Biomedical subjects

Aleksander S Popel

Publications and source records attributed to Aleksander S Popel.

At least 19 recordsLinked to original sources

PubMed2006

Targeting neuropilin-1 to inhibit VEGF signaling in cancer: Comparison of therapeutic approaches.

Angiogenesis (neovascularization) plays a crucial role in a variety of physiological and pathological conditions including cancer, cardiovascular disease, and wound healing. Vascular endothelial growth factor (VEGF) is a critical regulator of angiogenesis. Multiple VEGF receptors are expressed on endothelial cells, including signaling receptor tyrosine kinases (VEGFR1 and VEGFR2) and the nonsignaling co-receptor Neuropilin-1. Neuropilin-1 binds only the isoform of VEGF responsible for pathological angiogenesis (VEGF165), and is thus a potential target for inhibiting VEGF signaling. Using the first molecularly detailed computational model of VEGF and its receptors, we have shown previously that the VEGFR-Neuropilin interactions explain the observed differential effects of VEGF isoforms on VEGF signaling in vitro, and demonstrated potent VEGF inhibition by an antibody to Neuropilin-1 that does not block ligand binding but blocks subsequent receptor coupling. In the present study, we extend that computational model to simulation of in vivo VEGF transport and binding, and predict the in vivo efficacy of several Neuropilin-targeted therapies in inhibiting VEGF signaling: (a) blocking Neuropilin-1 expression; (b) blocking VEGF binding to Neuropilin-1; (c) blocking Neuropilin-VEGFR coupling. The model predicts that blockade of Neuropilin-VEGFR coupling is significantly more effective than other approaches in decreasing VEGF-VEGFR2 signaling. In addition, tumor types with different receptor expression levels respond differently to each of these treatments. In designing human therapeutics, the mechanism of attacking the target plays a significant role in the outcome: of the strategies tested here, drugs with similar properties to the Neuropilin-1 antibody are predicted to be most effective. The tumor type and the microenvironment of the target tissue are also significant in determining therapeutic efficacy of each of the treatments studied.

Biological Transport↗

PubMed2006

VEGF gradients, receptor activation, and sprout guidance in resting and exercising skeletal muscle.

Extensive experimental studies have identified vascular endothelial growth factor (VEGF) concentrations and concentration gradients as major factors in angiogenesis; however, localized in vivo measurements of these parameters have not been possible. We developed a three-dimensional computational model of skeletal muscle fibers, blood vessels, and interstitial space. Here it is applied to rat extensor digitorum longus. VEGF isoforms are secreted by myocytes, diffuse through extracellular matrix and basement membranes, and bind endothelial cell surface receptors on blood vessels. In addition, one isoform, VEGF164, binds to proteoglycans in the interstitial space. VEGF secretion rate is determined from the predicted tissue oxygen level through its effect on the hypoxia inducible factor-1alpha transcription factor. We estimate VEGF secretion and its concentrations and gradients in resting muscle and for different levels of exercise. The effects of low levels of inspired oxygen are also studied. We predict that the high spatial heterogeneity of muscle fiber VEGF secretion in hypoxic tissue leads to significant gradients of VEGF concentration and VEGF receptor activation. VEGF concentration gradients are predicted to be significant in both resting and exercising muscle (4% and 6-8% change in VEGF over 10 microm, respectively), sufficient for chemotactic guidance of 50-microm-long sprout tip cells. VEGF gradients also result in heterogeneity in VEGF receptor activation--a possible explanation for the stochasticity of sprout location. In the absence of interstitial flow, gradients are 10-fold steeper in the transverse direction (i.e., perpendicular to the muscle fibers) than in the longitudinal direction. This may explain observed perpendicular anastomoses in skeletal muscle.

Animals↗

PubMed2006

Interactions of VEGF isoforms with VEGFR-1, VEGFR-2, and neuropilin in vivo: a computational model of human skeletal muscle.

The vascular endothelial growth factor (VEGF) family of cytokines is involved in the maintenance of existing adult blood vessels as well as in angiogenesis, the sprouting of new vessels. To study the proangiogenic activation of VEGF receptors (VEGFRs) by VEGF family members in skeletal muscle, we develop a computational model of VEGF isoforms (VEGF(121), VEGF(165)), their cell surface receptors, and the extracellular matrix in in vivo tissue. We build upon our validated model of the biochemical interactions between VEGF isoforms and receptor tyrosine kinases (VEGFR-1 and VEGFR-2) and nonsignaling neuropilin-1 coreceptors in vitro. The model is general and could be applied to any tissue; here we apply the model to simulate the transport of VEGF isoforms in human vastus lateralis muscle, which is extensively studied in physiological experiments. The simulations predict the distribution of VEGF isoforms in resting (nonexercising) muscle and the activation of VEGFR signaling. Little of the VEGF protein in muscle is present as free, unbound extracellular cytokine; the majority is bound to the cell surface receptors or to the extracellular matrix. However, interstitial sequestration of VEGF(165) does not affect steady-state receptor binding. In the absence of neuropilin, VEGF(121) and VEGF(165) behave similarly, but neuropilin enhances the binding of VEGF(165) to VEGFR-2. This model is the first to study VEGF tissue distribution and receptor activation in human muscle, and it provides a platform for the design and evaluation of therapeutic approaches.

Computer Simulation↗

PubMed2006

A computational model of intracellular oxygen sensing by hypoxia-inducible factor HIF1 alpha.

Hypoxia-inducible factor-1, HIF1, transcriptionally activates over 200 genes vital for cell homeostasis and angiogenesis. We developed a computational model to gain a detailed quantitative understanding of how HIF1 acts to sense oxygen and respond to hypoxia. The model consists of kinetic equations describing the intracellular variation of 17 compounds, including HIF1, iron, prolyl hydroxylase, oxygen, ascorbate, 2-oxoglutarate, von Hippel Lindau protein and associated complexes. We tested an existing hypothesis of a switch-like change in HIF1 expression in response to a gradual decrease in O2 concentration. Our model predicts that depending on the molecular environment, such as intracellular iron levels, the hypoxic response varies considerably. We show HIF1-activated cellular responses can be divided into two categories: a steep, switch-like response to O2 and a gradual one. Discovery of this dual response prompted comparison of two therapeutic strategies, ascorbate and iron supplementation, and prolyl hydroxylase targeting, to predict under what microenvironments either effectively increases HIF1alpha hydroxylation. Results provide crucial insight into the effects of iron and prolyl hydroxylase on oxygen sensing. The model advances quantitative molecular level understanding of HIF1 pathways--an endeavor that will help elucidate the diverse responses to hypoxia found in cancer, ischemia and exercise.

Ascorbic Acid↗

PubMed2006

Computational model of vascular endothelial growth factor spatial distribution in muscle and pro-angiogenic cell therapy.

Members of the vascular endothelial growth factor (VEGF) family of proteins are critical regulators of angiogenesis. VEGF concentration gradients are important for activation and chemotactic guidance of capillary sprouting, but measurement of these gradients in vivo is not currently possible. We have constructed a biophysically and molecularly detailed computational model to study microenvironmental transport of two isoforms of VEGF in rat extensor digitorum longus skeletal muscle under in vivo conditions. Using parameters based on experimental measurements, the model includes: VEGF secretion from muscle fibers; binding to the extracellular matrix; binding to and activation of endothelial cell surface VEGF receptors; and internalization. For 2-D cross sections of tissue, we analyzed predicted VEGF distributions, gradients, and receptor binding. Significant VEGF gradients (up to 12% change in VEGF concentration over 10 mum) were predicted in resting skeletal muscle with uniform VEGF secretion, due to non-uniform capillary distribution. These relative VEGF gradients were not sensitive to extracellular matrix composition, or to the overall VEGF expression level, but were dependent on VEGF receptor density and affinity, and internalization rate parameters. VEGF upregulation in a subset of fibers increased VEGF gradients, simulating transplantation of pro-angiogenic myoblasts, a possible therapy for ischemic diseases. The number and relative position of overexpressing fibers determined the VEGF gradients and distribution of VEGF receptor activation. With total VEGF expression level in the tissue unchanged, concentrating overexpression into a small number of adjacent fibers can increase the number of capillaries activated. The VEGF concentration gradients predicted for resting muscle (average 3% VEGF/10 mum) is sufficient for cellular sensing; the tip cell of a vessel sprout is approximately 50 mum long. The VEGF gradients also result in heterogeneity in the activation of blood vessel VEGF receptors. This first model of VEGF tissue transport and heterogeneity provides a platform for the design and evaluation of therapeutic approaches.

Cell- and Tissue-Based Therapy↗

PubMed2006

Theoretical analysis of biochemical pathways of nitric oxide release from vascular endothelial cells.

Vascular endothelium expressing endothelial nitric oxide synthase (eNOS) produces nitric oxide (NO), which has a number of important physiological functions in the microvasculature. The rate of NO production by the endothelium is a critical determinant of NO distribution in the vascular wall. We have analyzed the biochemical pathways of NO synthesis and formulated a model to estimate NO production by the microvascular endothelium under physiological conditions. The model quantifies the NO produced by eNOS based on the kinetics of NO synthesis and the availability of eNOS and its intracellular substrates. The predicted NO production from microvessels was in the range of 0.005-0.1 microM/s. This range of predicted values is in agreement with some experimental values but is much lower than other rates previously measured or estimated from experimental data with the help of mathematical modeling. Paradoxical discrepancies between the model predictions and previously reported results based on experimental measurements of NO concentration in the vicinity of the arteriolar wall suggest that NO can also be released through eNOS-independent mechanisms, such as catalysis by neuronal NOS (nNOS). We also used our model to test the sensitivity of NO production to substrate availability, eNOS concentration, and potential rate-limiting factors. The results indicated that the predicted low level of NO production can be attributed primarily to a low expression of eNOS in the microvascular endothelial cells.

Endothelium, Vascular↗

PubMed2006

A computational model of oxygen transport in skeletal muscle for sprouting and splitting modes of angiogenesis.

Oxygen transport from capillary networks in muscle at a high oxygen consumption rate was simulated using a computational model to assess the relative efficacies of sprouting and splitting modes of angiogenesis. Efficacy was characterized by the volumetric fraction of hypoxic tissue and overall heterogeneity of oxygen distribution at steady state. Oxygen transport was simulated for a three-dimensional vascular network using parameters for rat extensor digitorum longus (EDL) muscle when oxygen consumption by tissue reached 6, 12, and 18 times basal consumption. First, a control network was generated by using straight non-anastomosed capillaries to establish baseline capillarity. Two networks were then constructed simulating either abluminal lateral sprouting or intraluminal splitting angiogenesis such that capillary surface area was equal in both networks. The sprouting network was constructed by placing anastomosed capillaries between straight capillaries of the control network with a higher probability of placement near hypoxic tissue. The splitting network was constructed by splitting capillaries from the control network into two branches at randomly chosen branching points. Under conditions of moderate oxygen consumption (6 times basal), only minor differences in oxygen delivery resulted between the sprouting and splitting networks. At higher consumption levels (12 and 18 times basal), the splitting network had the lowest volume of hypoxic tissue of the three networks. However, when total blood flow in all three networks was made equal, the sprouting network had the lowest volume of hypoxic tissue. This study also shows that under the steady-state conditions the effect of myoglobin (Mb) on oxygen transport was small.

Animals↗

PubMed2005

Monte Carlo simulations of VEGF binding to cell surface receptors in vitro.

The vascular endothelial growth factor (VEGF) family binds multiple endothelial cell surface receptors. Our goal is to build comprehensive models of these interactions for the purpose of simulating angiogenesis. In view of low concentrations of growth factors in vivo and in vitro, stochastic modeling of molecular interactions may be necessary. Here, we compare Monte Carlo simulations of the stochastic binding of VEGF and two of its major receptors on cells in vitro to equivalent deterministic simulations. In the range of typical VEGF concentrations, the stochastic and deterministic models are in agreement. However, we observe significant variability in receptor binding, which may be linked to biological stochastic events, e.g., blood vessel sprout initiation. We study patches of cell surface of varying sizes to investigate spatial integration of the signal by the cell, which impacts directly the variability of binding, and find significant variability up to the single-cell level. Dimerization of VEGF receptors does not significantly alter the variability in ligand binding. A 'sliding window' approach demonstrated no reduction in the variability of binding by temporal integration. The variability is expected to be more prominent in in vivo situations where the number of ligand molecules available for binding is less.

Algorithms↗

PubMed2005

Effects of chlorpromazine on mechanical properties of the outer hair cell plasma membrane.

An optical tweezers system was used to characterize the effects of chlorpromazine (CPZ) on the mechanical properties of the mammalian outer hair cell (OHC) through the formation of plasma membrane tethers. Such tethers exhibited force relaxation when held at a constant length for several minutes. We used a second-order generalized Kelvin body to model tether-force behavior from which several mechanical parameters were then calculated including stiffness, viscosity-associated measures, and force relaxation time constants. The results of the analysis portray a two-part relaxation process characterized by significantly different rates of force decay, which we propose is due to the local reorganization of lipids within the tether and the flow of external lipid into the tether. We found that CPZ's effect was limited to the latter phenomenon since only the second phase of relaxation was significantly affected by the drug. This finding coupled with an observed large reduction in overall tether forces implies a common basis for the drug's effects, the plasma membrane-cytoskeleton interaction. The CPZ-induced changes in tether viscoelastic behavior suggest that alterations in the mechanical properties of the OHC lateral wall could play a role in the modulation of OHC electromotility by CPZ.

Animals↗

PubMed2005

Effect of erythrocyte aggregation at normal human levels on functional capillary density in rat spinotrapezius muscle.

Previous studies have shown that functional capillary density (FCD) is substantially reduced by erythrocyte aggregation. However, only supranormal levels of aggregability were studied. To investigate the effect of erythrocyte aggregability at the level seen in healthy humans, the FCD of selected capillary fields in rat spinotrapezius muscle was determined with high-speed video microscopy under normal (nonaggregating) conditions and after induction of erythrocyte aggregation with Dextran 500 (200 mg/kg). To examine shear rate dependence, the effect was studied both at normal and reduced arterial pressures (50 and 25 mmHg), the latter achieved by short periods of hemorrhage. In a separate study, volume flow was determined in arterioles (52.1 +/- 3.7 microm) under the same conditions. Before Dextran 500 infusion, FCD fell to 91% and 76% of control values, respectively, when arterial pressure was reduced to 50 and 25 mmHg. After Dextran 500 infusion, FCD was 96% at normal arterial pressure and fell to 79% and 37% of normal control values at 50 and 25 mmHg. All FCD values were significantly lower after dextran infusion. FCD reduction after lowering arterial pressure or dextran infusion appeared to be due to plasma skimming rather than capillary plugging. Reduction of FCD by dextran at reduced pressure was compensated by increased red blood cell flux in capillaries with red blood cell flow. We conclude that the level of aggregability seen in healthy humans is an important determinant of FCD only at reduced arterial pressure.

Animals↗

PubMed2005

Venular endothelium-derived NO can affect paired arteriole: a computational model.

Venular endothelial cells can release nitric oxide (NO) in response to intraluminal flow both in isolated venules and in vivo. Experimental studies suggest that venular endothelium-released NO causes dilation of the adjacent paired arteriole. In the vascular wall, NO stimulates its target hemoprotein, soluble guanylate cyclase (sGC), which relaxes smooth muscle cells. In this study, a computational model of NO transport for an arteriole and venule pair was developed to determine the importance of the venular endothelium-released NO and its transport to the adjacent arteriole in the tissue. The model predicts that the tissue NO levels are affected within a wide range of parameters, including NO-red blood cell reaction rate and NO production rate in the arteriole and venule. The results predict that changes in the venular NO production affected not only venular endothelial and smooth muscle NO concentration but also endothelial and smooth muscle NO concentration in the adjacent arteriole. This suggests that the anatomy of microvascular tissue can permit the transport of NO from arteriolar to venular side, and vice versa, and may provide a mechanism for dilation of proximal arterioles by venules. These results will have significant implications for our understanding of tissue NO levels in both physiological and pathophysiological conditions.

Animals↗

PubMed2005

Distinct modes of collagen type I proteolysis by matrix metalloproteinase (MMP) 2 and membrane type I MMP during the migration of a tip endothelial cell: insights from a computational model.

Matrix metalloproteinases (MMPs) are a family of enzymes responsible for the proteolytic processing of extracellular matrix (ECM) structural proteins under physiological and pathological conditions. During sprouting angiogenesis, the MMPs expressed by a single "tip" endothelial cell exhibit proteolytic activity that allows the cells of the sprouting vessel bud to migrate into the ECM. Membrane type I matrix metalloproteinase (MT1-MMP) and the diffusible matrix metalloproteinase MMP2, in the presence of the tissue inhibitor of metalloproteinases TIMP2, constitute a system of proteins that play an important role during the proteolysis of collagen type I matrices. Here, we have formulated a computational model to investigate the proteolytic potential of such a tip endothelial cell. The cell expresses MMP2 in its proenzyme form, pro-MMP2, as well as MT1-MMP and TIMP2. The interactions of the proteins are described by a biochemically detailed reaction network. Assuming that the rate-limiting step of the migration is the ability of the tip cell to carry out proteolysis, we have estimated cell velocities for matrices of different collagen content. The estimated velocities of a few microns per hour are in agreement with experimental data. At high collagen content, proteolysis was carried out primarily by MT1-MMP and localized to the cell leading edge, whereas at lower concentrations, MT1-MMP and MMP2 were found to act in parallel, causing proteolysis in the vicinity of the leading edge. TIMP2 is a regulator of the proteolysis localization because it can shift the activity of MT1-MMP from its enzymatic toward its activatory mode, suggesting a tight mechanosensitive regulation of the enzymes and inhibitor expression. The model described here provides a foundation for quantitative studies of angiogenesis in extracellular matrices of different compositions, both in vitro and in vivo. It also identifies critical parameters whose values are not presently available and which should be determined in future experiments.

Cell Movement↗

PubMed2005

Differential binding of VEGF isoforms to VEGF receptor 2 in the presence of neuropilin-1: a computational model.

A comprehensive, biophysically accurate, computational model of vascular endothelial growth factor (VEGF) family member interactions with endothelial cell surface receptors was developed to study angiogenesis. Neuropilin-1 (NRP1) and the signaling VEGF receptor, VEGFR2, do not interact directly but are bridged by one VEGF isoform, VEGF(165). Using the model and published experimental data, we estimated the kinetic rate of this VEGFR2-NRP1 coupling in vitro. With the use of this rate, our model gives predictions in good quantitative agreement with several independent in vitro experiments involving VEGF(121) and VEGF(165) isoforms, confirming that VEGFR2-NRP1 coupling through VEGF(165) can fully explain the observed differences in receptor binding and phosphorylation in response to these isoforms. Model predictions also determine the mechanism of action of a commonly used NRP1 antibody and predict the results of potential future experiments. This is the first model to include VEGF isoforms or NRPs, and it is a necessary step toward a quantitative molecular level description of VEGF that can be extended to in vivo situations. The model has applications for both proangiogenic and antiangiogenic therapies, such as for heart disease and cancer, as well as in tissue engineering.

Kinetics↗

PubMed2005

High-frequency force generation in the constrained cochlear outer hair cell: a model study.

Cochlear outer hair cell (OHC) electromotility is believed to be responsible for the sensitivity and frequency selectivity of the mammalian hearing process. Its contribution to hearing is better understood by examining the force generated by the OHC as a feedback to vibration of the basilar membrane (BM). In this study, we examine the effects of the constraints imposed on the OHC and of the surrounding fluids on the cell's high-frequency active force generated under in vitro and in vivo conditions. The OHC is modeled as a viscoelastic and piezoelectric cylindrical shell coupled with viscous intracellular and extracellular fluids, and the constraint is represented by a spring with adjustable stiffness. The solution is obtained in the form of a Fourier series. The model results are consistent with previously reported experiments under both low- and high-frequency conditions. We find that constrained OHCs achieve a much higher corner frequency than free OHCs, depending on the stiffness of the constraint. We analyze cases in which the stiffness of the constraint is similar to that of the BM, reticular lamina, and tectorial membrane, and find that the force per unit transmembrane potential generated by the OHC can be constant up to several tens of kHz. This model, describing the OHC as a local amplifier, can be incorporated into a global cochlear model that considers cochlear hydrodynamics and frequency modulation of the receptor potential, as well as the graded BM stiffness and OHC length.

Acoustics↗

PubMed2005

Mechanosensitive channels in the lateral wall can enhance the cochlear outer hair cell frequency response.

We present the results of a modeling study on the impact of mechanosensitive channels in the lateral wall of the outer hair cell on the cell frequency response. The model includes the electrical properties of the cell membrane, piezoelectricity associated with a membrane motor mechanism, and mechanosensitive channels in the cell lateral wall. The outer hair cell is loaded by the vibrating basilar and tectorial membranes, and this loading generates strain in the lateral wall. Our analysis reveals a property, the strain rate sensitivity, that, in concert with the piezoelectric effect, can enhance the cell frequency response. We discuss possible viscoelastic-type mechanisms of the channel's strain rate sensitivity that is consistent with the organization of the composite cell lateral wall. The parameters of our model are chosen on the basis of the previously estimated electrical and piezoelectric properties as well as typical conductance and density of the mechanosensitive channels in cells. We found that the strain rate sensitivity of the channels can result in receptor potentials greater than those predicted by the RC (resistance and capacitance) analysis. The effect of the channels is especially significant in an intermediate range of sound frequencies, and the channel-related gain is up to 3-4 times between 3 and 15 kHz.

Acoustics↗

PubMed2005

Computational fluid dynamic simulation of aggregation of deformable cells in a shear flow.

We present computational fluid dynamic (CFD) simulation of aggregation of two deformable cells in a shearflow. This work is motivated by an attempt to develop computational models of aggregation of red blood cells (RBCs). Aggregation of RBCs is a major determinant of blood viscosity in microcirculation under physiological and pathological conditions. Deformability of the RBCs plays a major role in determining their aggregability. Deformability depends on the viscosity of the cytoplasmic fluid and on the rigidity of the cell membrane, in a macroscopic sense. This paper presents a computational study of RBC aggregation that takes into account the rheology of the cells as well as cell-cell adhesion kinetics. The simulation technique considered here is two dimensional and based on the front tracking/immersed boundary method for multiple fluids. Results presented here are on the dynamic events of aggregate formation between two cells, and its subsequent motion, rolling, deformation, and breakage. We show that the rheological properties of the cells have significant effects on the dynamics of the aggregate. A stable aggregate is formed at higher cytoplasmic viscosity and membrane rigidity. We also show that the bonds formed between the cells change in a cyclic manner as the aggregate rolls in a shearflow. The cyclic behavior is related to the rolling orientation of the aggregate. The frequency and amplitude of oscillation in the number of bonds also depend on the rheological properties.

Animals↗

PubMed2005

Modeling high-frequency electromotility of cochlear outer hair cell in microchamber experiment.

Cochlear outer hair cells (OHC) are critically important for the amplification and sharp frequency selectivity of the mammalian ear. The microchamber experiment has been an effective tool to analyze the OHC high-frequency performance. In this study, the OHC electrical stimulation in the microchamber is simulated. The model takes into account the inertial and viscous properties of fluids inside and outside the cell as well as the viscoelastic and piezoelectric properties of the cell composite membrane (wall). The closed ends of the cylindrical cell were considered as oscillatory rigid plates. The final solution was obtained in terms of Fourier series, and it was checked against the available results of the microchamber experiment. The conditions of the interaction between the cell and pipette was analyzed, and it was found that the amount of slip along the contact surface has a significant effect on the cell electromotile response. The cell's length changes were computed as a function of frequency, and their dependence on the viscosities of both fluids and the cell wall was analyzed. The distribution of the viscous losses inside the fluids was also estimated. The proposed approach can help in a better understanding of the high-frequency OHC electromotility under experimental and physiological conditions.

Cell Movement↗

PubMed2005

Effect of voltage-dependent membrane properties on active force generation in cochlear outer hair cell.

A computational model is proposed to analyze the active force production in an individual outer hair cell (OHC) under high-frequency conditions. The model takes into account important biophysical properties of the cell as well as constraints imposed by the surrounding environment. The biophysical properties include the elastic, piezoelectric, and viscous characteristics of the cell wall. The effect of the environment is associated with the stiffness of the constraint and the drag forces acting on the cell due to the interaction with the external and internal viscous fluids. The study concentrated on a combined effect of the transmembrane potential, frequency, and stiffness of the constraints. The effect of the voltage-dependent stiffness of the cell was particularly investigated and it was found to be twofold. First, it results in higher sensitivity and nonlinearity of the OHC active force production in the physiological range. Second, it determines smaller active forces in the hyperpolarization range. The resonant properties of the active force as functions of voltage and the constraint stiffness were also analyzed. The obtained results can be important for a better understanding of the OHC active force production and the contribution of cell electromotility to the cochlear amplification, sensitivity, and nonlinearity.

Acoustics↗