Computational biology analysis of platelet signaling reveals roles of feedbacks through phospholipase C and inositol 1,4,5-trisphosphate 3-kinase in controlling amplitude and duration of calcium oscillations

Numerical Analysis of Compound Biochemical Calcium Oscillations Process in Hepatocyte Cells

The hepatocyte cells regulate the wide range of liver function by moderating cellular activities such as lipid, protein metabolism, carbohydrate, and interact with other cells for proliferation and maintenance. In hepatocyte cells, the concentration of calcium uptake is quite extensive from various agonists such as activeG α ${G_\alpha}$ subunit, active phospholipase C, free calcium in the cytosol, and endoplasmic reticulum. The overproduction and degradation of calcium signals can cause homeostasis, liver inflammation, and liver diseases. The spatiotemporal behavior of calcium oscillation reveals the physiological role of these cellular entities in understanding the process of production and degradation. No computational attempt has been registered to date on the compound calcium regulation of these cellular entities including the memory of cells. Hence, the authors proposed a fractional order compartmental model that systematically simulates the exchange of calcium intake in cellular entities. The nonlinear equations of the rate of changes in the activeG α ${G_\alpha}$ subunit, active phospholipase C, free calcium in the cytosol, and endoplasmic reticulum are coupled to form a nonlinear fractional order initial value problem. The existence and uniqueness, stability analysis of the model is performed that validate the theoretical results and explore the dynamic behaviour of calcium oscillation in each compartment.

Control of Platelet CLEC-2-Mediated Activation by Receptor Clustering and Tyrosine Kinase Signaling

Platelets are blood cells responsible for vascular integrity preservation. The activation of platelet receptor C-type lectin-like receptor II-type (CLEC-2) could partially mediate the latter function. Although this receptor is considered to be of importance for hemostasis, the rate-limiting steps of CLEC-2-induced platelet activation are not clear. Here, we aimed to investigate CLEC-2-induced platelet signal transduction using computational modeling in combination with experimental approaches. We developed a stochastic multicompartmental computational model of CLEC-2 signaling. The model described platelet activation beginning with CLEC-2 receptor clustering, followed by Syk and Src family kinase phosphorylation, determined by the cluster size. Active Syk mediated linker adaptor for T cell protein phosphorylation and membrane signalosome formation, which resulted in the activation of Bruton's tyrosine kinase, phospholipase and phosphoinositide-3-kinase, calcium, and phosphoinositide signaling. The model parameters were assessed from published experimental data. Flow cytometry, total internal reflection fluorescence and confocal microscopy, and western blotting quantification of the protein phosphorylation were used for the assessment of the experimental dynamics of CLEC-2-induced platelet activation. Analysis of the model revealed that the CLEC-2 receptor clustering leading to the membrane-based signalosome formation is a critical element required for the accurate description of the experimental data. Both receptor clustering and signalosome formation are among the rate-limiting steps of CLEC-2-mediated platelet activation. In agreement with these predictions, the CLEC-2-induced platelet activation, but not activation mediated by G-protein-coupled receptors, was strongly dependent on temperature conditions and cholesterol depletion. Besides, the model predicted that CLEC-2-induced platelet activation results in cytosolic calcium spiking, which was confirmed by single-platelet total internal reflection fluorescence microscopy imaging. Our results suggest a refined picture of the platelet signal transduction network associated with CLEC-2. We show that tyrosine kinase activation is not the only rate-limiting step in CLEC-2-induced activation of platelets. Translocation of receptor-agonist complexes to the signaling region and linker adaptor for T cell signalosome formation in this region are limiting CLEC-2-induced activation as well.

Review of quantitative systems pharmacological modeling in thrombosis

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.

Effects of Juglans regia Root Bark Extract on Platelet Aggregation, Bleeding Time, and Plasmatic Coagulation: In Vitro and Ex Vivo Experiments

Platelets have an important role in thrombosis and haemostasis. Hyperactivity of the platelets has been associated with thromboembolic diseases and represents the main cause of complications of cardiovascular diseases. Crude aqueous extract (CAE) of Juglans regia root bark was evaluated for bleeding time, antiaggregant activity by using agonists, thrombin, ADP, collagen, or arachidonic acid (in vitro and ex vivo), and anticoagulant activity by measuring the clotting parameters: activated partial thromboplastin time, prothrombin time, thrombin time, and fibrinogen dosage (in vitro and ex vivo). The result of this study reported that the strongest antiaggregant effect of CAE in vitro was observed on the ADP-induced aggregation with inhibitions up to 90 %, while, in ex vivo experiments, the inhibition (more than 80 %) was observed with all agonists. Anticoagulant effect of CAE significantly prolonged the TT and decreased the fibrinogen level in vitro and ex vivo without interfering with APTT and PT. The bleeding time in mice and rats was significantly increased by CAE. The antiplatelet and anticoagulant effect observed in this study suggest that Juglans regia could have antithrombotic and/or thrombolytic activities and provide an alternative therapy against thrombotic complications related to cardiovascular diseases.

Modeling thrombosis in silico: Frontiers, challenges, unresolved problems and milestones

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.

Mathematical Techniques for Understanding Platelet Regulation and the Development of New Pharmacological Approaches

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.

Temporal Bias: Time-Encoded Dynamic GPCR Signaling

Evidence suggests that cells can time-encode signals for secure transport and perception of information, and it appears that this dynamic signaling is a common principle of nature to code information in time. G-protein-coupled receptor (GPCR) signaling networks are no exception as their composition and signal transduction appear temporally flexible. In this review, we discuss the potential mechanisms by which GPCRs code biological information in time to create 'temporal bias.' We highlight dynamic signaling patterns from the second messenger to the receptor-ligand level and shed light on the dynamics of G-protein cycles, the kinetics of ligand-receptor interaction, and the occurrence of distinct signaling waves within the cell. A dynamic feature such as temporal bias adds to the complexity of GPCR signaling bias and gives rise to the question whether this trait could be exploited to gain control over time-encoded cell physiology.

Systems biology insights into the meaning of the platelet's dual-receptor thrombin signaling

Essentials Roles of the two thrombin receptors in platelet signaling are poorly understood. Computational systems biology modeling was used together with continuous flow cytometry. Dual-receptor system has wide-range sensitivity to thrombin and optimal response dynamics. Procoagulant platelet formation is determined by donor-specific activities of the two receptors.

SUMMARY

Background Activation of human platelets with thrombin proceeds via two protease-activated receptors (PARs), PAR1 and PAR4, that have identical main intracellular signaling responses. Although there is evidence that they have different cleavage/inactivation kinetics (and some secondary variations in signaling), the reason for such redundancy is not clear. Methods We developed a multicompartmental stochastic computational systems biology model of dual-receptor thrombin signaling in platelets to gain insight into the mechanisms and roles of PAR1 and PAR4 functioning. Experiments employing continuous flow cytometry of washed human platelets were used to validate the model and test its predictions. Activity of PAR receptors in donors was evaluated by mRNA measurement and by polymorphism sequencing. Results Although PAR1 activation produced rapid and short-lived response, signaling via PAR4 developed slowly and propagated in time. Response of the dual-receptor system was both rapid and prolonged in time. Inclusion of PAR1/PAR4 heterodimer formation promoted PAR4 signaling in the medium range of thrombin concentration (about 10 nm), with little contribution at high and low thrombin. Different dynamics and dose-dependence of procoagulant platelet formation in healthy donors was associated with individual variations in PAR1 and PAR4 activities and particularly by the Ala120Thr polymorphism in the F2RL3 gene encoding PAR4. Conclusions The dual-receptor combination is critical to produce a response combining three critical advantages: sensitivity to thrombin concentration, rapid onset and steady propagation; specific features of the protease-activated receptors do not allow combination of all three in a single receptor.

Dynamics of calcium spiking, mitochondrial collapse and phosphatidylserine exposure in platelet subpopulations during activation

Essentials The sequence and logic of events leading to platelet procoagulant activity are poorly understood. Confocal time-lapse microscopy was used to investigate activation of single adherent platelets. Platelet transition to the procoagulant state followed cytosolic calcium oscillations. Mitochondria did not collapse simultaneously and membrane potential loss could be reversible.

SUMMARY

Background Activated platelets form two subpopulations, one of which is able to efficiently aggregate, and another that externalizes phosphatidylserine (PS) and thus accelerates membrane-dependent reactions of blood coagulation. The latter, procoagulant subpopulation is characterized by a high cytosolic calcium level and the loss of inner mitochondrial membrane potential, and there are conflicting opinions on their roles in its formation. Methods We used confocal microscopy to investigate the dynamics of subpopulation formation by imaging single, fibrinogen-bound platelets with individual mitochondria in them upon loading with calcium-sensitive and mitochondrial potential-sensitive dyes. Stimulation was performed with thrombin or the protease-activated receptor (PAR) 1 agonist SFLLRN. Stochastic simulations with a computational systems biology model of PAR1 calcium signaling were employed for analysis. Results Platelet activation resulted in a series of cytosolic calcium spikes and mitochondrial calcium uptake in all platelets. The frequency of spikes decreased with time for SFLLRN stimulation, but remained high for a long period of time for thrombin. In some platelets, uptake of calcium by mitochondria led to the mitochondrial permeability transition pore opening and inner mitochondrial membrane potential loss, which could be either reversible or irreversible. The latter resulted in an increase in the cytosolic calcium level and PS exposure. These platelets had higher cytosolic calcium levels before activation, and their mitochondria collapsed not simultaneously but one after another. Conclusions These results support a model of procoagulant subpopulation development following a series of stochastic cytosolic calcium spikes that are accumulated by mitochondria, leading to a collapse, and suggest important roles of individual platelet reactivity and signal exchange between different mitochondria of a platelet.