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Berger M, Hell T, Tobiasch A, Martini J, Lindner A, Tauber H, Bachler M, Hermann M. Analysis of fibrin networks using topological data analysis - a feasibility study. Sci Rep 2024; 14:13123. [PMID: 38849447 PMCID: PMC11161616 DOI: 10.1038/s41598-024-63935-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
Blood clot formation, a crucial process in hemostasis and thrombosis, has garnered substantial attention for its implications in various medical conditions. Microscopic examination of blood clots provides vital insights into their composition and structure, aiding in the understanding of clot pathophysiology and the development of targeted therapeutic strategies. This study explores the use of topological data analysis (TDA) to assess plasma clot characteristics microscopically, focusing on the identification of the elements components, holes and Wasserstein distances. This approach should enable researchers to objectively classify fibrin networks based on their topologic architecture. We tested this mathematical characterization approach on plasma clots formed in static conditions from porcine and human citrated plasma samples, where the effect of dilution and direct thrombin inhibition was explored. Confocal microscopy images showing fluorescence labeled fibrin networks were analyzed. Both treatments resulted in visual differences in plasma clot architecture, which could be quantified using TDA. Significant differences between baseline and diluted samples, as well as blood anticoagulated with argatroban, were detected mathematically. Therefore, TDA could be indicative of clots with compromised stability, providing a valuable tool for thrombosis risk assessment. In conclusion, microscopic examination of plasma clots, coupled with Topological Data Analysis, offers a promising avenue for comprehensive characterization of clot microstructure. This method could contribute to a deeper understanding of clot pathophysiology and thereby refine our ability to assess clot characteristics.
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Affiliation(s)
| | - Tobias Hell
- Data Lab Hell, Europastraße 2a, Zirl, Austria
| | - Anna Tobiasch
- organLife Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University Innsbruck, Innsbruck, Austria.
| | - Judith Martini
- Department of Anaesthesia and Intensive Care Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Andrea Lindner
- Department of Urology and Andrology, District Hospital Hall, Hall in Tirol, Austria
| | - Helmuth Tauber
- Department of Anaesthesiology and Intensive Care Medicine, Sanatorium Kettenbruecke der Barmherzigen Schwestern GmbH, Innsbruck, Austria
| | - Mirjam Bachler
- Institute for Sports Medicine, Alpine Medicine and Health Tourism, UMIT - University for Health Sciences, Medical Informatics and Technology, Austria, Hall in Tirol, Austria
| | - Martin Hermann
- Department of Anaesthesia and Intensive Care Medicine, Medical University of Innsbruck, Innsbruck, Austria
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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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Paszek E, Malinowski KP, Ząbczyk M, Butenas S, Undas A. Elevated factor XIa as a modulator of plasma fibrin clot properties in coronary artery disease. Eur J Clin Invest 2023; 53:e14007. [PMID: 37042848 DOI: 10.1111/eci.14007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/12/2023] [Accepted: 04/11/2023] [Indexed: 04/13/2023]
Abstract
INTRODUCTION Patients with coronary artery disease (CAD) display a prothrombotic fibrin clot phenotype, involving low permeability and resistance to lysis. The determinants of this phenotype remain elusive. Circulating tissue factor (TF) and activated factor XI (FXIa) are linked to arterial thromboembolism. We investigated whether detectable active TF and FXIa influence fibrin clot properties in CAD. METHODS In 118 CAD patients (median age 65 years, 78% men), we assessed Ks, an indicator of clot permeability, and clot lysis time (CLT) in plasma-based assays, along with the presence of active TF and FXIa. We also analysed proteins involved in clotting and thrombolysis, including fibrinogen, plasminogen activator inhibitor-1 (PAI-1) and thrombin activatable thrombolysis inhibitor (TAFI). During a median 106 month (interquartile range 95-119) follow-up, myocardial infarction (MI), stroke, systemic thromboembolism (SE) and cardiovascular (CV) death were recorded. RESULTS Circulating TF and FXIa, detected in 20.3% and 39.8% of patients, respectively, were associated with low Ks and prolonged CLT. Solely FXIa remained an independent predictor of low Ks and high CLT on multivariable analysis. Additionally, fibrinogen and PAI-1 were associated with low Ks, while PAI-1 and TAFI-with prolonged CLT. During follow-up low Ks and prolonged CLT increased the risk of MI and the latter also a composite endpoint of MI, stroke/SE or CV death. CONCLUSIONS To our knowledge, this study is the first to show that circulating FXIa is associated with prothrombotic fibrin clot properties in CAD, suggesting additional mechanisms through which FXIa inhibitors could act as novel antithrombotic agents in CAD.
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Affiliation(s)
- Elżbieta Paszek
- Clinical Department of Interventional Cardiology, John Paul II Hospital, Krakow, Poland
- Department of Thromboembolic Disorders, Institute of Cardiology, Jagiellonian University Medical College, Krakow, Poland
| | - Krzysztof P Malinowski
- Department of Bioinformatics and Telemedicine, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
- Center for Digital Medicine and Robotics, Jagiellonian University Medical College, Krakow, Poland
| | - Michał Ząbczyk
- Department of Thromboembolic Disorders, Institute of Cardiology, Jagiellonian University Medical College, Krakow, Poland
- Krakow Center for Medical Research and Technologies, John Paul II Hospital, Krakow, Poland
| | - Saulius Butenas
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Anetta Undas
- Department of Thromboembolic Disorders, Institute of Cardiology, Jagiellonian University Medical College, Krakow, Poland
- Krakow Center for Medical Research and Technologies, John Paul II Hospital, Krakow, Poland
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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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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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6
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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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7
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Méndez Rojano R, Lai A, Zhussupbekov M, Burgreen GW, Cook K, Antaki JF. A fibrin enhanced thrombosis model for medical devices operating at low shear regimes or large surface areas. PLoS Comput Biol 2022; 18:e1010277. [PMID: 36190991 PMCID: PMC9560616 DOI: 10.1371/journal.pcbi.1010277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/13/2022] [Accepted: 09/15/2022] [Indexed: 11/06/2022] Open
Abstract
Over the past decade, much of the development of computational models of device-related thrombosis has focused on platelet activity. While those models have been successful in predicting thrombus formation in medical devices operating at high shear rates (> 5000 s−1), they cannot be directly applied to low-shear devices, such as blood oxygenators and catheters, where emerging information suggest that fibrin formation is the predominant mechanism of clotting and platelet activity plays a secondary role. In the current work, we augment an existing platelet-based model of thrombosis with a partial model of the coagulation cascade that includes contact activation of factor XII and fibrin production. To calibrate the model, we simulate a backward-facing-step flow channel that has been extensively characterized in-vitro. Next, we perform blood perfusion experiments through a microfluidic chamber mimicking a hollow fiber membrane oxygenator and validate the model against these observations. The simulation results closely match the time evolution of the thrombus height and length in the backward-facing-step experiment. Application of the model to the microfluidic hollow fiber bundle chamber capture both gross features such as the increasing clotting trend towards the outlet of the chamber, as well as finer local features such as the structure of fibrin around individual hollow fibers. Our results are in line with recent findings that suggest fibrin production, through contact activation of factor XII, drives the thrombus formation in medical devices operating at low shear rates with large surface area to volume ratios. Patients treated with blood-contacting medical devices suffer from clotting complications. Over the past decades, a great effort has been made to develop computational tools to predict and prevent clot formation in these devices. However, most models have focused on platelet activity and neglected other important parts of the problem such as the coagulation cascade reactions that lead to fibrin formation. In the current work, we incorporate this missing element into a well-established and validated model for platelet activity. We then use this novel approach to predict thrombus formation in two experimental configurations. Our results confirm that to accurately predict the clotting process in devices where surface area to volume ratios are large and flow velocity and shear stresses remain low, coagulation reactions and subsequent fibrin formation must be considered. This new model could have great implications for the design and optimization of medical devices such as blood oxygenators. In the long term, the model could evolve into a functional tool to inform anticoagulation therapies for these patients.
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Affiliation(s)
- Rodrigo Méndez Rojano
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Angela Lai
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Mansur Zhussupbekov
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, United States of America
| | - Greg W. Burgreen
- Center for Advanced Vehicular Systems, Mississippi State University, Starkville, Mississippi, United States of America
| | - Keith Cook
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - James F. Antaki
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, United States of America
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8
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Zhang Y, Trigani KT, Shankar KN, Crossen J, Liu Y, Sinno T, Diamond SL. Anti-GPVI Fab reveals distinct roles for GPVI signaling in the first platelet layer and subsequent layers during microfluidic clotting on collagen with or without tissue factor. Thromb Res 2022; 218:112-129. [PMID: 36037547 DOI: 10.1016/j.thromres.2022.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/09/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022]
Abstract
The collagen receptor glycoprotein VI (GPVI) drives strong platelet activation, however its role at later stages of clotting remains less clear. Controlled timing of addition of anti-human GPVI Fab (clone E12) with microfluidic venous whole blood flow over collagen (± lipidated tissue factor, TF) produced distinct effects on platelets, fibrin, P-selectin exposure, and phosphatidylserine (PS) exposure. On collagen alone, Fab present initially potently reduced platelet deposition on collagen, while Fab added 90 s after initial platelet deposition, stopped subsequent platelet accumulation (despite the absence of fibrin). With thrombin generation via TF, Fab added at either t = 0 or 90 s had no effect on platelet deposition. However, Fab added initially, but not at 90-s, blocked fibrin formation. Gly-Pro-Arg-Pro ablated fibrin formation without effect on platelet accumulation (regardless of Fab added at t = 0 or 90 s), indicating thrombin signaling can suffice over GPVI signaling. Still, Fab moderately reduced P-selectin exposure with thrombin present and fibrin absent. On collagen/TF, Fab present initially ablated PS exposure, but had no effect when added 30 to 90-s later. The thrombin generated via PS exposure had an important role in driving platelet deposition in the presence of Fab, since inhibition of PS via annexin V binding in the presence of Fab significantly inhibited platelet deposition. We conclude GPVI signaling in the first platelet layer on collagen dictates thrombin and fibrin production, but the role of GPVI at subsequent times after formation of the first monolayer is obscured by thrombin-induced signaling.
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Affiliation(s)
- Y Zhang
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - K T Trigani
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - K N Shankar
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - J Crossen
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Y Liu
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - T Sinno
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - S L Diamond
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
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9
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Kelley MA, Leiderman K. Mathematical modeling to understand the role of bivalent thrombin-fibrin binding during polymerization. PLoS Comput Biol 2022; 18:e1010414. [PMID: 36107837 PMCID: PMC9477365 DOI: 10.1371/journal.pcbi.1010414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Thrombin is an enzyme produced during blood coagulation that is crucial to the formation of a stable clot. Thrombin cleaves soluble fibrinogen into fibrin, which polymerizes and forms an insoluble, stabilizing gel around the growing clot. A small fraction of circulating fibrinogen is the variant γA/γ′, which has been associated with high-affinity thrombin binding and implicated as a risk factor for myocardial infarctions, deep vein thrombosis, and coronary artery disease. Thrombin is also known to be strongly sequestered by polymerized fibrin for extended periods of time in a way that is partially regulated by γA/γ′. However, the role of γA/γ′-thrombin interactions during fibrin polymerization is not fully understood. Here, we present a mathematical model of fibrin polymerization that considered the interactions between thrombin, fibrinogen, and fibrin, including those with γA/γ′. In our model, bivalent thrombin-fibrin binding greatly increased thrombin residency times and allowed for thrombin-trapping during fibrin polymerization. Results from the model showed that early in fibrin polymerization, γ′ binding to thrombin served to localize the thrombin to the fibrin(ogen), which effectively enhanced the enzymatic conversion of fibrinogen to fibrin. When all the fibrin was fully generated, however, the fibrin-thrombin binding persisted but the effect of fibrin on thrombin switched quickly to serve as a sink, essentially removing all free thrombin from the system. This dual role for γ′-thrombin binding during polymerization led to a paradoxical decrease in trapped thrombin as the amount of γ′ was increased. The model highlighted biochemical and biophysical roles for fibrin-thrombin interactions during polymerization and agreed well with experimental observations.
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Affiliation(s)
- Michael A. Kelley
- Department of Applied Mathematics and Statistics, Colorado School of Mines, Golden, Colorado, United States of America
| | - Karin Leiderman
- Department of Applied Mathematics and Statistics, Colorado School of Mines, Golden, Colorado, United States of America
- * E-mail:
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10
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Carlo A, Yan Q, Ten Cate H, De Laat-Kremers R, De Laat B, Ninivaggi M. Semi-automated thrombin dynamics applying the ST Genesia thrombin generation assay. Front Cardiovasc Med 2022; 9:912433. [PMID: 35958413 PMCID: PMC9360406 DOI: 10.3389/fcvm.2022.912433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/30/2022] [Indexed: 01/15/2023] Open
Abstract
Background The haemostatic balance is an equilibrium of pro- and anticoagulant factors that work synergistically to prevent bleeding and thrombosis. As thrombin is the central enzyme in the coagulation pathway, it is desirable to measure thrombin generation (TG) in order to detect possible bleeding or thrombotic phenotypes, as well as to investigate the capacity of drugs affecting the formation of thrombin. By investigating the underlying processes of TG (i.e., prothrombin conversion and inactivation), additional information is collected about the dynamics of thrombin formation. Objectives To obtain reference values for thrombin dynamics (TD) analysis in 112 healthy donors using an automated system for TG. Methods TG was measured on the ST Genesia, fibrinogen on the Start, anti-thrombin (AT) on the STA R Max and α2Macroglobulin (α2M) with an in-house chromogenic assay. Results TG was measured using STG-BleedScreen, STG-ThromboScreen and STG-DrugScreen. The TG data was used as an input for TD analysis, in combination with plasma levels of AT, α2M and fibrinogen that were 113% (108-118%), 2.6 μM (2.2 μM-3.1 μM) and 2.9 g/L (2.6-3.2 g/L), respectively. The maximum rate of the prothrombinase complex (PCmax) and the total amount of prothrombin converted (PCtot) increased with increasing tissue factor (TF) concentration. PCtot increased from 902 to 988 nM, whereas PCmax increased from 172 to 508 nM/min. Thrombin (T)-AT and T-α2M complexes also increased with increasing TF concentration (i.e., from 860 to 955 nM and from 28 to 33 nm, respectively). PCtot, T-AT and T-α2M complex formation were strongly inhibited by addition of thrombomodulin (-44%, -43%, and -48%, respectively), whereas PCmax was affected less (-24%). PCtot, PCmax, T-AT, and T-α2M were higher in women using oral contraceptives (OC) compared to men/women without OC, and inhibition by thrombomodulin was also significantly less in women on OC (p < 0.05). Conclusions TG measured on the ST Genesia can be used as an input for TD analysis. The data obtained can be used as reference values for future clinical studies as the balance between prothrombin conversion and thrombin inactivation has shown to be useful in several clinical settings.
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Affiliation(s)
- Audrey Carlo
- Diagnostica Stago S.A.S., Asnières-sur-Seine, France
| | - Qiuting Yan
- Department of Functional Coagulation, Synapse Research Institute, Maastricht, Netherlands.,Department of Biochemistry, Maastricht University, Maastricht, Netherlands
| | - Hugo Ten Cate
- Department of Biochemistry, Maastricht University, Maastricht, Netherlands
| | - Romy De Laat-Kremers
- Department of Functional Coagulation, Synapse Research Institute, Maastricht, Netherlands.,Department of Data Analysis and Artificial Intelligence, Synapse Research Institute, Maastricht, Netherlands
| | - Bas De Laat
- Department of Functional Coagulation, Synapse Research Institute, Maastricht, Netherlands.,Department of Data Analysis and Artificial Intelligence, Synapse Research Institute, Maastricht, Netherlands
| | - Marisa Ninivaggi
- Department of Functional Coagulation, Synapse Research Institute, Maastricht, Netherlands
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11
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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: 11] [Impact Index Per Article: 5.5] [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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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: 7] [Impact Index Per Article: 3.5] [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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Pancaldi F, Kim OV, Weisel JW, Alber M, Xu Z. Computational Biomechanical Modeling of Fibrin Networks and Platelet-Fiber Network Interactions. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2022; 22. [DOI: 10.1016/j.cobme.2022.100369] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Shankar KN, Zhang Y, Sinno T, Diamond SL. A three-dimensional multiscale model for the prediction of thrombus growth under flow with single-platelet resolution. PLoS Comput Biol 2022; 18:e1009850. [PMID: 35089923 PMCID: PMC8827456 DOI: 10.1371/journal.pcbi.1009850] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/09/2022] [Accepted: 01/18/2022] [Indexed: 11/18/2022] Open
Abstract
Modeling thrombus growth in pathological flows allows evaluation of risk under patient-specific pharmacological, hematological, and hemodynamical conditions. We have developed a 3D multiscale framework for the prediction of thrombus growth under flow on a spatially resolved surface presenting collagen and tissue factor (TF). The multiscale framework is composed of four coupled modules: a Neural Network (NN) that accounts for platelet signaling, a Lattice Kinetic Monte Carlo (LKMC) simulation for tracking platelet positions, a Finite Volume Method (FVM) simulator for solving convection-diffusion-reaction equations describing agonist release and transport, and a Lattice Boltzmann (LB) flow solver for computing the blood flow field over the growing thrombus. A reduced model of the coagulation cascade was embedded into the framework to account for TF-driven thrombin production. The 3D model was first tested against in vitro microfluidics experiments of whole blood perfusion with various antiplatelet agents targeting COX-1, P2Y1, or the IP receptor. The model was able to accurately capture the evolution and morphology of the growing thrombus. Certain problems of 2D models for thrombus growth (artifactual dendritic growth) were naturally avoided with realistic trajectories of platelets in 3D flow. The generalizability of the 3D multiscale solver enabled simulations of important clinical situations, such as cylindrical blood vessels and acute flow narrowing (stenosis). Enhanced platelet-platelet bonding at pathologically high shear rates (e.g., von Willebrand factor unfolding) was required for accurately describing thrombus growth in stenotic flows. Overall, the approach allows consideration of patient-specific platelet signaling and vascular geometry for the prediction of thrombotic episodes. The excessive formation of blood clots under flow within the circulatory system (thrombosis) is known to initiate heart attacks and strokes. Therefore, obtaining insights into the formation and progression of these clots will be useful in evaluating pharmacological options. To this end, we have developed a 3D computational model that tracks the growth of a blood clot under flow from initial platelet deposition to full vessel occlusion in the presence of soluble platelet agonists. We first validated the model against experimental predictions of blood clots formed in vitro. Due to the construction of the model in 3D, we were able to carry out simulations of clot formation under important clinical situations, namely cylindrical blood vessels and acute flow narrowings (stenoses). To our knowledge, our model is the first of its kind that can account for patient-specific platelet phenotypes to perform robust 3D simulations of thrombus growth in geometries of clinical relevance.
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Affiliation(s)
- Kaushik N. Shankar
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yiyuan Zhang
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Talid Sinno
- 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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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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Abstract
Distinct from dilute, isotropic, and homogeneous reaction systems typically used in laboratory kinetic assays, blood is concentrated, two-phase, flowing, and highly anisotropic when clotting on a surface. This review focuses on spatial gradients that are generated and can dictate thrombus structure and function. Novel experimental and computational tools have recently emerged to explore reaction-transport coupling during clotting. Multiscale simulations help bridge tissue length scales (the coronary arteries) to millimeter scales of a growing clot to the microscopic scale of single-cell signaling and adhesion. Microfluidic devices help create and control pathological velocity profiles, albeit at a low Reynolds number. Since rate processes and force loading are often coupled, this review highlights prevailing convective-diffusive transport physics that modulate cellular and molecular processes during thrombus formation.
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Yeh HH, Yu K, Vappala S, Kalathottukaren MT, Abbina S, Luo HD, Grecov D, Kizhakkedathu JN. Rheological and clot microstructure evaluation of heparin neutralization by UHRA and protamine. J Mech Behav Biomed Mater 2021; 124:104851. [PMID: 34600430 DOI: 10.1016/j.jmbbm.2021.104851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/16/2021] [Accepted: 09/19/2021] [Indexed: 11/27/2022]
Abstract
The current study reports the use of small amplitude oscillatory rheometry to investigate the dynamics of blood clot formation upon heparin neutralization under three different oscillatory frequencies, two of which were mimicking physiological heart rates. We utilized two different heparin antidotes, namely protamine and newly developed universal heparin reversal agent (UHRA-7), at different concentrations to determine the quality of blood clot formed upon heparin neutralization by analyzing several key rheological parameters. Scanning electron microscopy (SEM) was used to determine the morphology and microstructure of the blood clot after heparin neutralization to support the rheological observations. The current study revealed that the structure of blood clots formed had significant differences when an oscillatory frequency that mimicked the physiological heart rate was used in comparison to a lower frequency commonly used in current clinical measurements. The limited working dose range for protamine and its intrinsic anticoagulation behaviour was observed. The neutralization profile of UHRA-7 showed a large window of activity. The global assessment of rheological parameters and microstructure of the clot together revealed additional details describing anticoagulant reversal and blood coagulation dynamics by relating the blood clot's fiber thickness and the oscillatory measurements, including storage modulus and blood clot's contractile force. Additionally, a mechanical characterization was conducted to provide a further assessment of blood coagulation using the rheological data.
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Affiliation(s)
- Han Hung Yeh
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada; Department of Mechanical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Kai Yu
- Centre for Blood Research and Life Science Institute, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Sreeparna Vappala
- Centre for Blood Research and Life Science Institute, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Manu Thomas Kalathottukaren
- Centre for Blood Research and Life Science Institute, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Srinivas Abbina
- Centre for Blood Research and Life Science Institute, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Haiming D Luo
- Centre for Blood Research and Life Science Institute, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Dana Grecov
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada; Department of Mechanical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Jayachandran N Kizhakkedathu
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada; Centre for Blood Research and Life Science Institute, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
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18
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Ngoepe MN, Pretorius E, Tshimanga IJ, Shaikh Z, Ventikos Y, Ho WH. Thrombin-Fibrinogen In Vitro Flow Model of Thrombus Growth in Cerebral Aneurysms. TH OPEN 2021; 5:e155-e162. [PMID: 34007954 PMCID: PMC8116173 DOI: 10.1055/s-0041-1728790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/01/2021] [Indexed: 12/16/2022] Open
Abstract
Cerebral aneurysms are balloon-like structures that develop on weakened areas of cerebral artery walls, with a significant risk of rupture. Thrombi formation is closely associated with cerebral aneurysms and has been observed both before and after intervention, leading to a wide variability of outcomes in patients with the condition. The attempt to manage the outcomes has led to the development of various computational models of cerebral aneurysm thrombosis. In the current study, we developed a simplified thrombin–fibrinogen flow system, based on commercially available purified human-derived plasma proteins, which enables thrombus growth and tracking in an idealized cerebral aneurysm geometry. A three-dimensional printed geometry of an idealized cerebral aneurysm and parent vessel configuration was developed. An unexpected outcome was that this phantom-based flow model allowed us to track clot growth over a period of time, by using optical imaging to record the progression of the growing clot into the flow field. Image processing techniques were subsequently used to extract important quantitative metrics from the imaging dataset, such as end point intracranial thrombus volume. The model clearly demonstrates that clot formation, in cerebral aneurysms, is a complex interplay between mechanics and biochemistry. This system is beneficial for verifying computational models of cerebral aneurysm thrombosis, particularly those focusing on initial angiographic occlusion outcomes, and will also assist manufacturers in optimizing interventional device designs.
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Affiliation(s)
- Malebogo N Ngoepe
- Department of Mechanical Engineering, University of Cape Town, Cape Town, South Africa.,Stellenbosch Institute for Advanced Study, Wallenberg Research Centre, Stellenbosch University, Stellenbosch, South Africa
| | - Etheresia Pretorius
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Ilunga J Tshimanga
- Department of Mechanical Engineering, University of South Africa, Johannesburg, South Africa
| | - Zahra Shaikh
- Department of Mechanical Engineering, University of South Africa, Johannesburg, South Africa
| | - Yiannis Ventikos
- Department of Mechanical Engineering, University College London, London, United Kingdom
| | - Wei Hua Ho
- Department of Mechanical Engineering, University of South Africa, Johannesburg, South Africa.,School of Mechanical, Industrial and Aeronautical Engineering, University of the Witwatersrand, Johannesburg, South Africa
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Crossen J, Diamond SL. Thermal shift assay to probe melting of thrombin, fibrinogen, fibrin monomer, and fibrin: Gly-Pro-Arg-Pro induces a fibrin monomer-like state in fibrinogen. Biochim Biophys Acta Gen Subj 2021; 1865:129805. [PMID: 33276061 PMCID: PMC7752828 DOI: 10.1016/j.bbagen.2020.129805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/30/2020] [Accepted: 11/24/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Thrombin activates fibrinogen and binds the fibrin E-domain (Kd ~ 2.8 μM) and the splice variant γ'-domain (Kd ~ 0.1 μM). We investigated if the loading of D-Phe-Pro-Arg-chloromethylketone inhibited thrombin (PPACK-thrombin) onto fibrin could enhance fibrin stability. METHODS A 384-well plate thermal shift assay (TSA) with SYPRO-orange provided melting temperatures (Tm) of thrombin, PPACK-thrombin, fibrinogen, fibrin monomer, and fibrin. RESULTS Large increases in Tm indicated that calcium led to protein stabilization (0 vs. 2 mM Ca2+) for fibrinogen (54.0 vs. 62.3 °C) and fibrin (62.3 vs. 72.2 °C). Additionally, active site inhibition with PPACK dramatically increased the Tm of thrombin (58.3 vs. 78.3 °C). Treatment of fibrinogen with fibrin polymerization inhibitor GPRP increased fibrinogen stability by ΔTm = 9.3 °C, similar to the ΔTm when fibrinogen was converted to fibrin monomer (ΔTm = 8.8 °C) or to fibrin (ΔTm = 10.4 °C). Addition of PPACK-thrombin at high 5:1 M ratio to fibrin(ogen) had little effect on fibrin(ogen) Tm values, indicating that thrombin binding does not detectably stabilize fibrin via a putative bivalent E-domain to γ'-domain interaction. CONCLUSIONS TSA was a sensitive assay of protein stability and detected: (1) the effects of calcium-stabilization, (2) thrombin active site labeling, (3) fibrinogen conversion to fibrin, and (4) GPRP induced changes in fibrinogen stability being essentially equivalent to that of fibrin monomer or polymerized fibrin. SIGNIFICANCE The low volume, high throughput assay has potential for use in understanding interactions with rare or mutant fibrin(ogen) variants.
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Affiliation(s)
- J Crossen
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, United States..
| | - S L Diamond
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, United States..
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20
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Zhang N, Sun J, Ji C, Zhou Y, Bao X, Yuan C. Clinical significance and influencing factors of fibrinogen in ANCA-associated vasculitis: A single-center retrospective study from Southwest China. Medicine (Baltimore) 2020; 99:e22424. [PMID: 32991476 PMCID: PMC7523770 DOI: 10.1097/md.0000000000022424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Hypercoagulable is an important pathological state in anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV). Fibrinogen (FIB) is the main protein in coagulation process. In this study, we aimed to investigate the clinical significance and influencing factors of FIB in AAV from Southwest China.A retrospective study was performed on AAV patients from Peoples Hospital of Deyang City from January 2007 to December 2018. Demographic and clinical characteristics were collected.A total of 463 AAV patients were included. In Wilcoxon rank sum test, FIB was significantly higher in AAV active group than inactive group (P = .005). FIB was also higher in bacterial infection group than in non-infection group both in active group (P = .008) and inactive group (P = .017). In receiver operating characteristic (ROC) curve analysis, the critical value of FIB for diagnosis of bacterial infection between AAV active and inactive groups was 3.385 g/L (P = .030), with sensitivity of 70.2% and specificity of 52.9%. In the multivariate analysis of variance (MANOVA), estimated glomerular filtration rate (eGFR) was shown to be an independent factor for FIB (P = .001). Least-significant difference showed the concentration of FIB (P < .05) increased with renal impairment, especially in endstage kidney disease (ESKD).FIB identified a certain reference value in distinguishing AAV activity from bacterial infection. ESKD had a statistical effect on it. Influencing factors of FIB should be evaluated based on the renal function impairment of patients.
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Affiliation(s)
- Naidan Zhang
- Department of Clinical Laboratory, Peoples Hospital of Deyang City, Deyang
- Department of Clinical Laboratory, West China Hospital of Sichuan University, Chengdu
| | - Jiaxiang Sun
- Department of Clinical Laboratory, Peoples Hospital of Deyang City, Deyang
| | - Chaixia Ji
- Department of Clinical Laboratory, Peoples Hospital of Deyang City, Deyang
| | - Yusha Zhou
- Department of Clinical Laboratory, Peoples Hospital of Deyang City, Deyang
| | - Xiao Bao
- Department of Rheumatology, Peoples Hospital of Deyang City, Deyang, China
| | - Chengliang Yuan
- Department of Clinical Laboratory, Peoples Hospital of Deyang City, Deyang
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21
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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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