing models are extrapolated to experimental parameters for which they have not been calibrated, careful adjustments are required.
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Affiliation(s)
- Alexandre Ranc
- Department of Haematology Biology, CHU, Univ Montpellier, Montpellier, France
| | - Salome Bru
- Polytech, Univ Montpellier, Montpellier, France
| | - Simon Mendez
- IMAG, Univ Montpellier, CNRS, Montpellier, France
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5
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Fu X, Su Z, Wang Y, Sun A, Wang L, Deng X, Chen Z, Fan Y. Comparison of hemodynamic features and thrombosis risk of membrane oxygenators with different structures: A numerical study. Comput Biol Med 2023; 159:106907. [PMID: 37075599 DOI: 10.1016/j.compbiomed.2023.106907] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/27/2023] [Accepted: 04/10/2023] [Indexed: 04/21/2023]
Abstract
PURPOSE The geometric structure of the membrane oxygenator can exert an impact on its hemodynamic features, which contribute to the development of thrombosis, thereby affecting the clinical efficacy of ECMO treatment. The purpose of this study is to investigate the impact of varying geometric structures on hemodynamic features and thrombosis risk of membrane oxygenators with different designs. METHODS Five oxygenator models with different structures, including different number and location of blood inlet and outlet, as well as variations in blood flow path, were established for investigation. These models are referred to as Model 1 (Quadrox-i Adult Oxygenator), Model 2 (HLS Module Advanced 7.0 Oxygenator), Model 3 (Nautilus ECMO Oxygenator), Model 4 (OxiaACF Oxygenator) and Model 5 (New design oxygenator). The hemodynamic features of these models were numerically analyzed using the Euler method combined with computational fluid dynamics (CFD). The accumulated residence time (ART) and coagulation factor concentrations (C[i], where i represents different coagulation factors) were calculated by solving the convection diffusion equation. The resulting relationships between these factors and the development of thrombosis in the oxygenator were then investigated. RESULTS Our results show that the geometric structure of the membrane oxygenator, including the location of the blood inlet and outlet as well as the design of the flow path, has a significant impact on the hemodynamic surroundings within the oxygenator. In comparison to Model 4, which had the inlet and outlet located in the center position, Model 1 and Model 3, which had the inlet and outlet at the edge of the blood flow field, exhibited a more uneven distribution of blood flow within the oxygenator, particularly in areas distant from the inlet and outlet, which was accompanied with lower flow velocity and higher values of ART and C[i], leading to the formation of flow dead zones and an elevated risk of thrombosis. The oxygenator of Model 5 is designed with a structure that features multiple inlets and outlets, which greatly improves the hemodynamic environment inside the oxygenator. This results in a more even distribution of blood flow within the oxygenator, reducing areas with high values of ART and C[i], and ultimately lowering the risk of thrombosis. The oxygenator of Model 3 with circular flow path section shows better hemodynamic performance compared to the oxygenator of Model 1 with square circular flow path. The overall ranking of hemodynamic performance for all five oxygenators is as follows: Model 5 > Model 4 > Model 2 > Model 3 > Model 1, indicating that Model 1 has the highest thrombosis risk while Model 5 has the lowest. CONCLUSION The study reveals that the different structures can affect the hemodynamic characteristics inside membrane oxygenators. The design of multiple inlets and outlets can improve the hemodynamic performance and reduce the thrombosis risk in membrane oxygenators. These findings of this study can be used to guide the optimization design of membrane oxygenators for improving hemodynamic surroundings and reducing thrombosis risk.
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Affiliation(s)
- Xingji Fu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zihua Su
- Beijing Aerospace Changfeng Co., Ltd., Beijing, 100854, China
| | - Yawei Wang
- Beijing Aerospace Changfeng Co., Ltd., Beijing, 100854, China
| | - Anqiang Sun
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Lizhen Wang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Xiaoyan Deng
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zengsheng Chen
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Yubo Fan
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
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6
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Nicoud F. An adjoint-based method for the computation of gradients in coagulation schemes. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2023; 39:e3698. [PMID: 36929230 DOI: 10.1002/cnm.3698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/25/2022] [Accepted: 03/04/2023] [Indexed: 05/13/2023]
Abstract
An adjoint-based methodology is proposed to compute the gradient of the outcomes of mathematical models for the coagulation cascade. The method is first exposed and validated by considering a simple, analytically tractable case involving only 3 species. Its potential is further illustrated by considering a detailed model for the extrinsic pathway involving 34 chemical species interacting through 45 chemical reactions and for which the gradient of Endogeneous Thrombin Potential, clotting time, maximum rate and peak value of thrombin with respect to the initial concentrations and reactions rates are computed. It is shown that the method produces gradients estimates that are fully consistent with the finite differences approximation used so far in the literature, but at a much lower computational cost.
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Affiliation(s)
- Franck Nicoud
- IMAG, University of Montpellier, CNRS, Montpellier, 34095, France
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7
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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: 3] [Impact Index Per Article: 3.0] [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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8
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Crossen J, Shankar KN, Diamond SL. Investigating thrombin-loaded fibrin in whole blood clot microfluidic assay via fluorogenic peptide. Biophys J 2023; 122:697-712. [PMID: 36635963 PMCID: PMC9989883 DOI: 10.1016/j.bpj.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/19/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
During clotting under flow, thrombin rapidly generates fibrin, whereas fibrin potently sequesters thrombin. This co-regulation was studied using microfluidic whole blood clotting on collagen/tissue factor, followed by buffer wash, and a start/stop cycling flow assay using the thrombin fluorogenic substrate, Boc-Val-Pro-Arg-AMC. After 3 min of clotting (100 s-1) and 5 min of buffer wash, non-elutable thrombin activity was easily detected during cycles of flow cessation. Non-elutable thrombin was similarly detected in plasma clots or arterial whole blood clots (1000 s-1). This thrombin activity was ablated by Phe-Pro-Arg-chloromethylketone (PPACK), apixaban, or Gly-Pro-Arg-Pro to inhibit fibrin. Reaction-diffusion simulations predicted 108 nM thrombin within the clot. Heparin addition to the start/stop assay had little effect on fibrin-bound thrombin, whereas addition of heparin-antithrombin (AT) required over 6 min to inhibit the thrombin, indicating a substantial diffusion limitation. In contrast, heparin-AT rapidly inhibited thrombin within microfluidic plasma clots, indicating marked differences in fibrin structure and functionality between plasma clots and whole blood clots. Addition of GPVI-Fab to blood before venous or arterial clotting (200 or 1000 s-1) markedly reduced fibrin-bound thrombin, whereas GPVI-Fab addition after 90 s of clotting had no effect. Perfusion of AF647-fibrinogen over washed fluorescein isothiocyanate (FITC)-fibrin clots resulted in an intense red layer around, but not within, the original FITC-fibrin. Similarly, introduction of plasma/AF647-fibrinogen generated substantial red fibrin masses that did not penetrate the original green clots, demonstrating that fibrin cannot be re-clotted with fibrinogen. Overall, thrombin within fibrin is non-elutable, easily accessed by peptides, slowly accessed by average-sized proteins (heparin/AT), and not accessible to fresh fibrinogen.
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Affiliation(s)
- Jennifer Crossen
- Institute for Medicine and Engineering, Department of Chemical and Biomolecular Engineering, 1024 Vagelos Research Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Kaushik N Shankar
- Institute for Medicine and Engineering, Department of Chemical and Biomolecular Engineering, 1024 Vagelos Research Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Scott L Diamond
- Institute for Medicine and Engineering, Department of Chemical and Biomolecular Engineering, 1024 Vagelos Research Laboratory, University of Pennsylvania, Philadelphia, PA 19104.
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9
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Zhu G, Modepalli S, Anand M, Li H. Computational modeling of hypercoagulability in COVID-19. Comput Methods Biomech Biomed Engin 2023; 26:338-349. [PMID: 36154346 DOI: 10.1080/10255842.2022.2124858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 100 million people worldwide and claimed millions of lives. While the leading cause of mortality in COVID-19 patients is the hypoxic respiratory failure from acute respiratory distress syndrome, there is accumulating evidence that shows excessive coagulation also increases the fatalities in COVID-19. Thus, there is a pressing demand to understand the association between COVID-19-induced hypercoagulability and the extent of formation of undesired blood clots. Mathematical modeling of coagulation has been used as an important tool to identify novel reaction mechanisms and to identify targets for new drugs. Here, we employ the coagulation factor data of COVID-19 patients reported from published studies as inputs for two mathematical models of coagulation to identify how the concentrations of coagulation factors change in these patients. Our simulation results show that while the levels of many of the abnormal coagulation factors measured in COVID-19 patients promote the generation of thrombin and fibrin, two key components of blood clots, the increased level of fibrinogen and then the reduced level of antithrombin are the factors most responsible for boosting the level of fibrin and thrombin, respectively. Altogether, our study demonstrates the potential of mathematical modeling to identify coagulation factors responsible for the increased clot formation in COVID-19 patients where clinical data is scarce.
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Affiliation(s)
- Ge Zhu
- Center for Biomedical Engineering, Brown University, Providence, USA
| | | | - Mohan Anand
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - He Li
- School of Chemical, Materials & Biomedical Engineering, University of Georgia, Athens, USA
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10
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Qureshi A, Lip GYH, Nordsletten DA, Williams SE, Aslanidi O, de Vecchi A. Imaging and biophysical modelling of thrombogenic mechanisms in atrial fibrillation and stroke. Front Cardiovasc Med 2023; 9:1074562. [PMID: 36733827 PMCID: PMC9887999 DOI: 10.3389/fcvm.2022.1074562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
Atrial fibrillation (AF) underlies almost one third of all ischaemic strokes, with the left atrial appendage (LAA) identified as the primary thromboembolic source. Current stroke risk stratification approaches, such as the CHA2DS2-VASc score, rely mostly on clinical comorbidities, rather than thrombogenic mechanisms such as blood stasis, hypercoagulability and endothelial dysfunction-known as Virchow's triad. While detection of AF-related thrombi is possible using established cardiac imaging techniques, such as transoesophageal echocardiography, there is a growing need to reliably assess AF-patient thrombogenicity prior to thrombus formation. Over the past decade, cardiac imaging and image-based biophysical modelling have emerged as powerful tools for reproducing the mechanisms of thrombogenesis. Clinical imaging modalities such as cardiac computed tomography, magnetic resonance and echocardiographic techniques can measure blood flow velocities and identify LA fibrosis (an indicator of endothelial dysfunction), but imaging remains limited in its ability to assess blood coagulation dynamics. In-silico cardiac modelling tools-such as computational fluid dynamics for blood flow, reaction-diffusion-convection equations to mimic the coagulation cascade, and surrogate flow metrics associated with endothelial damage-have grown in prevalence and advanced mechanistic understanding of thrombogenesis. However, neither technique alone can fully elucidate thrombogenicity in AF. In future, combining cardiac imaging with in-silico modelling and integrating machine learning approaches for rapid results directly from imaging data will require development under a rigorous framework of verification and clinical validation, but may pave the way towards enhanced personalised stroke risk stratification in the growing population of AF patients. This Review will focus on the significant progress in these fields.
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Affiliation(s)
- Ahmed Qureshi
- School of Biomedical Engineering and Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, United Kingdom,*Correspondence: Ahmed Qureshi,
| | - Gregory Y. H. Lip
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, United Kingdom
| | - David A. Nordsletten
- School of Biomedical Engineering and Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, United Kingdom,Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Steven E. Williams
- School of Biomedical Engineering and Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, United Kingdom,Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, United Kingdom
| | - Oleg Aslanidi
- School of Biomedical Engineering and Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, United Kingdom
| | - Adelaide de Vecchi
- School of Biomedical Engineering and Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, United Kingdom
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11
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Wang Y, Luan J, Luo K, Fan J, Zhu T. Model reduction of coagulation cascade based on genetic algorithm. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2022; 38:e3652. [PMID: 36167948 DOI: 10.1002/cnm.3652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/18/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Fibrin is an important product of the coagulation cascade, and plays an eminent role in platelet stabilization. Since coagulation cascade models typically involve the reaction kinetics of dozens of proteins, which will incur burdensome computational costs when coupled to blood flow in complex geometries, researchers often ignore this process when constructing thrombosis models. However, previous studies have shown that fundamental aspects of coagulation can be reproduced with simpler models, which motivated us to obtain a reduced-order model of fibrin generation through a systematic approach. Therefore, we introduced a semi-automatic framework to perform model-reduction of cascade reactions in this study, which consisted of two processes. Specifically, the retained protein species and cascade reactions were determined based on published studies and simulation results from the full cascade model, while the optimal reaction rates for the new cascade network were determined using a genetic algorithm. The framework has been applied to a 19-species coagulation model that triggers fibrin generation in internal fields via reactive boundaries, and a 10-species reduced-order model was obtained to reproduce the kinetics of fibrinogenesis in the full cascade model at different boundary tissue factor concentrations. This reduced-order model of fibrinogenesis would be valuable for thrombosis modeling that considers both the coagulation cascade and platelet activity. Furthermore, the framework proposed herein can also be applied to the reductions of other cascade reaction models.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, China
| | - Jingyang Luan
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Kun Luo
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, China
| | - Jianren Fan
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, China
| | - Ting Zhu
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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12
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Lakshmanan HHS, Estonilo A, Reitsma SE, Melrose AR, Subramanian J, Zheng TJ, Maddala J, Tucker EI, Gailani D, McCarty OJT, Jurney PL, Puy C. Revised model of the tissue factor pathway of thrombin generation: Role of the feedback activation of FXI. J Thromb Haemost 2022; 20:1350-1363. [PMID: 35352494 PMCID: PMC9590754 DOI: 10.1111/jth.15716] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/26/2022] [Accepted: 03/16/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Biochemical reaction networks are self-regulated in part due to feedback activation mechanisms. The tissue factor (TF) pathway of blood coagulation is a complex reaction network controlled by multiple feedback loops that coalesce around the serine protease thrombin. OBJECTIVES Our goal was to evaluate the relative contribution of the feedback activation of coagulation factor XI (FXI) in TF-mediated thrombin generation using a comprehensive systems-based analysis. MATERIALS AND METHODS We developed a systems biology model that improves the existing Hockin-Mann (HM) model through an integrative approach of mathematical modeling and in vitro experiments. Thrombin generation measured using in vitro assays revealed that the feedback activation of FXI contributes to the propagation of thrombin generation based on the initial concentrations of TF or activated coagulation factor X (FXa). We utilized experimental data to improve the robustness of the HM model to capture thrombin generation kinetics without a role for FXI before including the feedback activation of FXI by thrombin to construct the extended (ext.) HM model. RESULTS AND CONCLUSIONS Using the ext.HM model, we predicted that the contribution of positive feedback of FXI activation by thrombin can be abolished by selectively eliminating the inhibitory function of tissue factor pathway inhibitor (TFPI), a serine protease inhibitor of FXa and TF-activated factor VII (FVIIa) complex. This prediction from the ext.HM model was experimentally validated using thrombin generation assays with function blocking antibodies against TFPI and plasmas depleted of FXI. Together, our results demonstrate the applications of combining experimental and modeling techniques in predicting complex biochemical reaction systems.
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Affiliation(s)
| | - Aldrich Estonilo
- Department of Biomedical Engineering, San Jose State University, San Jose, California, USA
| | - Stéphanie E. Reitsma
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | - Alexander R. Melrose
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | | | - Tony J. Zheng
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | - Jeevan Maddala
- Department of Chemical and Biomedical Engineering, West Virginia University, Morgantown, West Virginia, USA
| | - Erik I. Tucker
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
- Aronora, Inc., Portland, Oregon, USA
| | - David Gailani
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Owen J. T. McCarty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | - Patrick L. Jurney
- Department of Biomedical Engineering, San Jose State University, San Jose, California, USA
| | - Cristina Puy
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
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Yin W, Dimatteo A, Kumpfbeck A, Leung S, Fandaros M, Musmacker B, Rubenstein DA, Frame MD. An in situ inferior vena cava ligation-stenosis model to study thrombin generation rates with flow. Thromb J 2022; 20:30. [PMID: 35614456 PMCID: PMC9131541 DOI: 10.1186/s12959-022-00391-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/19/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Blood flow-induced shear stress affects platelet participation in coagulation and thrombin generation. We aimed to develop an in vivo model to characterize thrombin generation rates under flow. METHODS An in situ inferior vena cava (IVC) ligation-stenosis model was established using C57BL/6 mice. Wild type C57BL/6 mice were fed normal chow diet for two weeks before experiments. On the day of experiments, mice were anesthetized, followed by an incision through the abdominal skin to expose the IVC, which was then ligated (followed by reperfusion through a stenosis for up to 2 h). IVC blood flow rate was monitored using a Transonic ultrasound flow meter. In sham animals, the IVC was exposed following the same procedure, but no ligation was applied. Thrombin generation following IVC ligation was estimated by measuring mouse plasma prothrombin fragment 1-2 concentration. Mouse plasma factor Va concentration was measured using phospholipids and a modified prothrombinase assay. Blood vessel histomorphology, vascular wall ICAM-1, von Willebrand Factor, tissue factor, and PECAM-1 expression were measured using immunofluorescence microscopy. RESULTS IVC blood flow rate increased immediately following ligation and stenosis formation. Sizable clots formed in mouse IVC following ligation and stenosis formation. Both plasma factor Va and prothrombin fragment 1-2 concentration reduced significantly following IVC ligation/stenosis, while no changes were observed with ICAM-1, von Willebrand Factor, tissue factor and PECAM-1 expression. CONCLUSION Clot formation was successful. However, the prothrombin-thrombin conversion rate constant in vivo cannot be determined as local thrombin and FVa concentration (at the injury site) cannot be accurately measured. Modification to the animal model is needed to further the investigation.
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Affiliation(s)
- Wei Yin
- Department of Biomedical Engineering, Stony Brook University, Bioengineering Building, Room 109, Stony Brook, NY, 11794, USA.
| | - Andrew Dimatteo
- Department of Biomedical Engineering, Stony Brook University, Bioengineering Building, Room 109, Stony Brook, NY, 11794, USA
| | - Andrew Kumpfbeck
- Department of Biomedical Engineering, Stony Brook University, Bioengineering Building, Room 109, Stony Brook, NY, 11794, USA
| | - Stephen Leung
- Department of Biomedical Engineering, Stony Brook University, Bioengineering Building, Room 109, Stony Brook, NY, 11794, USA
| | - Marina Fandaros
- Department of Biomedical Engineering, Stony Brook University, Bioengineering Building, Room 109, Stony Brook, NY, 11794, USA
| | - Bryan Musmacker
- Department of Biomedical Engineering, Stony Brook University, Bioengineering Building, Room 109, Stony Brook, NY, 11794, USA
| | - David A Rubenstein
- Department of Biomedical Engineering, Stony Brook University, Bioengineering Building, Room 109, Stony Brook, NY, 11794, USA
| | - Mary D Frame
- Department of Biomedical Engineering, Stony Brook University, Bioengineering Building, Room 109, Stony Brook, NY, 11794, USA
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14
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Multiphysics and multiscale modeling of microthrombosis in COVID-19. PLoS Comput Biol 2022; 18:e1009892. [PMID: 35255089 PMCID: PMC8901059 DOI: 10.1371/journal.pcbi.1009892] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/02/2022] [Indexed: 12/21/2022] Open
Abstract
Emerging clinical evidence suggests that thrombosis in the microvasculature of patients with Coronavirus disease 2019 (COVID-19) plays an essential role in dictating the disease progression. Because of the infectious nature of SARS-CoV-2, patients’ fresh blood samples are limited to access for in vitro experimental investigations. Herein, we employ a novel multiscale and multiphysics computational framework to perform predictive modeling of the pathological thrombus formation in the microvasculature using data from patients with COVID-19. This framework seamlessly integrates the key components in the process of blood clotting, including hemodynamics, transport of coagulation factors and coagulation kinetics, blood cell mechanics and adhesive dynamics, and thus allows us to quantify the contributions of many prothrombotic factors reported in the literature, such as stasis, the derangement in blood coagulation factor levels and activities, inflammatory responses of endothelial cells and leukocytes to the microthrombus formation in COVID-19. Our simulation results show that among the coagulation factors considered, antithrombin and factor V play more prominent roles in promoting thrombosis. Our simulations also suggest that recruitment of WBCs to the endothelial cells exacerbates thrombogenesis and contributes to the blockage of the blood flow. Additionally, we show that the recent identification of flowing blood cell clusters could be a result of detachment of WBCs from thrombogenic sites, which may serve as a nidus for new clot formation. These findings point to potential targets that should be further evaluated, and prioritized in the anti-thrombotic treatment of patients with COVID-19. Altogether, our computational framework provides a powerful tool for quantitative understanding of the mechanism of pathological thrombus formation and offers insights into new therapeutic approaches for treating COVID-19 associated thrombosis. Emerging clinical evidence suggests that thrombosis in the microvasculature of patients with Coronavirus disease 2019 (COVID-19) plays an essential role in dictating the disease progression. We employ a novel multiphysics and multiscale computational framework to investigate the underlying mechanism of the pathological formation of microthrombi and circulating cell clusters in COVID-19. We quantify the contributions of many prothrombotic factors reported in the literature, such as stasis, the derangement in blood coagulation factor levels and activities, inflammatory responses of endothelial cells and leukocytes to the microthrombus formation in COVID-19, through which we identify the potential targets that should be further evaluated, and prioritized in the anti-thrombotic treatment of patients with COVID-19.
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15
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Chen J, Diamond SL. Sensitivity analysis of a reduced model of thrombosis under flow: Roles of Factor IX, Factor XI, and γ'-Fibrin. PLoS One 2021; 16:e0260366. [PMID: 34813608 PMCID: PMC8610249 DOI: 10.1371/journal.pone.0260366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
A highly reduced extrinsic pathway coagulation model (8 ODEs) under flow considered a thin 15-micron platelet layer where transport limitations were largely negligible (except for fibrinogen) and where cofactors (FVIIa, FV, FVIII) were not rate-limiting. By including thrombin feedback activation of FXI and the antithrombin-I activities of fibrin, the model accurately simulated measured fibrin formation and thrombin fluxes. Using this reduced model, we conducted 10,000 Monte Carlo (MC) simulations for ±50% variation of 5 plasma zymogens and 2 fibrin binding sites for thrombin. A sensitivity analysis of zymogen concentrations indicated that FIX activity most influenced thrombin generation, a result expected from hemophilia A and B. Averaging all MC simulations confirmed both the mean and standard deviation of measured fibrin generation on 1 tissue factor (TF) molecule per μm2. Across all simulations, free thrombin in the layer ranged from 20 to 300 nM (mean: 50 nM). The top 2% of simulations that produced maximal fibrin were dominated by conditions with low antithrombin-I activity (decreased weak and strong sites) and high FIX concentration. In contrast, the bottom 2% of simulations that produced minimal fibrin were dominated by low FIX and FX. The percent reduction of fibrin by an ideal FXIa inhibitor (FXI = 0) ranged from 71% fibrin reduction in the top 2% of MC simulations to only 34% fibrin reduction in the bottom 2% of MC simulations. Thus, the antithrombotic potency of FXIa inhibitors may vary depending on normal ranges of zymogen concentrations. This reduced model allowed efficient multivariable sensitivity analysis.
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Affiliation(s)
- Jason Chen
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Scott L. Diamond
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA, United States of America
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16
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Grande Gutiérrez N, Alber M, Kahn AM, Burns JC, Mathew M, McCrindle BW, Marsden AL. Computational modeling of blood component transport related to coronary artery thrombosis in Kawasaki disease. PLoS Comput Biol 2021; 17:e1009331. [PMID: 34491991 PMCID: PMC8448376 DOI: 10.1371/journal.pcbi.1009331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 09/17/2021] [Accepted: 08/07/2021] [Indexed: 11/25/2022] Open
Abstract
Coronary artery thrombosis is the major risk associated with Kawasaki disease (KD). Long-term management of KD patients with persistent aneurysms requires a thrombotic risk assessment and clinical decisions regarding the administration of anticoagulation therapy. Computational fluid dynamics has demonstrated that abnormal KD coronary artery hemodynamics can be associated with thrombosis. However, the underlying mechanisms of clot formation are not yet fully understood. Here we present a new model incorporating data from patient-specific simulated velocity fields to track platelet activation and accumulation. We use a system of Reaction-Advection-Diffusion equations solved with a stabilized finite element method to describe the evolution of non-activated platelets and activated platelet concentrations [AP], local concentrations of adenosine diphosphate (ADP) and poly-phosphate (PolyP). The activation of platelets is modeled as a function of shear-rate exposure and local concentration of agonists. We compared the distribution of activated platelets in a healthy coronary case and six cases with coronary artery aneurysms caused by KD, including three with confirmed thrombosis. Results show spatial correlation between regions of higher concentration of activated platelets and the reported location of the clot, suggesting predictive capabilities of this model towards identifying regions at high risk for thrombosis. Also, the concentration levels of ADP and PolyP in cases with confirmed thrombosis are higher than the reported critical values associated with platelet aggregation (ADP) and activation of the intrinsic coagulation pathway (PolyP). These findings suggest the potential initiation of a coagulation pathway even in the absence of an extrinsic factor. Finally, computational simulations show that in regions of flow stagnation, biochemical activation, as a result of local agonist concentration, is dominant. Identifying the leading factors to a pro-coagulant environment in each case—mechanical or biochemical—could help define improved strategies for thrombosis prevention tailored for each patient. Computational studies aiming to model thrombosis often rely on an arterial wall injury. Collagen and other extracellular matrix components are exposed to the bloodstream, which facilitates platelet adhesion to the wall and subsequent clot formation. However, these models are not adequate to explain thrombosis in other settings where even in the absence of a focal lesion, clots may still form under certain flow conditions. Coronary artery aneurysm thrombosis following KD is an example of the need to understand the mechanisms of thrombus initiation in the absence of an extrinsic factor. This study provides a new framework to investigate thrombus initiation in KD from a patient-specific perspective, which integrates fluid mechanics and biochemistry and which could help quantify the pro-coagulant environment induced by the aneurysm and become a predictive tool. The work presented here has broad relevance to other clinical situations where flow stagnation and transport are driving factors in thrombus formation.
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Affiliation(s)
- Noelia Grande Gutiérrez
- Department of Mechanical Engineering, Stanford University, Stanford, California, United States of America
| | - Mark Alber
- Department of Mathematics and Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, Riverside, California, United States of America
| | - Andrew M. Kahn
- Department of Medicine, University of California, San Diego, San Diego, California, United States of America
| | - Jane C. Burns
- Department of Pediatrics, University of California, San Diego, San Diego, California, United States of America
| | - Mathew Mathew
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Brian W. McCrindle
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Alison L. Marsden
- Department of Pediatrics, Bioengineering and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California, United States of America
- * E-mail:
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17
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Doran S, Arif M, Lam S, Bayraktar A, Turkez H, Uhlen M, Boren J, Mardinoglu A. Multi-omics approaches for revealing the complexity of cardiovascular disease. Brief Bioinform 2021; 22:bbab061. [PMID: 33725119 PMCID: PMC8425417 DOI: 10.1093/bib/bbab061] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/20/2021] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
The development and progression of cardiovascular disease (CVD) can mainly be attributed to the narrowing of blood vessels caused by atherosclerosis and thrombosis, which induces organ damage that will result in end-organ dysfunction characterized by events such as myocardial infarction or stroke. It is also essential to consider other contributory factors to CVD, including cardiac remodelling caused by cardiomyopathies and co-morbidities with other diseases such as chronic kidney disease. Besides, there is a growing amount of evidence linking the gut microbiota to CVD through several metabolic pathways. Hence, it is of utmost importance to decipher the underlying molecular mechanisms associated with these disease states to elucidate the development and progression of CVD. A wide array of systems biology approaches incorporating multi-omics data have emerged as an invaluable tool in establishing alterations in specific cell types and identifying modifications in signalling events that promote disease development. Here, we review recent studies that apply multi-omics approaches to further understand the underlying causes of CVD and provide possible treatment strategies by identifying novel drug targets and biomarkers. We also discuss very recent advances in gut microbiota research with an emphasis on how diet and microbial composition can impact the development of CVD. Finally, we present various biological network analyses and other independent studies that have been employed for providing mechanistic explanation and developing treatment strategies for end-stage CVD, namely myocardial infarction and stroke.
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Affiliation(s)
- Stephen Doran
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, United Kingdom
| | - Muhammad Arif
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Simon Lam
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, United Kingdom
| | - Abdulahad Bayraktar
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, United Kingdom
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Boren
- Institute of Medicine, Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital Gothenburg, Sweden
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, United Kingdom
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
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18
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Raynaud F, Rousseau A, Monteyne D, Perez-Morga D, Zouaoui Boudjeltia K, Chopard B. Investigating the two regimes of fibrin clot lysis: an experimental and computational approach. Biophys J 2021; 120:4091-4106. [PMID: 34384765 PMCID: PMC8510862 DOI: 10.1016/j.bpj.2021.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/07/2021] [Accepted: 08/04/2021] [Indexed: 12/03/2022] Open
Abstract
It has been observed in vitro that complete clot lysis is generally preceded by a slow phase of lysis during which the degradation seems to be inefficient. However, this slow regime was merely noticed, but not yet quantitatively discussed. In our experiments, we observed that the lysis ubiquitously occurred in two distinct regimes, a slow and a fast lysis regime. We quantified extensively the duration of these regimes for a wide spectrum of experimental conditions and found that on average, the slow regime lasts longer than the fast one, meaning that during most of the process, the lysis is ineffective. We proposed a computational model in which the properties of the binding of the proteins change during the lysis: first, the biochemical reactions take place at the surface of the fibrin fibers, then in the bulk, resulting in the observed fast lysis regime. This simple hypothesis appeared to be sufficient to reproduce with a great accuracy the lysis profiles obtained experimentally.
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Affiliation(s)
- Franck Raynaud
- Department of Computer Science, University of Geneva, Geneva, Switzerland.
| | - Alexandre Rousseau
- Laboratoire de Médecine Expérimentale, Medicine Faculty, Université libre de Bruxelles (ULB 222 Unit), ISPPC CHU de Charleroi, Hôpital A. Vésale, Montigny-le-Tilleul, Belgium
| | - Daniel Monteyne
- Laboratory of Molecular Parasitology, IBMM, Université libre de Bruxelles, Gosselies, Belgium; Center for Microscopy and Molecular Imaging, Université libre de Bruxelles, Gosselies, Belgium
| | - David Perez-Morga
- Laboratory of Molecular Parasitology, IBMM, Université libre de Bruxelles, Gosselies, Belgium; Center for Microscopy and Molecular Imaging, Université libre de Bruxelles, Gosselies, Belgium
| | - Karim Zouaoui Boudjeltia
- Laboratoire de Médecine Expérimentale, Medicine Faculty, Université libre de Bruxelles (ULB 222 Unit), ISPPC CHU de Charleroi, Hôpital A. Vésale, Montigny-le-Tilleul, Belgium
| | - Bastien Chopard
- Department of Computer Science, University of Geneva, Geneva, Switzerland
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19
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Zhang Z, Mei M, Yao J, Ye T, Quan J, Liu J. An off/on thrombin activated energy driven molecular machine for sensitive detection of human thrombin via non-enzymatic catalyst recycling amplification. Analyst 2021; 145:6868-6874. [PMID: 32820297 DOI: 10.1039/d0an01054e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this article, we report a novel dual on/off thrombin fluorescence aptasensor by combining the energy driven target induced strand displacement reaction and a non-enzyme catalyst recycling DNA machine. Firstly, the specific binding of an aptamer strand and thrombin induce the release of a catalyst which was used as a DNA machine trigger. Subsequently, the catalyst as the trigger initiated the DNA machine through nucleic acid hybridization and branch migration of the DNA machine, resulting in the DNA substrate melting and re-hybridization. In such a working model, the DNA machine achieved cooperative control of the circular strand displacement reaction, realizing catalyst recycling and dual-amplification. The fluorescence signal change of FAM and ROX accumulation had a good linear relationship with the thrombin concentration in the range of 1 fM to 1 nM. On account of catalyst recycling and dual recognition, the detection limit for thrombin was determined to be as low as 0.45 fM (S/N = 3).This biosensor also showed good selectivity for thrombin without being affected by some other proteins, such as PSA, lysozyme etc. Moreover, this assay can be applied to the detection of thrombin in diluted human serum.
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Affiliation(s)
- Zhang Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China.
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20
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Crépin R, Morin C, Montmartin A, Tardy-Poncet B, Chelle P. Use of population PK/PD approach to model the thrombin generation assay: assessment in haemophilia A plasma samples spiked by a TFPI antibody. J Pharmacokinet Pharmacodyn 2021; 48:563-580. [PMID: 33846873 DOI: 10.1007/s10928-021-09752-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/22/2021] [Indexed: 11/28/2022]
Abstract
The thrombin generation (TG) assay is a well-established tool to capture the clotting potential of any healthy or haemophiliac subject. It measures ex vivo the kinetics of thrombin activation throughout the coagulation. Clinical studies allowed to create two databases gathering the coagulation factor levels and the thrombin generation profile of 40 healthy and 40 haemophiliac A (HA) subjects. Besides, portions of all HA samples were spiked with increasing levels of a TFPI antibody (considered as a possible therapeutic target) and corresponding TG profiles were determined. The non-linear mixed-effect (NLME) modelling aims at describing and explaining the experimentally observed important variability of the TG curves between subjects and the individual effects of spiking with a TFPI antibody. The models consist of an empirical description of the TG kinetics, accounting for an additive residual error and between-subject variability on its parameters. Factor VIII and TFPI were found to significantly explain and reduce the variability of the TG of haemophilia A samples. Besides, the model is shown to correctly reproduce the variability in the response to the ex vivo spiking with the TFPI antibody, by combining the empirical description of TG to a simple Hill equation that accounts for the binding between TFPI and different doses of its antibody. Such models can be useful for clinical practice, with the analysis and comparison of the distributions of TG profiles in healthy and haemophilia populations; and also for research, with the analysis of the effect of TFPI and its neutralization on individual TG profiles.
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Affiliation(s)
- Raphaël Crépin
- Mines Saint-Etienne, Univ Lyon, Univ Jean Monnet, INSERM, U1059 Sainbiose, Centre CIS, 42023, Saint-Étienne, France
| | - Claire Morin
- Mines Saint-Etienne, Univ Lyon, Univ Jean Monnet, INSERM, U1059 Sainbiose, Centre CIS, 42023, Saint-Étienne, France.
| | - Aurélie Montmartin
- INSERM, U1059, SAINBIOSE, Université de Lyon, UJM Saint Etienne, Saint-Étienne, France
| | - Brigitte Tardy-Poncet
- INSERM, U1059, SAINBIOSE, Université de Lyon, UJM Saint Etienne, Saint-Étienne, France
| | - Pierre Chelle
- School of Pharmacy, University of Waterloo, Kitchener, ON, Canada
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21
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Study on the activity of recombinant mutant tissue-type plasminogen activator fused with the C-terminal fragment of hirudin. J Thromb Thrombolysis 2021; 52:880-888. [PMID: 33826053 DOI: 10.1007/s11239-021-02440-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/26/2021] [Indexed: 12/12/2022]
Abstract
In the present study, bifunctional fusion proteins were designed by fusing the kringle 2 and protease domains of tissue-type plasminogen activator (tPA) to the C-terminal fragment of hirudin. The thrombolytic and anticoagulant activities of these recombinant proteins from mammalian cells were investigated using in vitro coagulation models and chromogenic assays. The results showed that all assayed tPA mutants retained catalytic activity. The C-terminal fragment of hirudin may have weak affinity to thrombin and thus was insufficient to suppress thrombin-mediated fibrin agglutination. The strength of the thrombolytic activity only relied on the selected tPA sequences, and the fibrinolytic efficiency of single-chain protein significantly decreased. Our data indicate that truncated tPA combined with a hirudin peptide may provide a framework for the further development of a new antithrombotic agent.
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22
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Pearce KJ, Nellenbach K, Smith RC, Brown AC, Haider MA. Modeling and Parameter Subset Selection for Fibrin Polymerization Kinetics with Applications to Wound Healing. Bull Math Biol 2021; 83:47. [PMID: 33751272 PMCID: PMC8237246 DOI: 10.1007/s11538-021-00876-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/25/2021] [Indexed: 11/29/2022]
Abstract
During the hemostatic phase of wound healing, vascular injury leads to endothelial cell damage, initiation of a coagulation cascade involving platelets, and formation of a fibrin-rich clot. As this cascade culminates, activation of the protease thrombin occurs and soluble fibrinogen is converted into an insoluble polymerized fibrin network. Fibrin polymerization is critical for bleeding cessation and subsequent stages of wound healing. We develop a cooperative enzyme kinetics model for in vitro fibrin matrix polymerization capturing dynamic interactions among fibrinogen, thrombin, fibrin, and intermediate complexes. A tailored parameter subset selection technique is also developed to evaluate parameter identifiability for a representative data curve for fibrin accumulation in a short-duration in vitro polymerization experiment. Our approach is based on systematic analysis of eigenvalues and eigenvectors of the classical information matrix for simulations of accumulating fibrin matrix via optimization based on a least squares objective function. Results demonstrate robustness of our approach in that a significant reduction in objective function cost is achieved relative to a more ad hoc curve-fitting procedure. Capabilities of this approach to integrate non-overlapping subsets of the data to enhance the evaluation of parameter identifiability are also demonstrated. Unidentifiable reaction rate parameters are screened to determine whether individual reactions can be eliminated from the overall system while preserving the low objective cost. These findings demonstrate the high degree of information within a single fibrin accumulation curve, and a tailored model and parameter subset selection approach for improving optimization and reducing model complexity in the context of polymerization experiments.
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Affiliation(s)
- Katherine J Pearce
- Department of Mathematics, North Carolina State University, Box 8205, Raleigh, NC, 27695-8205, USA
| | - Kimberly Nellenbach
- Joint Department of Biomedical Engineering, North Carolina State University and The University of North Carolina at Chapel Hill, Raleigh, NC, 27695, USA
| | - Ralph C Smith
- Department of Mathematics, North Carolina State University, Box 8205, Raleigh, NC, 27695-8205, USA
| | - Ashley C Brown
- Joint Department of Biomedical Engineering, North Carolina State University and The University of North Carolina at Chapel Hill, Raleigh, NC, 27695, USA
| | - Mansoor A Haider
- Department of Mathematics, North Carolina State University, Box 8205, Raleigh, NC, 27695-8205, USA.
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23
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Comparative Analysis of Thrombin Calibration Algorithms and Correction for Thrombin-α2macroglobulin Activity. J Clin Med 2020; 9:jcm9103077. [PMID: 32987791 PMCID: PMC7650706 DOI: 10.3390/jcm9103077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/27/2022] Open
Abstract
Background: The thrombin generation (TG) test is useful for characterizing global hemostasis potential, but fluorescence substrate artifacts, such as thrombin-α2macroglobulin (T-α2MG) signal, inner filter effect (IFE), substrate consumption, and calibration algorithms have been suggested as sources of intra- and inter-laboratory variance, which may limit its clinical utility. Methods: Effects of internal vs. external normalization, IFE and T-α2MG on TG curves in normal plasma supplemented with coagulation factors, thrombomodulin, and tissue factor were studied using the Calibrated Automated Thrombinography (CAT; Diagnostica Stago, Parsippany, NJ, USA) and in-house software. Results: The various calibration methods demonstrated no significant difference in producing TG curves, nor increased the robustness of the TG assay. Several TG parameters, including thrombin peak height (TPH), produced from internal linear calibration did not differ significantly from uncalibrated TG parameters. Further, TPH values from internal linear and nonlinear calibration with or without T-α2MG correction correlated well with TPH from external calibration. Higher coefficients of variation (CVs) for TPH values were observed in both platelet-free and platelet-rich plasma with added thrombomodulin. Conclusions: Our work suggests minimal differences between distinct computational approaches toward calibrating and correcting fluorescence signals into TG levels, with most samples returning similar or equivalent TPH results.
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24
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Mitrophanov AY, Merrill-Skoloff G, Grover SP, Govindarajan V, Kolanjiyil A, Hariprasad DS, Unnikrishnan G, Flaumenhaft R, Reifman J. Injury Length and Arteriole Constriction Shape Clot Growth and Blood-Flow Acceleration in a Mouse Model of Thrombosis. Arterioscler Thromb Vasc Biol 2020; 40:2114-2126. [PMID: 32640902 DOI: 10.1161/atvbaha.120.314786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
OBJECTIVE Quantitative relationships between the extent of injury and thrombus formation in vivo are not well understood. Moreover, it has not been investigated how increased injury severity translates to blood-flow modulation. Here, we investigated interconnections between injury length, clot growth, and blood flow in a mouse model of laser-induced thrombosis. Approach and Results: Using intravital microscopy, we analyzed 59 clotting events collected from the cremaster arteriole of 14 adult mice. We regarded injury length as a measure of injury severity. The injury caused transient constriction upstream and downstream of the injury site resulting in a 50% reduction in arteriole diameter. The amount of platelet accumulation and fibrin formation did not depend on arteriole diameter or deformation but displayed an exponentially increasing dependence on injury length. The height of the platelet clot depended linearly on injury length and the arteriole diameter. Upstream arteriolar constriction correlated with delayed upstream velocity increase, which, in turn, determined downstream velocity. Before clot formation, flow velocity positively correlated with the arteriole diameter. After the onset of thrombus growth, flow velocity at the injury site negatively correlated with the arteriole diameter and with the size of the above-clot lumen. CONCLUSIONS Injury severity increased platelet accumulation and fibrin formation in a persistently steep fashion and, together with arteriole diameter, defined clot height. Arterial constriction and clot formation were characterized by a dynamic change in the blood flow, associated with increased flow velocity.
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Affiliation(s)
- Alexander Y Mitrophanov
- From the DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Development Command, Ft. Detrick, MD (A.Y.M., V.G., A.K., D.S.H., G.U., J.R.).,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD (A.Y.M., V.G., A.K., D.S.H., G.U.)
| | - Glenn Merrill-Skoloff
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA (G.M.-S., S.P.G., R.F.)
| | - Steven P Grover
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA (G.M.-S., S.P.G., R.F.)
| | - Vijay Govindarajan
- From the DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Development Command, Ft. Detrick, MD (A.Y.M., V.G., A.K., D.S.H., G.U., J.R.).,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD (A.Y.M., V.G., A.K., D.S.H., G.U.)
| | - Arun Kolanjiyil
- From the DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Development Command, Ft. Detrick, MD (A.Y.M., V.G., A.K., D.S.H., G.U., J.R.).,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD (A.Y.M., V.G., A.K., D.S.H., G.U.)
| | - Daniel S Hariprasad
- From the DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Development Command, Ft. Detrick, MD (A.Y.M., V.G., A.K., D.S.H., G.U., J.R.).,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD (A.Y.M., V.G., A.K., D.S.H., G.U.)
| | - Ginu Unnikrishnan
- From the DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Development Command, Ft. Detrick, MD (A.Y.M., V.G., A.K., D.S.H., G.U., J.R.).,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD (A.Y.M., V.G., A.K., D.S.H., G.U.)
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA (G.M.-S., S.P.G., R.F.)
| | - Jaques Reifman
- From the DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Development Command, Ft. Detrick, MD (A.Y.M., V.G., A.K., D.S.H., G.U., J.R.)
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25
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Modeling Thrombin Generation in Plasma under Diffusion and Flow. Biophys J 2020; 119:162-181. [PMID: 32544388 DOI: 10.1016/j.bpj.2020.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/03/2020] [Accepted: 04/23/2020] [Indexed: 11/21/2022] Open
Abstract
We investigate the capacity of published numerical models of thrombin generation to reproduce experimentally observed threshold behavior under conditions in which diffusion and/or flow are important. Computational fluid dynamics simulations incorporating species diffusion, fluid flow, and biochemical reactions are compared with published data for thrombin generation in vitro in 1) quiescent plasma exposed to patches of tissue factor and 2) plasma perfused through a capillary coated with tissue factor. Clot time is correctly predicted in individual cases, and some models qualitatively replicate thrombin generation thresholds across a series of tissue factor patch sizes or wall shear rates. Numerical results suggest that there is not a genuine patch size threshold in quiescent plasma-clotting always occurs given enough time-whereas the shear rate threshold observed under flow is a genuine physical limit imposed by flow-mediated washout of active coagulation factors. Despite the encouraging qualitative results obtained with some models, no single model robustly reproduces all experiments, demonstrating that greater understanding of the underlying reaction network, and particularly of surface reactions, is required. In this direction, additional simulations provide evidence that 1) a surface-localized enzyme, speculatively identified as meizothrombin, is significantly active toward the fluorescent thrombin substrate used in the experiments or, less likely, 2) thrombin is irreversibly inhibited at a faster-than-expected rate, possibly explained by a stimulatory effect of plasma heparin on antithrombin. These results highlight the power of simulation to provide novel mechanistic insights that augment experimental studies and build our understanding of complex biophysicochemical processes. Further validation work is critical to unleashing the full potential of coagulation models as tools for drug development and personalized medicine.
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26
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Zheng X, Yazdani A, Li H, Humphrey JD, Karniadakis GE. A three-dimensional phase-field model for multiscale modeling of thrombus biomechanics in blood vessels. PLoS Comput Biol 2020; 16:e1007709. [PMID: 32343724 PMCID: PMC7224566 DOI: 10.1371/journal.pcbi.1007709] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 05/14/2020] [Accepted: 02/03/2020] [Indexed: 01/10/2023] Open
Abstract
Mechanical interactions between flowing and coagulated blood (thrombus) are crucial in dictating the deformation and remodeling of a thrombus after its formation in hemostasis. We propose a fully-Eulerian, three-dimensional, phase-field model of thrombus that is calibrated with existing in vitro experimental data. This phase-field model considers spatial variations in permeability and material properties within a single unified mathematical framework derived from an energy perspective, thereby allowing us to study effects of thrombus microstructure and properties on its deformation and possible release of emboli under different hemodynamic conditions. Moreover, we combine this proposed thrombus model with a particle-based model which simulates the initiation of the thrombus. The volume fraction of a thrombus obtained from the particle simulation is mapped to an input variable in the proposed phase-field thrombus model. The present work is thus the first computational study to integrate the initiation of a thrombus through platelet aggregation with its subsequent viscoelastic responses to various shear flows. This framework can be informed by clinical data and potentially be used to predict the risk of diverse thromboembolic events under physiological and pathological conditions.
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Affiliation(s)
- Xiaoning Zheng
- Division of Applied Mathematics, Brown University, Providence, Rhode Island, United States of America
| | - Alireza Yazdani
- Division of Applied Mathematics, Brown University, Providence, Rhode Island, United States of America
| | - He Li
- Division of Applied Mathematics, Brown University, Providence, Rhode Island, United States of America
| | - Jay D. Humphrey
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
| | - George E. Karniadakis
- Division of Applied Mathematics, Brown University, Providence, Rhode Island, United States of America
- * E-mail:
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27
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Ngo BKD, Barry ME, Lim KK, Johnson JC, Luna DJ, Pandian NK, Jain A, Grunlan MA. Thromboresistance of Silicones Modified with PEO-Silane Amphiphiles. ACS Biomater Sci Eng 2020; 6:2029-2037. [DOI: 10.1021/acsbiomaterials.0c00011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Bryan Khai D. Ngo
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Mikayla E. Barry
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Kendrick K. Lim
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Jessica C. Johnson
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - David J. Luna
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Navaneeth K.R. Pandian
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Abhishek Jain
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Melissa A. Grunlan
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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28
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Link KG, Stobb MT, Sorrells MG, Bortot M, Ruegg K, Manco-Johnson MJ, Di Paola JA, Sindi SS, Fogelson AL, Leiderman K, Neeves KB. A mathematical model of coagulation under flow identifies factor V as a modifier of thrombin generation in hemophilia A. J Thromb Haemost 2020; 18:306-317. [PMID: 31562694 PMCID: PMC6994344 DOI: 10.1111/jth.14653] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/24/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND The variability in bleeding patterns among individuals with hemophilia A, who have similar factor VIII (FVIII) levels, is significant and the origins are unknown. OBJECTIVE To use a previously validated mathematical model of flow-mediated coagulation as a screening tool to identify parameters that are most likely to enhance thrombin generation in the context of FVIII deficiency. METHODS We performed a global sensitivity analysis (GSA) on our mathematical model to identify potential modifiers of thrombin generation. Candidates from the GSA were confirmed by calibrated automated thrombography (CAT) and flow assays on collagen-tissue factor (TF) surfaces at a shear rate of 100 per second. RESULTS Simulations identified low-normal factor V (FV) (50%) as the strongest modifier, with additional thrombin enhancement when combined with high-normal prothrombin (150%). Low-normal FV levels or partial FV inhibition (60% activity) augmented thrombin generation in FVIII-inhibited or FVIII-deficient plasma in CAT. Partial FV inhibition (60%) boosted fibrin deposition in flow assays performed with whole blood from individuals with mild and moderate FVIII deficiencies. These effects were amplified by high-normal prothrombin levels in both experimental models. CONCLUSIONS These results show that low-normal FV levels can enhance thrombin generation in hemophilia A. Further explorations with the mathematical model suggest a potential mechanism: lowering FV reduces competition between FV and FVIII for factor Xa (FXa) on activated platelet surfaces (APS), which enhances FVIII activation and rescues thrombin generation in FVIII-deficient blood.
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Affiliation(s)
- Kathryn G. Link
- Department of Applied Mathematics, University of California, Merced, Merced, CA, USA
| | - Michael T. Stobb
- Department of Mathematics, University of Utah, Salt Lake City, UT, USA
| | - Matthew G. Sorrells
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, USA
| | - Maria Bortot
- Department of Bioengineering, University of Colorado, Denver | Anschutz Medical Campus, Aurora, CO, USA
| | - Katherine Ruegg
- Hemophilia and Thrombosis Center, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Marilyn J. Manco-Johnson
- Hemophilia and Thrombosis Center, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Jorge A. Di Paola
- Hemophilia and Thrombosis Center, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Suzanne S. Sindi
- Department of Mathematics, University of Utah, Salt Lake City, UT, USA
| | - Aaron L. Fogelson
- Department of Applied Mathematics, University of California, Merced, Merced, CA, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Karin Leiderman
- Department of Applied Mathematics and Statistics, Colorado School of Mines, Golden, CO, USA
| | - Keith B. Neeves
- Department of Bioengineering, University of Colorado, Denver | Anschutz Medical Campus, Aurora, CO, USA
- Hemophilia and Thrombosis Center, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
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Stobb MT, Monroe DM, Leiderman K, Sindi SS. Assessing the impact of product inhibition in a chromogenic assay. Anal Biochem 2019; 580:62-71. [PMID: 31091429 DOI: 10.1016/j.ab.2019.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 12/30/2022]
Abstract
Chromogenic substrates (CS) are synthetic substrates used to monitor the activity of a target enzyme. It has been reported that some CSs display competitive product inhibition with their target enzyme. Thus, in assays where enzyme activity is continuously monitored over long periods of time, the product inhibition may significantly interfere with the reactions being monitored. Despite this knowledge, it is rare for CSs to be directly incorporated into mathematical models that simulate these assays. This devalues the predictive power of the models. In this study, we examined the interactions between a single enzyme, coagulation factor Xa, and its chromogenic substrate. We developed, and experimentally validated, a mathematical model of a chromogenic assay for factor Xa that explicitly included product inhibition from the CS. We employed Bayesian inference, in the form of Markov-Chain Monte Carlo, to estimate the strength of the product inhibition and other sources of uncertainty such as pipetting error and kinetic rate constants. Our model, together with carefully calibrated biochemistry experiments, allowed for full characterization of the strength and impact of product inhibition in the assay. The effect of CS product inhibition in more complex reaction mixtures was further explored using mathematical models.
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Affiliation(s)
- Michael T Stobb
- Department of Applied Mathematics, University of California, Merced, 5200 North Lake Road, Merced, CA, 95340, USA
| | - Dougald M Monroe
- Hematology/Oncology, 8202B Mary Ellen Jones Building, Campus Box 7035, Chapel Hill, NC, 27599-7035, USA
| | - Karin Leiderman
- Department of Applied Mathematics and Statistics, Colorado School of Mines, 1500 Illinois St, Golden, CO, 80401, USA.
| | - Suzanne S Sindi
- Department of Applied Mathematics, University of California, Merced, 5200 North Lake Road, Merced, CA, 95340, USA
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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: 21] [Impact Index Per Article: 4.2] [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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Bravo MC, Tejiram S, McLawhorn MM, Moffatt LT, Orfeo T, Jett-Tilton M, Pusateri AE, Shupp JW, Brummel-Ziedins KE. Utilizing Plasma Composition Data to Help Determine Procoagulant Dynamics in Patients with Thermal Injury: A Computational Assessment. Mil Med 2019; 184:392-399. [PMID: 30901410 DOI: 10.1093/milmed/usy397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/19/2018] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION The development of methods that generate individualized assessments of the procoagulant potential of burn patients could improve their treatment. Beyond its role as an essential intermediate in the formation of thrombin, factor (F)Xa has systemic effects as an agonist to inflammatory processes. In this study, we use a computational model to study the FXa dynamics underlying tissue factor-initiated thrombin generation in a small cohort of burn patients. MATERIALS AND METHODS Plasma samples were collected upon admission (Hour 0) from nine subjects (five non-survivors) with major burn injuries and then at 48 hours. Coagulation factor concentrations (II, V, VII, VIII, IX, X, TFPI, antithrombin (AT), protein C (PC)) were measured and used in a computational model to generate time course profiles for thrombin (IIa), FXa, extrinsic tenase, intrinsic tenase and prothrombinase complexes upon a 5 pM tissue factor stimulus in the presence of 1 nM thrombomodulin. Parameters were extracted from the thrombin and FXa profiles (including max rate (MaxRIIa and MaxRFXa) and peak level (MaxLIIa and MaxLFXa)). Procoagulant potential was also evaluated by determining the concentration of the complexes at select times. Parameter values were compared between survivors and non-survivors in the burn cohort and between the burn cohort and a simulation based on the mean physiological (100%) concentration for all factor levels. RESULTS Burn patients differed at Hour 0 (p < 0.05) from 100% mean physiological levels for all coagulation factor levels except FV and FVII. The concentration of FX, FII, TFPI, AT and PC was lower; FIX and FVIII were increased. The composition differences resulted in all nine burn patients at Hour 0 displaying a procoagulant phenotype relative to 100% mean physiological simulation (MaxLIIa (306 ± 90 nM vs. 52 nM), MaxRIIa (2.9 ± 1.1 nM/s vs. 0.3 nM/s), respectively p < 0.001); MaxRFXa and MaxLFXa were also an order of magnitude greater than 100% mean physiological simulation (p < 0.001). When grouped by survival status and compared at the time of admission, non-survivors had lower PC levels (56 ± 18% vs. 82 ± 9%, p < 0.05), and faster MaxRFXa (29 ± 6 pM/s vs. 18 ± 6 pM/s, p < 0.05) than those that survived; similar trends were observed for all other procoagulant parameters. At 48 hours when comparing non-survivors to survivors, TFPI levels were higher (108 ± 18% vs. 59 ± 18%, p < 0.05), and MaxRIIa (1.5 ± 1.4 nM/s vs. 3.6 ± 0.7 nM/s, p < 0.05) and MaxRFXa (13 ± 12 pM/s vs. 35 ± 4 pM/s, p < 0.05) were lower; similar trends were observed with all other procoagulant parameters. Overall, between admission and 48 hours, procoagulant potential, as represented by MaxR and MaxL parameters for thrombin and FXa, in non-survivors decreased while in survivors they increased (p < 0.05). In patients that survived, there was a positive correlation between FX levels and MaxLFXa (r = 0.96) and reversed in mortality (r= -0.91). CONCLUSIONS Thrombin and FXa generation are increased in burn patients at admission compared to mean physiological simulations. Over the first 48 hours, burn survivors became more procoagulant while non-survivors became less procoagulant. Differences between survivors and non-survivors appear to be present in the underlying dynamics that contribute to FXa dynamics. Understanding how the individual specific balance of procoagulant and anticoagulant proteins contributes to thrombin and FXa generation could ultimately guide therapy and potentially reduce burn injury-related morbidity and mortality.
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Affiliation(s)
- Maria Cristina Bravo
- The Department of Biochemistry, College of Medicine, University of Vermont, 360 South Park Drive, Colchester, VT
| | - Shawn Tejiram
- The Burn Center, Department of Surgery, MedStar Washington Hospital Center, 110 Irving Street, NW; Suite 3B-55, Washington, DC
| | - Melissa M McLawhorn
- The Burn Center, Department of Surgery, MedStar Washington Hospital Center, 110 Irving Street, NW; Suite 3B-55, Washington, DC
| | - Lauren T Moffatt
- The Burn Center, Department of Surgery, MedStar Washington Hospital Center, 110 Irving Street, NW; Suite 3B-55, Washington, DC
| | - Thomas Orfeo
- The Department of Biochemistry, College of Medicine, University of Vermont, 360 South Park Drive, Colchester, VT
| | - Marti Jett-Tilton
- United States Army Center for Environmental Health Research, US Army Medical Command, 568 Doughten Drive, Fort Detrick, MD
| | - Anthony E Pusateri
- US Army Institute of Surgical Research, 3698 Chambers Pass, JBSA - Fort Sam Houston, TX
| | - Jeffrey W Shupp
- The Burn Center, Department of Surgery, MedStar Washington Hospital Center, 110 Irving Street, NW; Suite 3B-55, Washington, DC
| | - Kathleen E Brummel-Ziedins
- The Department of Biochemistry, College of Medicine, University of Vermont, 360 South Park Drive, Colchester, VT
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Méndez Rojano R, Mendez S, Lucor D, Ranc A, Giansily-Blaizot M, Schved JF, Nicoud F. Kinetics of the coagulation cascade including the contact activation system: sensitivity analysis and model reduction. Biomech Model Mechanobiol 2019; 18:1139-1153. [DOI: 10.1007/s10237-019-01134-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/16/2019] [Indexed: 12/14/2022]
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Manuchehrfar F, Tian W, Chou T, Liang J. Evolution of Coagulation-Fragmentation Stochastic Processes Using Accurate Chemical Master Equation Approach. COMMUNICATIONS IN INFORMATION AND SYSTEMS 2019; 19:37-55. [PMID: 34421394 DOI: 10.4310/cis.2019.v19.n1.a3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Coagulation and fragmentation (CF) is a fundamental process in which smaller particles attach to each other to form larger clusters while existing clusters break up into smaller particles . It is a ubiquitous process that plays important roles in many physical and biological phenomena. CF is typically a stochastic process that often occurs in confined spaces with a limited number of available particles . Here, we study the CF process formulated with the discrete Chemical Master Equation (dCME). Using the newly developed Accurate Chemical Master Equation (ACME) method, we examine the time-dependent behavior of the CF system. We investigate the effects of a number of important factors that influence the overall behavior of the system, including the dimensionality, the ratio of attachment to detachment rates among clusters, and the initial conditions. By comparing CF in one and three dimensions, we conclude that systems in three dimensions are more likely to form large clusters. We also demonstrate how the ratio of the attachment to detachment rates affects the dynamics and the steady-state of the system. Finally, we demonstrate the relationship between the formation of large clusters and the initial condition.
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Affiliation(s)
- Farid Manuchehrfar
- Department of Bioengineering, University of Illinois at Chicago (UIC), Chicago, Illinois, USA
| | - Wei Tian
- Department of Bioengineering, University of Illinois at Chicago (UIC), Chicago, Illinois, USA
| | - Tom Chou
- Departments of Biomathematics and Mathematics, University of California at Los Angeles (UCLA), Los Angeles, California
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago (UIC), Chicago, Illinois, USA
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Cheng L, Wei GW, Leil T. Review of quantitative systems pharmacological modeling in thrombosis. COMMUNICATIONS IN INFORMATION AND SYSTEMS 2019; 19:219-240. [PMID: 34045928 DOI: 10.4310/cis.2019.v19.n3.a1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hemostasis and thrombosis are often thought as two sides of the same clotting mechanism whereas hemostasis is a natural protective mechanism to prevent bleeding and thrombosis is a blood clot abnormally formulated inside a blood vessel, blocking the normal blood flow. The evidence to date suggests that at least arterial thrombosis results from the same critical pathways of hemostasis. Analysis of these complex processes and pathways using quantitative systems pharmacological model-based approach can facilitate the delineation of the causal pathways that lead to the emergence of thrombosis. In this paper, we provide an overview of the main molecular and physiological mechanisms associated with hemostasis and thrombosis, and review the models and quantitative system pharmacological modeling approaches that are relevant in characterizing the interplay among the multiple factors and pathways of thrombosis. An emphasis is given to computational models for drug development. Future trends are discussed.
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Affiliation(s)
- Limei Cheng
- Clinical Pharmacology and Pharmacometrics Bristol-Myers Squibb, Princeton, NJ 08540, USA
| | - Guo-Wei Wei
- Department of Mathematics Michigan State University East Lansing, MI 48824 USA
| | - Tarek Leil
- Clinical Pharmacology and Pharmacometrics Bristol-Myers Squibb, Princeton, NJ 08540, USA
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Ruberto MF, Marongiu F, Mandas A, Mameli A, Porru M, Cianchetti E, Barcellona D. The venous thromboembolic risk and the clot wave analysis: a useful relationship? Clin Chem Lab Med 2018; 56:448-453. [PMID: 29031015 DOI: 10.1515/cclm-2017-0678] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 09/12/2017] [Indexed: 11/15/2022]
Abstract
BACKGROUND Hospitalized patients with acute medical conditions have higher venous thromboembolism (VTE) risk. A patient with a final Padua Prediction Score (PPS) of ≥4 is considered to be at high risk for VTE. The aim of this study was to investigate on a possible relationship between PPS, the dynamics of the clot formation, i.e. the clot waveform analysis (CWA) of aPTT, fibrinogen and D-Dimer in a large group of medical patients. METHODS CWA in terms of velocity (first derivative), acceleration (second derivative), density (Delta) of aPTT, fibrinogen, D-Dimer and PPS for VTE were determined in 801 medical patients divided in three groups (without antithrombotic prophylaxis and high PPS, without antithrombotic prophylaxis and low PPS, with antithrombotic prophylaxis and high PPS) and a group of healthy subjects. RESULTS CWA, fibrinogen and D-Dimer values were higher in the medical patients with high PPS with or without antithrombotic prophylaxis when compared with patients without antithrombotic prophylaxis with low PPS and healthy subjects. The second derivative, fibrinogen and D-Dimer were significantly associated with a high PPS score (≥4): odds ratio (OR) = 1.53, 95% confidence interval (CI) = 1.03-2.28; OR = 1.91, 95% CI = 1.3-2.79; OR = 3.16, 95% CI = 2.29-4.36, respectively. Interactions between first derivative and D-Dimer (OR = 2.14, 95% CI = 1.23-3.72) and first derivative and fibrinogen (OR = 1.75, 95% CI = 1.02-2.98) were found. CONCLUSIONS CWA could give useful information to recognize a hypercoagulable state in patients admitted to a medical ward with high and low PPS. First and second derivative aPTT, D-Dimer and fibrinogen levels could be added to PPS to better assess the global thromboembolic risk of these patients.
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Affiliation(s)
- Maria Filomena Ruberto
- Department of Medical Science and Public Health, University of Cagliari, Cagliari, Italy
| | - Francesco Marongiu
- Internal Medicine and Haemostasis and Thrombosis Unit, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy, Phone: +39070 6754188
| | - Antonella Mandas
- Department of Medical Science and Public Health, University of Cagliari, Cagliari, Italy
| | - Antonella Mameli
- Department of Medical Science and Public Health, University of Cagliari, Cagliari, Italy
| | - Mariagrazia Porru
- Department of Medical Science and Public Health, University of Cagliari, Cagliari, Italy
| | - Elisabetta Cianchetti
- Department of Medical Science and Public Health, University of Cagliari, Cagliari, Italy
| | - Doris Barcellona
- Department of Medical Science and Public Health, University of Cagliari, Cagliari, Italy
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Lu Y, Lee MY, Zhu S, Sinno T, Diamond SL. Multiscale simulation of thrombus growth and vessel occlusion triggered by collagen/tissue factor using a data-driven model of combinatorial platelet signalling. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2018; 34:523-546. [PMID: 27672182 PMCID: PMC5798174 DOI: 10.1093/imammb/dqw015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/23/2016] [Indexed: 12/23/2022]
Abstract
During clotting under flow, platelets bind and activate on collagen and release autocrinic factors such as ADP and thromboxane, while tissue factor (TF) on the damaged wall leads to localized thrombin generation. Towards patient-specific simulation of thrombosis, a multiscale approach was developed to account for: platelet signalling [neural network (NN) trained by pairwise agonist scanning (PAS), PAS-NN], platelet positions (lattice kinetic Monte Carlo, LKMC), wall-generated thrombin and platelet-released ADP/thromboxane convection–diffusion (partial differential equation, PDE) and flow over a growing clot (lattice Boltzmann). LKMC included shear-driven platelet aggregate restructuring. The PDEs for thrombin, ADP and thromboxane were solved by finite element method using cell activation-driven adaptive triangular meshing. At all times, intracellular calcium was known for each platelet by PAS-NN in response to its unique exposure to local collagen, ADP, thromboxane and thrombin. When compared with microfluidic experiments of human blood clotting on collagen/TF driven by constant pressure drop, the model accurately predicted clot morphology and growth with time. In experiments and simulations at TF at 0.1 and 10 molecule-TF/\documentclass[12pt]{minimal}
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}{}$_{1}$\end{document} and IP-receptor. This multiscale approach facilitates patient-specific simulation of thrombosis under hemodynamic and pharmacological conditions.
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Affiliation(s)
- Yichen Lu
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Mei Yan Lee
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Shu Zhu
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Talid Sinno
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Scott L Diamond
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia PA 19104, USA
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Sagar A, LeCover R, Shoemaker C, Varner J. Dynamic Optimization with Particle Swarms (DOPS): a meta-heuristic for parameter estimation in biochemical models. BMC SYSTEMS BIOLOGY 2018; 12:87. [PMID: 30314484 PMCID: PMC6186122 DOI: 10.1186/s12918-018-0610-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 09/17/2018] [Indexed: 01/28/2023]
Abstract
BACKGROUND Mathematical modeling is a powerful tool to analyze, and ultimately design biochemical networks. However, the estimation of the parameters that appear in biochemical models is a significant challenge. Parameter estimation typically involves expensive function evaluations and noisy data, making it difficult to quickly obtain optimal solutions. Further, biochemical models often have many local extrema which further complicates parameter estimation. Toward these challenges, we developed Dynamic Optimization with Particle Swarms (DOPS), a novel hybrid meta-heuristic that combined multi-swarm particle swarm optimization with dynamically dimensioned search (DDS). DOPS uses a multi-swarm particle swarm optimization technique to generate candidate solution vectors, the best of which is then greedily updated using dynamically dimensioned search. RESULTS We tested DOPS using classic optimization test functions, biochemical benchmark problems and real-world biochemical models. We performed [Formula: see text] = 25 trials with [Formula: see text] = 4000 function evaluations per trial, and compared the performance of DOPS with other commonly used meta-heuristics such as differential evolution (DE), simulated annealing (SA) and dynamically dimensioned search (DDS). On average, DOPS outperformed other common meta-heuristics on the optimization test functions, benchmark problems and a real-world model of the human coagulation cascade. CONCLUSIONS DOPS is a promising meta-heuristic approach for the estimation of biochemical model parameters in relatively few function evaluations. DOPS source code is available for download under a MIT license at http://www.varnerlab.org .
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Affiliation(s)
- Adithya Sagar
- Robert Fredrick Smith School of Chemical and Biomolecular Engineering, Cornell University, 244 Olin Hall, Ithaca, NY, USA
| | - Rachel LeCover
- Robert Fredrick Smith School of Chemical and Biomolecular Engineering, Cornell University, 244 Olin Hall, Ithaca, NY, USA
| | - Christine Shoemaker
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Jeffrey Varner
- Robert Fredrick Smith School of Chemical and Biomolecular Engineering, Cornell University, 244 Olin Hall, Ithaca, NY, USA.
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Susree M, Panteleev MA, Anand M. Coated platelets introduce significant delay in onset of peak thrombin production: Theoretical predictions. J Theor Biol 2018; 453:108-116. [PMID: 29782929 DOI: 10.1016/j.jtbi.2018.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/26/2018] [Accepted: 05/17/2018] [Indexed: 11/16/2022]
Abstract
Platelets play a crucial role in the initiation, progress, termination as well as regulation of blood coagulation. Recent studies have confirmed that not all but only a small percentage of thrombin-activated platelets ("coated" platelets) exhibit procoagulant properties (namely the expression of phosphatidylserine binding sites) required for the acceleration and progress of coagulation. A mechanistic model is developed for in vitro coagulation whose key features are distinct equations for coated platelets, thrombin dose-dependence for coated platelets, and competitive binding of coagulation factors to platelet membrane. Model predictions show significant delay in the onset of peak Va production, and peak thrombin production when dose-dependence is incorporated instead of a fixed theoretical maximum percentage of coated platelets. Further, peak thrombin concentration is significantly overestimated when either fractional presence of coated platelets is ignored (by 299.4%) or when dose-dependence on thrombin is ignored (by 24.7%).
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Affiliation(s)
- M Susree
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285 Telangana, India
| | - Mikhail A Panteleev
- Center for Theoretical Problems of Physicochemical Pharmacology, Federal Research and Clinical Center of Pediatric Hematology, Oncology and Immunology, Lomonosov Moscow State University, Moscow, Russia
| | - M Anand
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285 Telangana, India.
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40
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Link KG, Stobb MT, Di Paola J, Neeves KB, Fogelson AL, Sindi SS, Leiderman K. A local and global sensitivity analysis of a mathematical model of coagulation and platelet deposition under flow. PLoS One 2018; 13:e0200917. [PMID: 30048479 PMCID: PMC6062055 DOI: 10.1371/journal.pone.0200917] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/04/2018] [Indexed: 11/23/2022] Open
Abstract
The hemostatic response involves blood coagulation and platelet aggregation to stop blood loss from an injured blood vessel. The complexity of these processes make it difficult to intuit the overall hemostatic response without quantitative methods. Mathematical models aim to address this challenge but are often accompanied by numerous parameters choices and thus need to be analyzed for sensitivity to such choices. Here we use local and global sensitivity analyses to study a model of coagulation and platelet deposition under flow. To relate with clinical assays, we measured the sensitivity of three specific thrombin metrics: lag time, maximum relative rate of generation, and final concentration after 20 minutes. In addition, we varied parameters of three different classes: plasma protein levels, kinetic rate constants, and platelet characteristics. In terms of an overall ranking of the model’s sensitivities, we found that the local and global methods provided similar information. Our local analysis, in agreement with previous findings, shows that varying parameters within 50-150% of baseline values, in a one-at-a-time (OAT) fashion, always leads to significant thrombin generation in 20 minutes. Our global analysis gave a different and novel result highlighting groups of parameters, still varying within the normal 50-150%, that produced little or no thrombin in 20 minutes. Variations in either plasma levels or platelet characteristics, using either OAT or simultaneous variations, always led to strong thrombin production and overall, relatively low output variance. Simultaneous variation in kinetics rate constants or in a subset of all three parameter classes led to the highest overall output variance, incorporating instances with little to no thrombin production. The global analysis revealed multiple parameter interactions in the lag time and final concentration leading to relatively high variance; high variance was also observed in the thrombin generation rate, but parameters attributed to that variance acted independently and additively.
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Affiliation(s)
- Kathryn G. Link
- Department of Bioengineering, University of Utah, Salt Lake City, UT, United States of America
| | - Michael T. Stobb
- Department of Applied Mathematics, University of California Merced, Merced, CA, United States of America
| | - Jorge Di Paola
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Keith B. Neeves
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States of America
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, United States of America
| | - Aaron L. Fogelson
- Department of Mathematics, University of Utah, Salt Lake City, UT, United States of America
- Department of Bioengineering, University of Utah, Salt Lake City, UT, United States of America
| | - Suzanne S. Sindi
- Department of Applied Mathematics, University of California Merced, Merced, CA, United States of America
| | - Karin Leiderman
- Department of Applied Mathematics and Statistics, Colorado School of Mines, Golden, CO, United States of America
- * E-mail:
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41
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Xu S, Xu Z, Kim OV, Litvinov RI, Weisel JW, Alber M. Model predictions of deformation, embolization and permeability of partially obstructive blood clots under variable shear flow. J R Soc Interface 2018; 14:rsif.2017.0441. [PMID: 29142014 DOI: 10.1098/rsif.2017.0441] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/19/2017] [Indexed: 01/20/2023] Open
Abstract
Thromboembolism, one of the leading causes of morbidity and mortality worldwide, is characterized by formation of obstructive intravascular clots (thrombi) and their mechanical breakage (embolization). A novel two-dimensional multi-phase computational model is introduced that describes active interactions between the main components of the clot, including platelets and fibrin, to study the impact of various physiologically relevant blood shear flow conditions on deformation and embolization of a partially obstructive clot with variable permeability. Simulations provide new insights into mechanisms underlying clot stability and embolization that cannot be studied experimentally at this time. In particular, model simulations, calibrated using experimental intravital imaging of an established arteriolar clot, show that flow-induced changes in size, shape and internal structure of the clot are largely determined by two shear-dependent mechanisms: reversible attachment of platelets to the exterior of the clot and removal of large clot pieces. Model simulations predict that blood clots with higher permeability are more prone to embolization with enhanced disintegration under increasing shear rate. In contrast, less permeable clots are more resistant to rupture due to shear rate-dependent clot stiffening originating from enhanced platelet adhesion and aggregation. These results can be used in future to predict risk of thromboembolism based on the data about composition, permeability and deformability of a clot under specific local haemodynamic conditions.
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Affiliation(s)
- Shixin Xu
- Department of Mathematics, Division of Clinical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
| | - Zhiliang Xu
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Oleg V Kim
- Department of Mathematics, Division of Clinical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rustem I Litvinov
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan 420008, Russian Federation
| | - John W Weisel
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Alber
- Department of Mathematics, Division of Clinical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA .,Department of Internal Medicine, Division of Clinical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA.,Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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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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43
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Zhu S, Chen J, Diamond SL. Establishing the Transient Mass Balance of Thrombosis: From Tissue Factor to Thrombin to Fibrin Under Venous Flow. Arterioscler Thromb Vasc Biol 2018; 38:1528-1536. [PMID: 29724819 PMCID: PMC6023760 DOI: 10.1161/atvbaha.118.310906] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/19/2018] [Indexed: 11/16/2022]
Abstract
Supplemental Digital Content is available in the text. Objective— We investigated the coregulation of thrombin and fibrin as blood flows over a procoagulant surface. Approach and Results— Using microfluidic perfusion of factor XIIa-inhibited human whole blood (200 s−1 wall shear rate) over a 250-μm long patch of collagen/TF (tissue factor; ≈1 molecule per μm2) and immunoassays of the effluent for F1.2 (prothrombin fragment 1.2), TAT (thrombin–antithrombin complex), and D-dimer (post–end point plasmin digest), we sought to establish the transient mass balance for clotting under venous flow. F1.2 (but almost no free thrombin detected via TAT assay) continually eluted from clots when fibrin was allowed to form. Low-dose fluorescein-Phe-Pro-Arg-chloromethylketone stained fibrin-bound thrombin—a staining ablated by anti–γ′-fibrinogen or the fibrin inhibitor glypro-arg-pro but highly resistant to 7-minute buffer rinse, demonstrating tight binding of thrombin to γ′-fibrin. With fibrin polymerizing for 500 seconds, 92 000 thrombin molecules and 203 000 clot-associated fibrin monomer equivalents were generated per TF molecule (or per μm2). Fibrin reached 15 mg/mL in the pore space (porosity ≈0.5) of a 15-μm-thick thrombus core by 500 seconds and 30 mg/mL by 800 seconds. For a known rate of ≈60 FPA (fibrinopeptide-A) per thrombin per second, each thrombin molecule generated only 3 fibrin monomer equivalents during 500 seconds, indicating an intraclot thrombin half-life of ≈70 ms, much shorter than its diffusional escape time (≈10 seconds). By 800 seconds, gly-pro-arg-pro allowed 4-fold more F1.2 generation, consistent with gly-pro-arg-pro ablating fibrin’s antithrombin-I activity and facilitating thrombin-mediated FXIa activation. Conclusions— Under flow, fibrinogen continually penetrates the clot, and γ′-fibrin regulates thrombin.
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Affiliation(s)
- Shu Zhu
- From the Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia
| | - Jason Chen
- From the Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia
| | - Scott L Diamond
- From the Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia.
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44
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Computational Model for Hyperfibrinolytic Onset of Acute Traumatic Coagulopathy. Ann Biomed Eng 2018; 46:1173-1182. [PMID: 29675813 DOI: 10.1007/s10439-018-2031-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/16/2018] [Indexed: 12/16/2022]
Abstract
The onset of acute traumatic coagulopathy in trauma patients exacerbates hemorrhaging and dramatically increases mortality. The disease is characterized by increased localized bleeding, and the mechanism for its onset is not yet known. We propose that the fibrinolytic response, specifically the release of tissue-plasminogen activator (t-PA), within vessels of different sizes leads to a variable susceptibility to local coagulopathy through hyperfibrinolysis which can explain many of the clinical observations in the early stages from severely injured coagulopathic patients. We use a partial differential equation model to examine the consequences of vessel geometry and extent of injury on fibrinolysis profiles. In addition, we simulate the efficacy of tranexamic acid treatment on coagulopathy initiated through endothelial t-PA release, and are able to reproduce the time-sensitive nature of the efficacy of this treatment as observed in clinical studies.
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45
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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: 44] [Impact Index Per Article: 7.3] [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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46
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Tsiklidis E, Sims C, Sinno T, Diamond SL. Multiscale systems biology of trauma-induced coagulopathy. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 10:e1418. [PMID: 29485252 DOI: 10.1002/wsbm.1418] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/03/2018] [Accepted: 01/09/2018] [Indexed: 01/26/2023]
Abstract
Trauma with hypovolemic shock is an extreme pathological state that challenges the body to maintain blood pressure and oxygenation in the face of hemorrhagic blood loss. In conjunction with surgical actions and transfusion therapy, survival requires the patient's blood to maintain hemostasis to stop bleeding. The physics of the problem are multiscale: (a) the systemic circulation sets the global blood pressure in response to blood loss and resuscitation therapy, (b) local tissue perfusion is altered by localized vasoregulatory mechanisms and bleeding, and (c) altered blood and vessel biology resulting from the trauma as well as local hemodynamics control the assembly of clotting components at the site of injury. Building upon ongoing modeling efforts to simulate arterial or venous thrombosis in a diseased vasculature, computer simulation of trauma-induced coagulopathy is an emerging approach to understand patient risk and predict response. Despite uncertainties in quantifying the patient's dynamic injury burden, multiscale systems biology may help link blood biochemistry at the molecular level to multiorgan responses in the bleeding patient. As an important goal of systems modeling, establishing early metrics of a patient's high-dimensional trajectory may help guide transfusion therapy or warn of subsequent later stage bleeding or thrombotic risks. This article is categorized under: Analytical and Computational Methods > Computational Methods Biological Mechanisms > Regulatory Biology Models of Systems Properties and Processes > Mechanistic Models.
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Affiliation(s)
- Evan Tsiklidis
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Carrie Sims
- Department of Trauma Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Talid Sinno
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Scott L Diamond
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
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47
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Méndez Rojano R, Mendez S, Nicoud F. Introducing the pro-coagulant contact system in the numerical assessment of device-related thrombosis. Biomech Model Mechanobiol 2018; 17:815-826. [PMID: 29302840 DOI: 10.1007/s10237-017-0994-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/14/2017] [Indexed: 11/28/2022]
Abstract
Thrombosis is a major concern in blood-coated medical devices. Contact activation, which is the initial part of the coagulation cascade in device-related thrombosis, is not considered in current thrombus formation models. In the present study, pro-coagulant reactions including the contact activation system are coupled with a fluid solver in order to evaluate the potential of the contact system to initiate thrombin production. The biochemical/fluid model is applied to a backward-facing step configuration, a flow configuration that frequently appears in medical devices. In contrast to the in vivo thrombosis models in which a specific thrombotic zone (injury region) is set a priori by the user to initiate the coagulation reaction, a reactive surface boundary condition is applied to the whole device wall. Simulation results show large thrombin concentration in regions related to recirculation zones without the need of an a priori knowledge of the thrombus location. The numerical results align well with the regions prone to thrombosis observed in experimental results reported in the literature. This approach could complement thrombus formation models that take into account platelet activity and thrombus growth to optimize a wide range of medical devices.
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Affiliation(s)
- Rodrigo Méndez Rojano
- Institut Montpelliérain Alexander Grothendieck, CNRS, Univ. Montpellier, 2 Place Eugène Bataillon, 34095, Montpellier Cedex 5, France.
| | - Simon Mendez
- Institut Montpelliérain Alexander Grothendieck, CNRS, Univ. Montpellier, 2 Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Franck Nicoud
- Institut Montpelliérain Alexander Grothendieck, CNRS, Univ. Montpellier, 2 Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
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48
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Dunster JL, Panteleev MA, Gibbins JM, Sveshnikova AN. Mathematical Techniques for Understanding Platelet Regulation and the Development of New Pharmacological Approaches. Methods Mol Biol 2018; 1812:255-279. [PMID: 30171583 DOI: 10.1007/978-1-4939-8585-2_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mathematical and computational modeling is currently in the process of becoming an accepted tool in the arsenal of methods utilized for the investigation of complex biological systems. For some problems in the field, like cellular metabolic regulation, neural impulse propagation, or cell cycle, progress is already unthinkable without use of such methods. Mathematical models of platelet signaling, function, and metabolism during the last years have not only been steadily increasing in their number, but have also been providing more in-depth insights, generating hypotheses, and allowing predictions to be made leading to new experimental designs and data. Here we describe the basic approaches to platelet mathematical model development and validation, highlighting the challenges involved. We then review the current theoretical models in the literature and how these are being utilized to increase our understanding of these complex cells.
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Affiliation(s)
- Joanna L Dunster
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, University of Reading, Reading, UK.
| | - Mikhail A Panteleev
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
- National Scientific and Practical Centre of Pediatric Hematology, Oncology and Immunology Named After Dmitry Rogachev, 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, University of Reading, Reading, UK
| | - Anastacia N Sveshnikova
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
- National Scientific and Practical Centre of Pediatric Hematology, Oncology and Immunology Named After Dmitry Rogachev, Moscow, Russia
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49
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Nobile MS, Cazzaniga P, Tangherloni A, Besozzi D. Graphics processing units in bioinformatics, computational biology and systems biology. Brief Bioinform 2017; 18:870-885. [PMID: 27402792 PMCID: PMC5862309 DOI: 10.1093/bib/bbw058] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Indexed: 01/18/2023] Open
Abstract
Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools.
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Affiliation(s)
- Marco S Nobile
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy
- SYSBIO.IT Centre of Systems Biology, Milano, Italy
| | - Paolo Cazzaniga
- Department of Human and Social Sciences, University of Bergamo, Bergamo, Italy
- SYSBIO.IT Centre of Systems Biology, Milano, Italy
| | - Andrea Tangherloni
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy
| | - Daniela Besozzi
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy
- SYSBIO.IT Centre of Systems Biology, Milano, Italy
- Corresponding author. Daniela Besozzi, Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy and SYSBIO.IT Centre of Systems Biology, Milano, Italy. Tel.: +39 02 6448 7874. E-mail:
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50
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A Short Review of Advances in the Modelling of Blood Rheology and Clot Formation. FLUIDS 2017. [DOI: 10.3390/fluids2030035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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