Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility

Background

Mathematical modelling of cellular networks is an integral part of Systems Biology and requires appropriate software tools. An important class of methods in Systems Biology deals with structural or topological (parameter-free) analysis of cellular networks. So far, software tools providing such methods for both mass-flow (metabolic) as well as signal-flow (signalling and regulatory) networks are lacking.

Results

Herein we introduce CellNetAnalyzer, a toolbox for MATLAB facilitating, in an interactive and visual manner, a comprehensive structural analysis of metabolic, signalling and regulatory networks. The particular strengths of CellNetAnalyzer are methods for functional network analysis, i.e. for characterising functional states, for detecting functional dependencies, for identifying intervention strategies, or for giving qualitative predictions on the effects of perturbations. CellNetAnalyzer extends its predecessor FluxAnalyzer (originally developed for metabolic network and pathway analysis) by a new modelling framework for examining signal-flow networks. Two of the novel methods implemented in CellNetAnalyzer are discussed in more detail regarding algorithmic issues and applications: the computation and analysis (i) of shortest positive and shortest negative paths and circuits in interaction graphs and (ii) of minimal intervention sets in logical networks.

Conclusion

CellNetAnalyzer provides a single suite to perform structural and qualitative analysis of both mass-flow- and signal-flow-based cellular networks in a user-friendly environment. It provides a large toolbox with various, partially unique, functions and algorithms for functional network analysis.CellNetAnalyzer is freely available for academic use.     

Continuum modeling and numerical simulation of cell motility

This work proposes a continuum-mechanical model of cell motility which accounts for the dynamics of motility-relevant protein species. For the special case of fish epidermal keratocytes, the stress and cell-substrate traction responses are postulated to depend on selected protein densities in accordance with the structural features of the cells. A one-dimensional version of the model is implemented using Arbitrary Lagrangian–Eulerian finite elements in conjunction with Lagrange multipliers for the treatment of kinematic constraints related to surface growth. Representative numerical tests demonstrate the capacity of the proposed model to simulate stationary and steady crawling states.     

Systems dynamic modeling of the stomatal guard cell predicts emergent behaviors in transport, signaling, and volume control

The dynamics of stomatal movements and their consequences for photosynthesis and transpirational water loss have long been incorporated into mathematical models, but none have been developed from the bottom up that are widely applicable in predicting stomatal behavior at a cellular level. We previously established a systems dynamic model incorporating explicitly the wealth of biophysical and kinetic knowledge available for guard cell transport, signaling, and homeostasis. Here we describe the behavior of the model in response to experimentally documented changes in primary pump activities and malate (Mal) synthesis imposed over a diurnal cycle. We show that the model successfully recapitulates the cyclic variations in H⁺, K⁺, Cl⁻, and Mal concentrations in the cytosol and vacuole known for guard cells. It also yields a number of unexpected and counterintuitive outputs. Among these, we report a diurnal elevation in cytosolic-free Ca²⁺ concentration and an exchange of vacuolar Cl⁻ with Mal, both of which find substantiation in the literature but had previously been suggested to require additional and complex levels of regulation. These findings highlight the true predictive power of the OnGuard model in providing a framework for systems analysis of stomatal guard cells, and they demonstrate the utility of the OnGuard software and HoTSig library in exploring fundamental problems in cellular physiology and homeostasis.The guard cells, which surround stomatal pores in the epidermis of plant leaves, regulate the pore aperture to balance the often conflicting demands for CO₂ in photosynthesis with the need to conserve water by the plant. Stomatal transpiration accounts for much of the nearly 70% of global water usage associated with agriculture and has a profound impact on the water and carbon cycles of the world (Gedney et al., 2006; UNESCO, 2009). Recent studies have associated increases in continental water runoff with the rise in available CO₂ and decreases in stomatal transpiration (Gedney et al., 2006) and have suggested that stomatal behavior skews the impact of greenhouse gasses on fresh water resources (Betts et al., 2007). The past half century has generated a vast wealth of knowledge for guard cell transport, signaling, and homeostasis, resolving the properties of all of the major transporters and many of the signaling pathways that control them (Blatt, 2000a; Schroeder et al., 2001; Blatt et al., 2007; Wang and Song, 2008; McAinsh and Pittman, 2009). Even so, resolving many aspects of stomatal dynamics remains a challenge. These studies have yet to yield any detail about how the entire network of transporters works as a unit to modulate solute flux and regulate stomatal aperture. Quantitative systems analysis offers one approach to this problem that is now much needed. Efforts to model stomatal function to date generally have been driven by a top-down approach: The mechanics of stomatal movements are subsumed within a few empirical parameters of linear hydraulic pathways and conductances (Farquhar and Wong, 1984; Ball, 1987; Williams et al., 1996; Eamus and Shanahan, 2002; West et al., 2005). These models have proven useful at the plant and community levels; but they have not incorporated the essential detail to support an understanding of the molecular and cellular mechanics that drive stomatal movements.In the previous article (Hills et al., 2012) we introduced a computational approach to developing a dynamic model of the stomatal guard cell based on the HoTSig library and OnGuard software. We resolved an OnGuard model that takes account of all of the fundamental properties for transporters at the plasma membrane and tonoplast, the salient features of osmolite metabolism, and key homeostatic and dynamic signaling characteristics that have been described in the literature. The model successfully integrated a number of the steady-state characteristics of guard cells, recapitulating the patterns in guard cell response to the extracellular variables of KCl and CaCl₂ concentrations and to extracellular pH. Here we explore the capacity of the model to reproduce diurnal oscillations in guard cell membrane transport and malate (Mal) metabolism, and its consequences for the dynamics of guard cell volume, turgor pressure, and stomatal aperture. We demonstrate the true predictive power of the OnGuard model in generating a number of unexpected and counterintuitive outputs. Among these, the model yields counterintuitive changes in cytosolic-free [Ca²⁺] ([Ca2+]_i) and a daily exchange of Cl⁻ with Mal that are well documented in the literature, but have been suggested to require additional and complex levels of regulation. These behaviors are accounted for entirely by the known kinetic features of the transporters encoded in the model. Thus, the results demonstrate the predictive power of the OnGuard model as a framework from which to test the basic tenets of the stomatal behavior and to explore the interactions of transport and metabolism in the guard cell system.     

Ensemble modeling for analysis of cell signaling dynamics

Systems biology iteratively combines experimentation with mathematical modeling. However, limited mechanistic knowledge, conflicting hypotheses and scarce experimental data severely hamper the development of predictive mechanistic models in many areas of biology. Even under such high uncertainty, we show here that ensemble modeling, when combined with targeted experimental analysis, can unravel key operating principles in complex cellular pathways. For proof of concept, we develop a library of mechanistically alternative dynamic models for the highly conserved target-of-rapamycin (TOR) pathway of Saccharomyces cerevisiae. In contrast to the prevailing view of a de novo assembly of type 2A phosphatases (PP2As), our integrated computational and experimental analysis proposes a specificity factor, based on Tap42p-Tip41p, for PP2As as the key signaling mechanism that is quantitatively consistent with all available experimental data. Beyond revising our picture of TOR signaling, we expect ensemble modeling to help elucidate other insufficiently characterized cellular circuits.     

One-eyed pinhead regulates cell motility independent of Squint/Cyclops signaling

In vertebrates, EGF-CFC factors are essential for Nodal signaling. Here, we show that the zygotic function of one-eyed pinhead, the zebrafish EGF-CFC factor, is necessary for cell movement throughout the blastoderm of the early embryo. During the blastula and gastrula stages, mutant cells are more cohesive and migrate slower than wild-type cells. Chimeric analysis reveals that these early motility defects are cell-autonomous; later, one-eyed pinhead mutant cells have a cell-autonomous tendency to acquire ectodermal rather than mesendodermal fates. Moreover, wild-type cells transplanted into the axial region of mutant hosts tend to form isolated aggregates of notochord tissue adjacent to the mutant notochord. Upon misexpressing the Nodal-like ligand Activin in whole embryos, which rescues aspects of the mutant phenotype, cell behavior retains the one-eyed pinhead motility phenotype. However, in squint;cyclops double mutants, which lack Nodal function and possess a more severe phenotype than zygotic one-eyed pinhead mutants, cells of the dorsal margin exhibit a marked tendency to widely disperse rather than cohere together. Elsewhere in the double mutants, for cells of the blastoderm and for rare cells of the gastrula that involute into the hypoblast, motility appears wild-type. Notably, cells at the animal pole, which are not under direct regulation by the Nodal pathway, behave normal in squint;cyclops mutants but exhibit defective motility in one-eyed pinhead mutants. We conclude that, in addition to a role in Nodal signaling, One-eyed pinhead is required for aspects of cell movement, possibly by regulating cell adhesion.     

Charge effects on phospholipid monolayers in relation to cell motility

A new sensitive method for the assay of retinyl ester hydrolase in vitro was developed and applied to liver homogenates of 18 young pigs with depleted-to-adequate liver vitamin A reserves. Radioactive substrate was not required, because the formation of retinol could be adequately quantitated by reversed-phase high-performance liquid chromatography. Optimal hydrolase activity was observed with 500 microM retinyl palmitate, 100 mM 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate, and 2 mg/ml Triton X-100 at pH 8.0. The relative rates of hydrolysis of six different retinyl esters by liver homogenate were: retinyl linolenate (100%), myristate (99%), palmitate (47%), oleate (38%), linoleate (31%), and stearate (29%). The enzyme was found primarily in the membrane-containing fractions of liver (59 +/- 3%, S.E.) and kidney (76 +/- 3%), with considerably lower overall activity in kidney (57-375 nmol/h per g of tissue) than in liver (394-1040 nmol/h per g). Retinyl ester hydrolase activity in these pigs was independent of serum retinol values, which ranged from 3 to 24 micrograms/dl, and of liver vitamin A concentrations from 0 to 32 micrograms/g. Pig liver retinyl ester hydrolase differs from the rat liver enzyme in its substrate specificity, bile acid stimulation, and interanimal variability.     

New method for modeling connective-tissue cell migration: improved accuracy on motility parameters

Mathematical models of cell migration based on persistent random walks have been successfully applied to describe the motility of several cell types. However, the migration of slowly moving connective-tissue cells, such as fibroblasts, is difficult to observe experimentally and difficult to describe theoretically. We identify two primary sources of this difficulty. First, cells such as fibroblasts tend to migrate slowly and change shape during migration. This makes accurate determination of cell position difficult. Second, the cell population is considerably heterogeneous with respect to cell speed. Here we develop a method for fitting connective-tissue cell migration data to persistent random walk models, which accounts for these two significant sources of error and enables accurate determination of the cell motility parameters. We demonstrate the usefulness of this method for modeling both isotropic cell motility and biased cell motility, where the migration of a population of cells is influenced by a gradient in a surface-bound adhesive peptide. This method can discern differences in the motility of populations of cells at different points along the peptide gradient and can therefore be used as a tool to quantify the effects of peptide concentration and gradient magnitude on cell migration.     

The effects of antimicrotubule agents on cell motility in fibroblast aggregates

Spherical aggregates of chick heart, sclera and skin fibroblasts were fused with tritiated thymidine-labelled aggregates of the identical cell type. After being placed in contact, the two aggregates cohered and broadened the area of contact to form a single aggregate with a planar interface between the labelled and unlabelled halves. The motility of cells in the aggregate was determined by measuring the movement of labelled cells across the boundary into the unlabelled half. Exposure to pharmacological doses of antimicrotubule agents resulted in a significant reduction in fibroblast motility in the three-dimensional aggregates.     

Tumour invasion: effects of cell adhesion and motility

Metastasis is the major cause of failure in cancer therapy. Recent studies of the molecular cell biology of the metastatic process have provided new insights into the mechanisms of cell-cell adhesion, cell-substrate adhesion and cell motility that underly invasion by tumour cells. In this review, Van Roy and Mareel discuss the role of proteins with invasion-promoting and invasion-suppressing functions in metastasis.     

Regulation of cell proliferation by autocrine motility factor/phosphoglucose isomerase signaling

Autocrine motility factor (AMF)/phosphoglucose isomerase (PGI; EC 5.3.1.9) is a housekeeping cytosolic enzyme that plays a key role in both glycolysis and gluconeogenesis pathways. AMF/PGI is also a multifunctional protein that displays cytokine properties, eliciting mitogenic, motogenic, and differentiation activities, and has been implicated in tumor progression and metastasis. Because little is known about AMF/PGI-dependent signaling in general and during tumorigenesis in particular, we sought to study its effect on the cell cycle. To elucidate the functional role of PGI, we stably transfected its cDNA into NIH/3T3 and BALB/c 3T3-A31 fibroblasts. Ectopic overexpression of PGI results in the acquisition of a transformed phenotype associated with an acceleration of G1 to S cell cycle transition. These were manifested by up-regulation of cyclin D1 expression and cyclin-dependent kinase activity and down-regulation of the cyclin-dependent kinase inhibitor p27Kip1. The reduced p27Kip1 protein expression level in PGI-overexpressing cells could be restored to control levels by treatment with proteasome inhibitor. PGI-overexpressing cells also exhibited elevated expression of Skp2 involved in p27Kip1 ubiquitination and elevation in the levels of retinoblastoma protein hyperphosphorylation. Thus, we may conclude that the overexpression of AMF/PGI enhances cell proliferation together with up-regulation of cyclin/cyclin-dependent kinase activities and down-regulation of p27Kip1, whereas the induction of 3T3 fibroblast transformation by PGI is regulated by the retinoblastoma protein pathway.     

Regulation of myocardial contractility and cell size by distinct PI3K-PTEN signaling pathways

The PTEN/PI3K signaling pathway regulates a vast array of fundamental cellular responses. We show that cardiomyocyte-specific inactivation of tumor suppressor PTEN results in hypertrophy, and unexpectedly, a dramatic decrease in cardiac contractility. Analysis of double-mutant mice revealed that the cardiac hypertrophy and the contractility defects could be genetically uncoupled. PI3Kalpha mediates the alteration in cell size while PI3Kgamma acts as a negative regulator of cardiac contractility. Mechanistically, PI3Kgamma inhibits cAMP production and hypercontractility can be reverted by blocking cAMP function. These data show that PTEN has an important in vivo role in cardiomyocyte hypertrophy and GPCR signaling and identify a function for the PTEN-PI3Kgamma pathway in the modulation of heart muscle contractility.     

Triptolide suppresses pancreatic cancer cell proliferation by inhibiting hedgehog signaling pathway activity

正Dear Editor,Pancreatic cancer (PCa) is a high-grade gastrointestinal malignancy more commonly occurring in elderly populations with lower than 5% overall 5-year survival rate (Hidalgo, 2010). PCa responds poorly to most chemotherapeutic agents, and therefore it is imperative to develop novel therapeutic agents that have anti-cancer activities against PCa.     

EPH/EPHRIN regulates cellular organization by actomyosin contractility effects on cell contacts

EPH/EPHRIN signaling is essential to many aspects of tissue self-organization and morphogenesis, but little is known about how EPH/EPHRIN signaling regulates cell mechanics during these processes. Here, we use a series of approaches to examine how EPH/EPHRIN signaling drives cellular self-organization. Contact angle measurements reveal that EPH/EPHRIN signaling decreases the stability of heterotypic cell:cell contacts through increased cortical actomyosin contractility. We find that EPH/EPHRIN-driven cell segregation depends on actomyosin contractility but occurs independently of directed cell migration and without changes in cell adhesion. Atomic force microscopy and live cell imaging of myosin localization support that EPH/EPHRIN signaling results in increased cortical tension. Interestingly, actomyosin contractility also nonautonomously drives increased EPHB2:EPHB2 homotypic contacts. Finally, we demonstrate that changes in tissue organization are driven by minimization of heterotypic contacts through actomyosin contractility in cell aggregates and by mouse genetics experiments. These data elucidate the biomechanical mechanisms driving EPH/EPHRIN-based cell segregation wherein differences in interfacial tension, regulated by actomyosin contractility, govern cellular self-organization.     

Smurf1 regulates tumor cell plasticity and motility through degradation of RhoA leading to localized inhibition of contractility

Rho GTPases participate in various cellular processes, including normal and tumor cell migration. It has been reported that RhoA is targeted for degradation at the leading edge of migrating cells by the E3 ubiquitin ligase Smurf1, and that this is required for the formation of protrusions. We report that Smurf1-dependent RhoA degradation in tumor cells results in the down-regulation of Rho kinase (ROCK) activity and myosin light chain 2 (MLC2) phosphorylation at the cell periphery. The localized inhibition of contractile forces is necessary for the formation of lamellipodia and for tumor cell motility in 2D tissue culture assays. In 3D invasion assays, and in in vivo tumor cell migration, the inhibition of Smurf1 induces a mesenchymal-amoeboid-like transition that is associated with a more invasive phenotype. Our results suggest that Smurf1 is a pivotal regulator of tumor cell movement through its regulation of RhoA signaling.     

On the effects of cycloheximide on cell motility and polarisation in Dictyostelium discoideum

Background  

Cycloheximide is a protein synthesis inhibitor that acts specifically on the 60S subunit of eukaryotic ribosomes. It has previously been shown that a short incubation of Dictyostelium discoideum amoebae in cycloheximide eliminates fluid phase endocytosis.     

Deguelin attenuates non-small cell lung cancer cell metastasis through inhibiting the CtsZ/FAK signaling pathway

Lung cancer is the leading cause of cancer-related death among both men and women every year, mainly due to metastasis. Although natural compound deguelin has been reported to inhibited cell migration and invasion in various cancer cells, the details of this regulation progress remain to be fully elucidated. In this study, we investigated the underlying mechanism of deguelin-suppressed metastasis of non-small cell lung cancer (NSCLC) cells. Our results demonstrate that deguelin inhibits NSCLC cell migration, invasion, and metastasis both in vitro and in vivo. These inhibitory effects of deguelin were mediated by suppressing of Cathepsin Z (CtsZ) expression and interrupting the interaction of CtsZ with integrin β3. Moreover, deguelin inhibits the activation of CtsZ downstream FAK/Src/Paxillin signaling. Knockdown of CtsZ mimicked the effect of deguelin on NSCLC cells migration and invasion. Our study reveals that deguelin exerts its anti-metastatic effect both in vitro and in vivo is partly dependent on the suppression of CtsZ signaling. Deguelin would be a potential anti-metastasis agent against NSCLC.     

Modeling cell protrusion predicts how myosin II and actin turnover affect adhesion-based signaling

Orchestration of cell migration is essential for development, tissue regeneration, and the immune response. This dynamic process integrates adhesion, signaling, and cytoskeletal subprocesses across spatial and temporal scales. In mesenchymal cells, adhesion complexes bound to extracellular matrix mediate both biochemical signal transduction and physical interaction with the F-actin cytoskeleton. Here, we present a mathematical model that offers insight into both aspects, considering spatiotemporal dynamics of nascent adhesions, active signaling molecules, mechanical clutching, actin treadmilling, and nonmuscle myosin II contractility. At the core of the model is a positive feedback loop, whereby adhesion-based signaling promotes generation of barbed ends at, and protrusion of, the cell’s leading edge, which in turn promotes formation and stabilization of nascent adhesions. The model predicts a switch-like transition and optimality of membrane protrusion, determined by the balance of actin polymerization and retrograde flow, with respect to extracellular matrix density. The model, together with new experimental measurements, explains how protrusion can be modulated by mechanical effects (nonmuscle myosin II contractility and adhesive bond stiffness) and F-actin turnover.