Interactions between mitogenic stimuli, or, a thousand and one connections

Role of Integrins in Modulating Smooth Muscle Cell Plasticity and Vascular Remodeling: From Expression to Therapeutic Implications

Smooth muscle cells (SMCs), present in the media layer of blood vessels, are crucial in maintaining vascular homeostasis. Upon vascular injury, SMCs show a high degree of plasticity, undergo a change from a “contractile” to a “synthetic” phenotype, and play an essential role in the pathophysiology of diseases including atherosclerosis and restenosis. Integrins are cell surface receptors, which are involved in cell-to-cell binding and cell-to-extracellular-matrix interactions. By binding to extracellular matrix components, integrins trigger intracellular signaling and regulate several of the SMC function, including proliferation, migration, and phenotypic switching. Although pharmacological approaches, including antibodies and synthetic peptides, have been effectively utilized to target integrins to limit atherosclerosis and restenosis, none has been commercialized yet. A clear understanding of how integrins modulate SMC biology is essential to facilitate the development of integrin-based interventions to combat atherosclerosis and restenosis. Herein, we highlight the importance of integrins in modulating functional properties of SMCs and their implications for vascular pathology.

Signal transduction in cognitive systems: Origin and dynamics of the inverted-U/U dose-response relations

Cognitive systems are indeed physical systems, but have behavioral patterns extending far beyond familiar physical changes. These behaviors are characterized by underlying symmetries and temperature measures much different from those driving phase transitions in non-cognitive systems. We define a temperature analog dependent on a scalarized synergism between rates of internal crosstalk, external sensory information, and material supply, and show that, if the analog fits a simple concavity relation with the rate index, then the dose-response curve of cognition rate with that index will be an inverted-U. If convex, the relation will be U-shaped. The basic results can be generalized at the expense of further mathematical detail to fit a broad spectrum of empirical patterns.

Design Considerations for Hydrogel Wound Dressings: Strategic and Molecular Advances

Wound dressings are traditionally used to protect a wound and to facilitate healing. Currently, their function is expanding. There is an urgent need for new smart products that not only act as a protective barrier but also actively support the wound healing process. Hydrogel dressings are an example of such innovative products and typically facilitate wound healing by providing a hospitable and moist environment in which cells can thrive, while the wound can still breathe and exudate can be drained. These dressings also tend to be less painful or have a soothing effect and allow for additional drug delivery. In this review, various strategic and molecular design considerations are discussed that are relevant for developing a hydrogel into a wound dressing product. These considerations vary from material choice to ease of use and determine the dressing's final properties, application potential, and benefits for the patient. The focus of this review lies on identifying and explaining key aspects of hydrogel wound dressings and their relevance in the different phases of wound repair. Molecular targets of wound healing are discussed that are relevant when tailoring hydrogels toward specific wound healing scenarios. In addition, the potential of hydrogels is reviewed as medicine advances from a repair-based wound healing approach toward a regenerative-based one. Hydrogels can play a key role in the transition toward personal wound care and facilitating regenerative medicine strategies by acting as a scaffold for (stem) cells and carrier/source of bioactive molecules and/or drugs. Impact statement Improved wound healing will lead to a better quality of life around the globe. It can be expected that this coincides with a reduction in health care spending, as the duration of treatment decreases. To achieve this, new and modern wound care products are desired that both facilitate healing and improve comfort and outcome for the patient. It is proposed that hydrogel wound dressings can play a pivotal role in improving wound care, and to that end, this review aims to summarize the various design considerations that can be made to optimize hydrogels for the purpose of a wound dressing.

Cannabinoid Actions on Neural Stem Cells: Implications for Pathophysiology

With the increase of life expectancy, neurodegenerative disorders are becoming not only a health but also a social burden worldwide. However, due to the multitude of pathophysiological disease states, current treatments fail to meet the desired outcomes. Therefore, there is a need for new therapeutic strategies focusing on more integrated, personalized and effective approaches. The prospect of using neural stem cells (NSC) as regenerative therapies is very promising, however several issues still need to be addressed. In particular, the potential actions of pharmacological agents used to modulate NSC activity are highly relevant. With the ongoing discussion of cannabinoid usage for medical purposes and reports drawing attention to the effects of cannabinoids on NSC regulation, there is an enormous, and yet, uncovered potential for cannabinoids as treatment options for several neurological disorders, specifically when combined with stem cell therapy. In this manuscript, we review in detail how cannabinoids act as potent regulators of NSC biology and their potential to modulate several neurogenic features in the context of pathophysiology.

Comparative analysis of the transcriptome of the overwintering desert beetle Microdera punctipennis

The cold tolerance mechanisms of insect have been studied extensively on the model species Drosophila and a few other species at the transcriptional level. However studies on insects that inherit strong cold tolerance are limited. Cold hardy Tenebrionid beetle Microdera punctipennis is endemic to Gurbantonggut Desert, northwest of China. However, its genomic information is lacking. To investigate the overwintering mechanisms of M. punctipennis adult, RNA-seq was performed on the winter adults and the control adults that were kept in laboratory at 30 °C. A total of 175,247 unigenes were acquired with an average length of 645 bp. By using DESeq package, we identified 3367 unigenes that were up-regulated and 7988 down-regulated in the winter adults compared with the controls. To further our understanding of these differentially expressed genes (DEGs), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Pathway analysis showed that the "ECM-receptor interaction", "PI3K-Akt signaling pathway", "Estrogen signaling pathway", "Tight junction", and "Regulation of actin cytoskeleton", etc. might play important roles in M. punctipennis overwintering. The DEGs results from the RNA-Seq were confirmed partially by qRT-PCR for 13 DEGs, which showed high consistence with a Pearson's correlation coefficient of 0.851. Overall, the sequence data will provide basic information for subsequent bioinformatical analysis and mining of the genes responsible for cold tolerance in M. punctipennis, as well as for understanding the molecular mechanisms of desert beetle overwintering.

Xaliproden (SR57746A) Induces 5-Ht1A Receptors-Mediated Map Kinase Activation in Pc12 Cells

Neurotrophic growth factors are involved in cell survival. However, natural growth factors have a very limited therapeutic use because of their short half-life. In the present study, we investigated the mechanism of action of a non peptidic neurotrophic drug, Xaliproden, a potential molecule for the treatment of motoneuron diseases, since the transduction pathways of this synthetic 5-HT1A agonist are very poorly understood. Xaliproden does not activate the Trk receptor but causes a rapid increase in the activities of the ERK1 and ERK2 isoforms of MAP kinase, which then rapidly decrease to the basal level. We demonstrate that isoforms of the she adapter protein are phosphorylated independently of each other and are probably not the source of the Xaliproden-induced MAP kinases activation. The inhibitor of Ras farnesylation, FPT-1, and the protein kinase C inhibitors, GF 109203X and chelerythrine, inhibited the Xaliproden-induced MAP kinase activation, suggesting p21Ras and PKC involvement. Moreover, the observations that the 5-HT1A antagonist, pindobind, and pertussis toxin abolished the Xaliproden-induced ERK stimulation suggested that Xaliproden activates the MAP kinase pathways by stimulating the G-protein-coupled receptor, 5-HT1A. These results demonstrated clearly that the non peptidic compound, Xaliproden, exerts its neurotrophic effects through a mechanism of action differing from that of neurotrophins. These findings suggest that this compound does not involve MAPK activation by TrkA receptor stimulation but acts by MAP Kinase pathway by a pertussis toxin-sensitive mechanism involving 5-HT1A receptors, p21 Ras and MEK-1 and by PKC and Akt pathways.

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast

Cells respond to environmental stimuli via specialized signaling pathways. Concurrent stimuli trigger multiple pathways that integrate information, predominantly via protein phosphorylation. Budding yeast responds to NaCl and pheromone via two mitogen-activated protein kinase cascades, the high osmolarity, and the mating pathways, respectively. To investigate signal integration between these pathways, we quantified the time-resolved phosphorylation site dynamics after pathway co-stimulation. Using shotgun mass spectrometry, we quantified 2,536 phosphopeptides across 36 conditions. Our data indicate that NaCl and pheromone affect phosphorylation events within both pathways, which thus affect each other at more levels than anticipated, allowing for information exchange and signal integration. We observed a pheromone-induced down-regulation of Hog1 phosphorylation due to Gpd1, Ste20, Ptp2, Pbs2, and Ptc1. Distinct Ste20 and Pbs2 phosphosites responded differently to the two stimuli, suggesting these proteins as key mediators of the information exchange. A set of logic models was then used to assess the role of measured phosphopeptides in the crosstalk. Our results show that the integration of the response to different stimuli requires complex interconnections between signaling pathways.

Lung epithelial stem cells and their niches: Fgf10 takes center stage

Throughout life adult animals crucially depend on stem cell populations to maintain and repair their tissues to ensure life-long organ function. Stem cells are characterized by their capacity to extensively self-renew and give rise to one or more differentiated cell types. These powerful stem cell properties are key to meet the changing demand for tissue replacement during normal lung homeostasis and regeneration after lung injury. Great strides have been made over the last few years to identify and characterize lung epithelial stem cells as well as their lineage relationships. Unfortunately, knowledge on what regulates the behavior and fate specification of lung epithelial stem cells is still limited, but involves communication with their microenvironment or niche, a local tissue environment that hosts and influences the behaviors or characteristics of stem cells and that comprises other cell types and extracellular matrix. As such, an intimate and dynamic epithelial-mesenchymal cross-talk, which is also essential during lung development, is required for normal homeostasis and to mount an appropriate regenerative response after lung injury. Fibroblast growth factor 10 (Fgf10) signaling in particular seems to be a well-conserved signaling pathway governing epithelial-mesenchymal interactions during lung development as well as between different adult lung epithelial stem cells and their niches. On the other hand, disruption of these reciprocal interactions leads to a dysfunctional epithelial stem cell-niche unit, which may culminate in chronic lung diseases such as chronic obstructive pulmonary disease (COPD), chronic asthma and idiopathic pulmonary fibrosis (IPF).

Metalloproteinase dependent reduction of cell surface cluster determinants upon the induction of apoptosis

LN18 glioblastoma cells were used as a model to examine changes in surface cluster determinants (CDs) as the cells undergo apoptosis. LN18 cells proceeding through apoptosis manifested a decrease in cell adhesion molecules, growth factor receptors and other surface proteins. Apoptosis was induced by MK886, a known FLAP and PPAR-α inhibitor, or staurosporine, a known inhibitor of protein kinases including protein kinase C (PKC). The detection and decrease of surface CDs were observed by flow cytometry using CD-specific primary antibodies followed by secondary antibodies conjugated to phycoerythrin. It was determined that there was an apoptotic induced decrease of α and β integrin determinants and the growth factor receptors EGFR and IGF1R. The MHC-1 cell surface marker HLA-ABC was also reduced in the apoptotic cells. The level of EGFR, IGF1R and detected α and β integrin determinants dropped dramatically. The degradation takes place in mid to late apoptosis. It was determined by real-time RT-PCR that the decrease in integrins, EGFR, IGF1R and MHC-1 determinants were not due to a reduction in transcription. Inhibitors of metalloproteinases blocked the apoptotic decrease in cell surface determinants indicating that metalloproteinases mediated the reduction in these CDs in a manner that can reduce growth and survival signals while stimulating the NK surveillance system. Overall, the data indicate that the final stages of the pharmacological induction of apoptosis, while proceeding to a full commitment to non-necrotic cell death, involves the degradation of integrin, insulin and epidermal growth factor receptors caused by a programmed dysregulation of the cell’s metalloproteinases.

Comparison on extreme pathways reveals nature of different biological processes

Background

Constraint-based reconstruction and analysis (COBRA) is used for modeling genome-scale metabolic networks (MNs). In a COBRA model, extreme pathways (ExPas) are the edges of its conical solution space, which is formed by all viable steady-state flux distributions. ExPa analysis has been successfully applied to MNs to reveal their phenotypic capabilities and properties. Recently, the COBRA framework has been extended to transcriptional regulatory networks (TRNs) and transcriptional and translational networks (TTNs), so efforts are needed to determine whether ExPa analysis is also effective on these two types of networks.

Results

In this paper, the ExPas resulting from the COBRA models of E.coli's MN, TRN and TTN were horizontally compared from 5 aspects: (1) Total number and the ratio of their amount to reaction amount; (2) Length distribution; (3) Reaction participation; (4) Correlated reaction sets (CoSets); (5) interconnectivity degree. Significant discrepancies in above properties were observed during the comparison, which reveals the biological natures of different biological processes. Besides, by demonstrating the application of ExPa analysis on E.coli, we provide a practical guidance of an improved approach to compute ExPas on COBRA models of TRNs.

Conclusions

ExPas of E.coli's MN, TRN and TTN have different properties, which are strongly connected with various biological natures of biochemical networks, such as topological structure, specificity and redundancy. Our study shows that ExPas are biologically meaningful on the newborn models and suggests the effectiveness of ExPa analysis on them.

Computational models of signalling networks for non-linear control

Artificial signalling networks (ASNs) are a computational approach inspired by the signalling processes inside cells that decode outside environmental information. Using evolutionary algorithms to induce complex behaviours, we show how chaotic dynamics in a conservative dynamical system can be controlled. Such dynamics are of particular interest as they mimic the inherent complexity of non-linear physical systems in the real world. Considering the main biological interpretations of cellular signalling, in which complex behaviours and robust cellular responses emerge from the interaction of multiple pathways, we introduce two ASN representations: a stand-alone ASN and a coupled ASN. In particular we note how sophisticated cellular communication mechanisms can lead to effective controllers, where complicated problems can be divided into smaller and independent tasks.

Extracellular regulated kinase5 is expressed in fetal mouse submandibular glands and is phosphorylated in response to epidermal growth factor and other ligands of the ErbB family of receptors

Growth factors and their receptors regulate development of many organs through activation of multiple intracellular signaling cascades including a mitogen-activated protein kinase (MAPK). Extracellular regulated kinases (ERK)1/2, classic MAPK family members, are expressed in fetal mouse submandibular glands (SMG), and stimulate branching morphogenesis. ERK5, also called big mitogen-activated protein kinase 1, was recently found as a new member of MAPK super family, and its biological roles are still largely unknown. In this study, we investigated the expression and function of ERK5 in developing fetal mouse SMGs. Western blotting analysis showed that the expression pattern of ERK5 was different from the pattern of ERK1/2 in developing fetal SMGs. Both ERK1/2 and ERK5 were phosphorylated after exposure to ligands of the ErbB family of receptor tyrosine kinases (RTKs). Phosphorylation of ERK1/2 was strongly induced by epidermal growth factor (EGF) in SMG rudiments at embryonic day 14 (E14), E16 and E18. However, ERK5 phosphorylation induced by EGF was clearly observed at E14 and E16, but not at E18. Branching morphogenesis of cultured E13 SMG rudiments was strongly suppressed by administration of U0126, an inhibitor for ERK1/2 activation, whereas the phosphorylation of ERK5 was not inhibited by U0126. BIX02188, a specific inhibitor for ERK5 activation, also inhibited branching morphogenesis in cultured SMG rudiments. These results show that EGF-responsive ERK5 is expressed in developing fetal mouse SMG, and suggest that both ERK1/2 and ERK5 signaling cascades might play an important role in the regulation of branching morphogenesis.

FAS1 domain protein inhibits VEGF165-induced angiogenesis by targeting the interaction between VEGFR-2 and αvβ3 integrin

It is known that VEGF receptors (VEGFR) and integrins interact with each other to regulate angiogenesis. We reported previously that the fasciclin 1 (FAS1) domain-containing protein, TGFBIp/βig-h3 (TGF-β-induced protein) is an angiogenesis regulator that inhibits both endothelial cell migration and growth via αvβ3 integrin. In an attempt to target the interaction between VEGFR-2 and αvβ3 integrin, we determined whether the FAS1 domain region of TGFBIp/βig-h3 (FAS1 domain protein) can block the interaction between the two receptors, leading to the suppression of angiogenesis. In this study, we showed that FAS1 domain protein inhibits VEGF165-induced endothelial cell proliferation and migration via αvβ3 integrin, resulting in the inhibition of VEGF165-induced angiogenesis. We also defined a molecular mechanism by which FAS1 domain protein blocks the association between αvβ3 integrin and VEGFR-2, showing that it binds to αvβ3 integrin but not to VEGFR-2. Blocking the association of these major angiogenic receptors with FAS1 domain protein inhibits signaling pathways downstream of VEGFR-2. Collectively, our results indicate that FAS1 domain protein, in addition to its inhibitory effect on αvβ3 integrin-mediated angiogenesis, also inhibits VEGF165-induced angiogenesis. Thus, FAS1 domain protein can be further developed into a potent anticancer drug that targets two principal angiogenic pathways.

Regulation of integrin adhesions by varying the density of substrate-bound epidermal growth factor

Substrates coated with specific bioactive ligands are important for tissue engineering, enabling the local presentation of extracellular stimulants at controlled positions and densities. In this study, we examined the cross-talk between integrin and epidermal growth factor (EGF) receptors following their interaction with surface-immobilized Arg-Gly-Asp (RGD) and EGF ligands, respectively. Surfaces of glass coverslips, modified with biotinylated silane-polyethylene glycol, were functionalized by either biotinylated RGD or EGF (or both) via the biotin-NeutrAvidin interaction. Fluorescent labeling of the adhering A431 epidermoid carcinoma cells for zyxin or actin indicated that EGF had a dual effect on focal adhesions (FA) and stress fibers: at low concentrations (0.1; 1 ng/ml), it stimulated their growth; whereas at higher concentrations, on surfaces with low to intermediate RGD densities, it induced their disassembly, leading to cell detachment. The EGF-dependent dissociation of FAs was, however, attenuated on higher RGD density surfaces. Simultaneous stimulation by both immobilized RGD and EGF suggest a strong synergy between integrin and EGFR signaling, in FA induction and cell spreading. A critical threshold level of EGF was required to induce significant variation in cell adhesion; beyond this critical density, the immobilized molecule had a considerably stronger effect on cell adhesion than did soluble EGF. The mechanisms underlying this synergy between the adhesion ligand and EGF are discussed.

NOISE-INDUCED ALTERNATIVE RESPONSE IN MAP KINASE PATHWAYS WITH MUTUAL INHIBITION

All organisms have the ability to detect and respond to changes in the environment for survival, and as a result, specific cellular signaling pathways have evolved by which organisms sense their environment and respond to signals that they detect. However, an important unsolved problem in cell biology is to understand how specificity from signal to cellular response is maintained between different signal transduction pathways that share similar or identical components. Here, we show, using mathematical and computational modeling, that two typical signaling pathways in a single cell, hyperosmolar and pheromone motigen-avtivated protein kinase in the yeast Saccharomyces cerevisiae with mutual inhibition, can respond alternatively to two costimulated signals in a stochastically fluctuated environment. Within a bistable region over two input signals, noise plays an essential role in achieving specificity of response, while outside it, these pathways achieve specificity by filtering out spurious crosstalk through mutual inhibition.

CROSSTALK FACILITATES SPATIAL SIGNAL PROPAGATION THROUGH MAPK CASCADES

In intracellular mitogen-activated protein kinase (MAPK) cascades, it has been shown that signals can be propagated across the cell cytosol in the form of phosphoprotein waves arising from the bistable response of MAPK to active MAPK kinase. Without such a bistable response, however, they can not propagate into distant cell compartments, although a long positive feedback endows a mechanistically-distinct bistable response of MAPK to extracellular signal. Here we provide a compensate means that uses crosstalk between parallel identical pathways of MAPK cascades. For a spherical cell, we find that both unidirectional and bidirectional crosstalk with enhancement of phosphorylation can facilitate phosphoprotein signal propagation from the plasma membrane to the periphery of cell nucleus. Moreover, different shallow spatial gradients of biphosphorylated MAPK occur in the cytosol under different strengths of pathway interactions. These results suggest that crosstalk would be utilized by living organisms for spatial information transfer and cellular decision-making processing.

Reconstruction and crosstalk of protein-protein interaction networks of Wnt and Hedgehog signaling in Drosophila melanogaster

In the last few years, researchers have an intense interest in the evolutionarily conserved signaling pathways which have crucial roles during embryonic development. The most intriguing factor of this interest is that malfunctioning of these signaling pathways (Hedgehog, Notch, Wnt etc.) leads to several human diseases, especially to cancer. This study deals with the β-catenin dependent branch of Wnt signaling and the Hedgehog signaling pathways which offer potential targeting points for cancer drug development. The identification of all proteins functioning in these signaling networks is crucial for the efforts of preventing tumor formation. Here, through integration of protein-protein interaction data and Gene Ontology annotations, Wnt/β-catenin and Hedgehog signaling networks consisting of proteins that have statistically high probability of being biologically related to these signaling pathways were reconstructed in Drosophila melanogaster. Next, by the structural network analyses, the crucial components functioning in these pathways were identified. The proteins Arm, Frizzled receptors (Fz and Fz2), Arr, Apc, Axn, Ci and Ptc were detected as the key proteins in these networks. Futhermore, the hub protein Mer having tumor suppressor function may be proposed as a putative drug target for cancer and deserves further investigation via experimental methods. Finally, the crosstalk analysis between the reconstructed networks reveals that these two signaling networks crosstalk to each other.

The effect of cell-ECM adhesion on signalling via the ErbB family of growth factor receptors

Integrins and growth factor receptors of the ErbB family are involved in the regulation of cellular interactions with the extracellular microenvironment. Cross-talk between these two groups of transmembrane receptors is essential for cellular responses and can be regulated through the formation of multimolecular complexes. Tetraspanins as facilitators and building blocks of specialized microdomains may be involved in this process. In the present study, we demonstrated that, in contrast with previous reports, integrin-mediated adhesion did not stimulate ligand-independent activation of ErbB receptors in epithelial cells. However, integrin-dependent adhesion potentiated ligand-induced activation of EGFR (epidermal growth factor receptor) and ErbB2 and facilitated receptor homo- and hetero-dimerization. The actin cytoskeleton appeared to play a critical role in this phenomenon.

Remodeling and homeostasis of the extracellular matrix: implications for fibrotic diseases and cancer

Dynamic remodeling of the extracellular matrix (ECM) is essential for development, wound healing and normal organ homeostasis. Life-threatening pathological conditions arise when ECM remodeling becomes excessive or uncontrolled. In this Perspective, we focus on how ECM remodeling contributes to fibrotic diseases and cancer, which both present challenging obstacles with respect to clinical treatment, to illustrate the importance and complexity of cell-ECM interactions in the pathogenesis of these conditions. Fibrotic diseases, which include pulmonary fibrosis, systemic sclerosis, liver cirrhosis and cardiovascular disease, account for over 45% of deaths in the developed world. ECM remodeling is also crucial for tumor malignancy and metastatic progression, which ultimately cause over 90% of deaths from cancer. Here, we discuss current methodologies and models for understanding and quantifying the impact of environmental cues provided by the ECM on disease progression, and how improving our understanding of ECM remodeling in these pathological conditions is crucial for uncovering novel therapeutic targets and treatment strategies. This can only be achieved through the use of appropriate in vitro and in vivo models to mimic disease, and with technologies that enable accurate monitoring, imaging and quantification of the ECM.

Design principles and specificity in biological networks with cross activation

Cells sense and respond to diverse environmental stimuli using a set of intracellular signaling components. Often, the signal transduction pathways contain shared components which lead to cross activation at different levels of the pathway. To discover the design principles that ensure signaling specificity is a challenging task, especially for pathways that contain numerous components. Here, we present an analysis of cross-activating pathways and show that a general inhibitory scheme, asymmetric hierarchical inhibition, is sufficient to ensure signaling specificity. Based on this inhibitory scheme, we are able to enumerate all possible network topologies containing two inhibitory links that guarantee specificity. Furthermore, we apply our methodology to the mating and filamentous growth pathways of the yeast model system Saccharomyces cerevisiae. We enumerate the possible ways to wire this model system and determine which topology is consistent with experimental data.

Inhibition of carcinoma cell motility by epoxyeicosatrienoic acid (EET) antagonists

Cytochrome P450 (CYP) epoxygenases, CYP2C8, 2C9 and 2J2 mRNA and proteins, were expressed in prostate carcinoma (PC-3, DU-145 and LNCaP) cells. 11,12-Epoxyeicosatrienoic acid (11,12-EET) was the major arachidonic acid metabolite in these cells. Blocking EET synthesis by a selective CYP epoxygenase inhibitor (N-methylsulfonyl-6-(2-propargyloxyphenyl)hexanamide [MS-PPOH]) inhibited tonic (basal) invasion and migration (motility) while exogenously added EET induced cell motility in a concentration-dependent manner. An epidermal growth factor receptor (EGFR) kinase inhibitor (AG494) or a PI3 kinase inhibitor (LY294002) inhibited cell migration and reduced 11,12-EET-induced cell migration. Importantly, synthetic EET antagonists (14,15-epoxyeicosa-5(Z)-enoic acid [14,15-EEZE], 14,15-epoxyeicosa-5(Z)-enoic acid 2-[2-(3-hydroxy-propoxy)-ethoxy]-ethyl ester [14,15-EEZE-PEG] and 14,15-epoxyeicosa-5(Z)-enoic-methylsulfonylimide [14,15-EEZE-mSI]) inhibited EET-induced cell invasion and migration. 11,12-EET induced cell stretching and myosin-actin microfilament formation as well as increased phosphorylation of EGFR and Akt (Ser473), while 14,15-EEZE inhibited these effects. These results suggest that EET induce and EET antagonists inhibit cell motility, possibly by putative EET receptor-mediated EGFR and PI3K/Akt pathways, and suggest that EET antagonists are potential therapeutic agents for prostate cancer.

Ultrasensitive responses and specificity in cell signaling

Background

Interconnected cell signaling pathways are able to efficiently and accurately transmit a multitude of different signals, despite an inherent potential for undesirable levels of cross-talk. To ensure that an appropriate response is produced, biological systems have evolved network-level mechanisms that insulate pathways from crosstalk and prevent 'leaking' or 'spillover' between pathways. Many signaling pathways have been shown to respond in an ultrasensitive (switch-like) fashion to graded input, and this behavior may influence specificity. The relationship of ultrasensitivity to signaling specificity has not been extensively explored.

Results

We studied the behavior of simple mathematical models of signaling networks composed of two interconnected pathways that share an intermediate component, asking if the two pathways in the network could exhibit both output specificity (preferentially activate their own output) and input fidelity (preferentially respond to their own input). Previous results with weakly-activated pathways indicated that neither mutual specificity nor mutual fidelity were obtainable in the absence of an insulating mechanism, such as cross-pathway inhibition, combinatorial signaling or scaffolding/compartmentalization. Here we found that mutual specificity is obtainable for hyperbolic or ultrasensitive pathways, even in the absence of an insulating mechanism. However, mutual fidelity is impossible at steady-state, even if pathways are hyperbolic or ultrasensitive. Nevertheless, ultrasensitivity does provide advantages in attaining specificity and fidelity to networks that contain an insulating mechanism. For networks featuring cross-pathway inhibition or combinatorial signaling, ultrasensitive activation can increase specificity in a limited way, and can only be utilized by one of the two pathways. In contrast, for networks featuring scaffolding/compartmentalization, ultrasensitive activation of both pathways can dramatically improve network specificity.

Conclusions

There are constraints to obtaining performance objectives associated with signaling specificity; such constraints may have influenced the evolution of signal transduction networks. Notably, input fidelity (preferential response to an authentic input) is a more difficult objective to achieve than output specificity (preferential targeting to an authentic output). Indeed, mutual fidelity is impossible in the absence of an insulating mechanism, even if pathways are ultrasensitive. Ultrasensitivity does, however, significantly enhance the performance of several insulating mechanisms. In particular, the ultrasensitive activation of both pathways can provide substantial improvement to networks containing scaffolding/compartmentalization.

Androgen and Src signaling regulate centrosome activity

Microtubules nucleated from gamma-tubulin ring complexes located at the centrosome regulate the localization of organelles, promote vesicular transport and direct cell migration. Although several signaling mechanisms have been identified that regulate microtubule dynamics during interphase, signaling pathways that promote microtubule nucleation remain elusive. We assayed microtubule regrowth following nocodazole washout in human fibroblasts and CHO-K1 cells adhered to fibronectin in either normal serum-free medium or the serum-free, growth-promoting medium, CCM1, which contains IGF1 and androgen, as well as other nutrients. The results indicate that integrin-mediated adhesion is not sufficient to promote rapid microtubule regrowth in either cell type. The addition of androgen, but not IGF1, for 5 minutes was sufficient to promote rapid regrowth and this occurred by a mechanism requiring the androgen receptor. Since Src is a component of the cytoplasmic androgen-receptor-signaling complex, we examined its role using Src siRNA, the Src kinase inhibitor SU6656, and the expression of a constitutively active Src mutant. The data show that Src signaling is both required and sufficient to promote rapid microtubule regrowth in cells adhered to fibronectin. Measurement of the density of microtubules close to the centrosome and the rates of GFP-EB1-labeled microtubules emanating from the centrosome indicated that Src signaling promotes microtubule nucleation. Furthermore, recovery of GFP-gamma-tubulin at the centrosome following photobleaching and measurements of endogenous gamma-tubulin levels at the centrosome showed that androgen and Src signaling regulate the levels of centrosomal gamma-tubulin. Thus, we propose that androgen and Src signaling regulate microtubule nucleation during interphase by promoting the centrosomal localization of gamma-tubulin.

Protein kinase D1 inhibits cell proliferation through matrix metalloproteinase-2 and matrix metalloproteinase-9 secretion in prostate cancer

We and others previously showed that protein kinase D1 (PKD1) is downregulated in several cancers including prostate; interacts with E-cadherin, a major cell adhesion epithelial protein; and causes increased cell aggregation and decreased motility of prostate cancer cells. In this study, we show that PKD1 complexes with beta3-integrin, resulting in activation of mitogen-activated protein kinase/extracellular signal-regulated kinase (ERK) kinase-ERK pathway, which causes increased production of matrix metalloproteinase (MMP)-2 and MMP-9, that is associated with shedding of soluble 80 kDa E-cadherin extracellular domain. Interestingly, decreased cell proliferation following PKD1 transfection was rescued by MMP-2 and MMP-9 inhibitors and augmented by recombinant MMP-2 (rMMP-2) and rMMP-9 proteins, suggesting an antiproliferative role for MMPs in prostate cancer. Translational studies by in silico analysis of publicly available DNA microarray data sets show a significant direct correlation between PKD1 and MMP-2 expression in human prostate tissues. The study shows a novel mechanism for antiproliferative effects of PKD1, a protein of emerging translational interest in several human cancers, through increased production of MMP-2 and MMP-9 in cancer cells.

Parameter inference and model selection in signaling pathway models

To support and guide an extensive experimental research into systems biology of signaling pathways, increasingly more mechanistic models are being developed with hopes of gaining further insight into biological processes. In order to analyze these models, computational and statistical techniques are needed to estimate the unknown kinetic parameters. This chapter reviews methods from frequentist and Bayesian statistics for estimation of parameters and for choosing which model is best for modeling the underlying system. Approximate Bayesian computation techniques are introduced and employed to explore different hypothesis about the JAK-STAT signaling pathway.

The GAB2 signaling scaffold promotes anchorage independence and drives a transcriptional response associated with metastatic progression of breast cancer

Acquisition of independence from anchorage to the extracellular matrix is a critical event for onset and progression of solid cancers. To identify and characterize new genes conferring anchorage independence, we transduced MCF10A human normal breast cells with a retroviral cDNA expression library and selected them by growth in suspension. Microarray analysis targeted on library-derived transcripts revealed robust and reproducible enrichment, after selection, of cDNAs encoding the scaffolding adaptor Gab2. Gab2 was confirmed to strongly promote anchorage-independent growth when overexpressed. Interestingly, downregulation by RNA interference of endogenous Gab2 in neoplastic cells did not affect their adherent growth, but abrogated their growth in soft agar. Gab2-driven anchorage independence was found to specifically involve activation of the Src-Stat3 signaling axis. A transcriptional 'signature' of 205 genes was obtained from GAB2-transduced, anchorage-independent MCF10A cells, and found to contain two main functional modules, controlling proliferation and cell adhesion/migration/invasion, respectively. Extensive validation on breast cancer data sets showed that the GAB2 signature provides a robust prognostic classifier for breast cancer metastatic relapse, largely independent from existing clinical and genomic indicators and from estrogen receptor status. This work highlights a pivotal role for GAB2 and its transcriptional targets in anchorage-independent growth and breast cancer metastatic progression.

Sustained activation of STAT5 is essential for chromatin remodeling and maintenance of mammary-specific function

Epithelial cells, once dissociated and placed in two-dimensional (2D) cultures, rapidly lose tissue-specific functions. We showed previously that in addition to prolactin, signaling by laminin-111 was necessary to restore functional differentiation of mammary epithelia. Here, we elucidate two additional aspects of laminin-111 action. We show that in 2D cultures, the prolactin receptor is basolaterally localized and physically segregated from its apically placed ligand. Detachment of the cells exposes the receptor to ligation by prolactin leading to signal transducers and activators of transcription protein 5 (STAT5) activation, but only transiently and not sufficiently for induction of milk protein expression. We show that laminin-111 reorganizes mammary cells into polarized acini, allowing both the exposure of the prolactin receptor and sustained activation of STAT5. The use of constitutively active STAT5 constructs showed that the latter is necessary and sufficient for chromatin reorganization and β-casein transcription. These results underscore the crucial role of continuous laminin signaling and polarized tissue architecture in maintenance of transcription factor activation, chromatin organization, and tissue-specific gene expression.

Coordinate integrin and c-Met signaling regulate Wnt gene expression during epithelial morphogenesis

Integrin receptors for the extracellular matrix and receptor tyrosine kinase growth factor receptors represent two of the major families of receptors that transduce into cells information about the surrounding environment. Wnt proteins are a major family of signaling molecules that regulate morphogenetic events. There is presently little understanding of how the expression of Wnt genes themselves is regulated. In this study, we demonstrate that alpha3beta1 integrin, a major laminin receptor involved in the development of the kidney, and c-Met, the receptor for hepatocyte growth factor, signal coordinately to regulate the expression of Wnt7b in the mouse. Wnt signals in turn appear to regulate epithelial cell survival in the papilla of the developing kidney, allowing for the elongation of epithelial tubules to form a mature papilla. Together, these results demonstrate how signals from integrins and growth factor receptors can be integrated to regulate the expression of an important family of signaling molecules so as to regulate morphogenetic events.

Decorin and its galactosaminoglycan chain: extracellular regulator of cellular function?

A molecular network of extracellular matrix molecules determines the tissue architecture and accounts for mechanical properties like compressibility or stretch resistance. It is widely accepted that the elements of the cellular microenvironment are important regulators of the cellular behavior in vitro and in vivo. One large group comprising these molecules is the family of proteoglycans. Both, the core proteins and, in particular, the attached galactosaminoglycans, contribute to the regulation network as they bind a variety of signaling molecules, e.g. cytokines, chemokines, growth, and differentiation factors. We would like to emphasize specific patterns of epimerization and sulfation within the galactosaminoglycans chains, because these result in "motifs" that are responsible for the modulation of signal factor binding, release and activity. This property is crucial in physiological and pathological conditions, for example development and wound healing.

Quantitative analysis of the responses of murine bone marrow mesenchymal stem cells to EGF, PDGF-BB and fibronectin by factorial design methodology

A 2-level full factorial design was firstly employed to explore the responses of murine bone marrow mesenchymal stem cells stimulated by various combinations of EGF, PDGF-BB, and fibronectin. EGF and PDGF-BB individually, rather than fibronectin, had significant effects on cell proliferation. The synergism between PDGF-BB and fibronectin, as well as the antagonism between EGF and PDGF-BB were also detected. Moreover, cells changed from a flattened and spread to a smaller and elongated shape with addition of factors. The factors also moved cells out of G0/G1 phase, increasing the fractions of cells in S and G2/M phases.

Drug targets for tumorigenesis: insights from structural analysis of EGFR signaling network

Deciphering the complex network structure is crucial in drug target identification. This study presents a framework incorporating graph theoretic and network decomposition methods to analyze system-level properties of the comprehensive map of the epidermal growth factor receptor (EGFR) signaling, which is a good candidate model system to study the general mechanisms of signal transduction. The graph theoretic analysis of the EGFR network indicates that it has small-world characteristics with scale-free topology. The employment of network decomposition analysis enlightened the system-level properties, such as network cross-talk, specific molecules in each pathway and participation of molecules in the network. Participating in a significant fraction of the fundamental paths connecting the ligands to the phenotypes, cofactor GTP and complex Gbeta/Ggamma were identified as "housekeeping" molecules, through which all pathways of EGFR network are cross-talking. c-Src-Shc complex is identified as important due to its role in all fundamental paths through tumorigenesis and being specific to this phenotype. Inhibitors of this complex may be good anti-cancer agents having very little or no effect on other phenotypes.

Integrins alpha1beta1 and alpha2beta1 are receptors for the rotavirus enterotoxin

Rotavirus NSP4 is a viral enterotoxin capable of causing diarrhea in neonatal mice. This process is initiated by the binding of extracellular NSP4 to target molecule(s) on the cell surface that triggers a signaling cascade leading to diarrhea. We now report that the integrins alpha1beta1 and alpha2beta1 are receptors for NSP4. NSP4 specifically binds to the alpha1 and alpha2 I domains with apparent K(d) = 1-2.7 muM. Binding is mediated by the I domain metal ion-dependent adhesion site motif, requires Mg(2+) or Mn(2+), is abolished with EDTA, and an NSP4 point mutant, E(120)A, fails to bind alpha2 integrin I domain. NSP4 has two distinct integrin interaction domains. NSP4 amino acids 114-130 are essential for binding to the I domain, and NSP4 peptide 114-135 blocks binding of the natural ligand, collagen I, to integrin alpha2. NSP4 amino acids 131-140 are not associated with the initial binding to the I domain, but elicit signaling that leads to the spreading of attached C2C12-alpha2 cells, mouse myoblast cells stably expressing the human alpha2 integrin. NSP4 colocalizes with integrin alpha2 on the basolateral surface of rotavirus-infected polarized intestinal epithelial (Caco-2) cells as well as surrounding noninfected cells. NSP4 mutants that fail to bind or signal through integrin alpha2 were attenuated in diarrhea induction in neonatal mice. These results indicate that NSP4 interaction with integrin alpha1 and alpha2 is an important component of enterotoxin function and rotavirus pathogenesis, further distinguishing this viral virulence factor from other microbial enterotoxins.

Restoration of PTEN expression alters the sensitivity of prostate cancer cells to EGFR inhibitors

INTRODUCTION

Prostate cancer (CaP) progression from an androgen-dependent to an androgen-independent state is associated with overexpression of EGFR family members or activation of their downstream signaling pathways, such as PI3K-Akt and MAPK. Although there are data implicating PI3K-Akt or MAPK pathway activation with resistance to EGFR inhibitors in CaP, the potential cross-talk between these pathways in response to EGFR or MAPK inhibitors remains to be examined.

METHODS

Cross-talk between PTEN and MAPK signaling and its effects on CaP cell sensitivity to EGFR or MAPK inhibitors were examined in a PTEN-null C4-2 CaP cell, pTetOn PTEN C4-2, where PTEN expression was restored conditionally.

RESULTS

Expression of PTEN in C4-2 cells exposed to EGF or serum was associated with increased phospho-ERK levels compared to cells without PTEN expression. Similar hypersensitivity of MAPK signaling was observed when cells were treated with a PI3K inhibitor LY294002. This enhanced sensitivity of MAPK signaling in PTEN-expressing cells was associated with a growth stimulatory effect in response to EGF. Furthermore, EGFR inhibitors gefitinib and lapatinib abrogated hypersensitivity of MAPK signaling and cooperated with PTEN expression to inhibit cell growth in both monolayer and anchorage-independent conditions. Similar cooperative growth inhibition was observed when cells were treated with the MEK inhibitor, CI1040, in combination with PTEN expression suggesting that inhibition of MAPK signaling could mediate the cooperation of EGFR inhibitors with PTEN expression.

CONCLUSIONS

Our results suggest that signaling cross-talk between the PI3K-Akt and MAPK pathways occurs in CaP cells, highlighting the potential benefit of targeting both the PI3K-Akt and MAPK pathways in CaP treatment.

Integrin alphavbeta3 mediates upregulation of epidermal growth-factor receptor expression and activity in human ovarian cancer cells

Upon overexpression of integrin alphavbeta3 and its engagement by vitronectin, we previously showed enhanced adhesion, proliferation, and motility of human ovarian cancer cells. By studying differential expression of genes possibly related to these tumor biological events, we identified the epidermal growth-factor receptor (EGF-R) to be under control of alphavbeta3 expression levels. Thus in the present study we characterized alphavbeta3-dependent changes of EGF-R and found significant upregulation of its expression and activity which was reflected by prominent changes of EGF-R promoter activity. Upon disruption of DNA-binding motifs for the transcription factors p53, ETF, the repressor ETR, p50, and c-rel, respectively, we sought to identify DNA elements contributing to alphavbeta3-mediated EGF-R promoter induction. Both, the p53- and ETF-mutant, while exhibiting considerably lower EGF-R promoter activity than the wild type promoter, retained inducibility by alphavbeta3. Mutation of the repressor motif ETR, as expected, enhanced EGF-R promoter activity with a further moderate increase upon alphavbeta3 elevation. The p50-mutant displayed EGF-R promoter activity almost comparable to that of the wild type promoter with no impairment of induction by alphavbeta3. However, the activity of an EGF-R promoter mutant displaying a disrupted c-rel-binding motif did not only prominently decline, but, moreover, was not longer responsive to enhanced alphavbeta3, involving this DNA element in alphavbeta3-dependent EGF-R upregulation. Moreover, alphavbeta3 did not only increase the EGF-R but, moreover, also led to obvious co-clustering on the cancer cell surface. By studying alphavbeta3/EGF-R-effects on the focal adhesion kinase (FAK) and the mitogen activated protein kinases (MAPK) p44/42 (erk(-1)/erk(-2)), having important functions in synergistic crosstalk between integrins and growth-factor receptors, we found for both significant enhancement of expression and activity upon alphavbeta3/VN interaction and cell stimulation by EGF. Upregulation of the EGF-R by integrin alphavbeta3, both receptor molecules with a well-defined role as targets for cancer treatment, might represent an additional mechanism to adapt synergistic receptor signaling and crosstalk in response to an altered tumor cell microenvironment during ovarian cancer progression.

Modelling dynamic processes in yeast

Yeast molecular and cell biology has accumulated large amounts of qualitative and quantitative data of diverse cellular processes. The results are often summarized as verbal or graphical descriptions. Moreover, a series of mathematical models has been developed that should help to interpret such data, to integrate them into a coherent picture and to allow for an understanding of the underlying processes. Dynamic modelling of regulatory processes in yeast focuses on central carbon metabolism, on a number of selected signalling pathways and on cell cycle regulation. These models can explain questions of general relevance, such as whether the dynamics of a network can be understood from the combination of in vitro kinetics of its individual reactions. They help to elucidate complicated dynamic features, such as glycolytic oscillations, effects of feedback regulation or the optimal regulation of gene expression. The availability of comprehensive qualitative information, such as protein interactions or pathway composition, and sets of quantitative data make yeast a perfect model organism. Therefore, yeast-related data are often used to develop and examine computational approaches and modelling methods.

Different regulation of hepatocyte behaviors between natural extracellular matrices and synthetic extracellular matrices by hepatocyte growth factor

The roles of growth factors and extracellular matrices (ECMs) in regulation of hepatocyte behaviors are very important for the establishment of liver-tissue engineering. Especially, collaboration between growth factors and ECMs is a big concern for liver-tissue engineering. In this study, the hepatocyte responses by hepatocyte growth factor (HGF) were compared between natural ECMs and a synthetic galactose-carrying polymer: poly(N-p-vinylbenzyl-4-O-beta-D-galactopyranosyl-D-gluconamide) (PVLA). Hepatocytes underwent proliferation on type I collagen- and fibronectin-coated surfaces in the presence of HGF, whereas hepatocytes formed spheroid on laminin-1-, PVLA-, and poly-L-lysine (PLL)-coated surfaces in the presence of HGF without the activation of proliferation. HGF accelerated ECM deposition, especially laminin-10/11, beneath the hepatocytes cultured on PVLA- and PLL-coated surfaces and the deposited laminin-10/11 activated integrin signaling to collaborate with HGF signaling. Therefore, the deposited ECM molecules should be focused to clear the mechanism of hepatocyte behaviors in the presence of HGF.

Jasmonate signalling network in Arabidopsis thaliana: crucial regulatory nodes and new physiological scenarios

Plant development and stress responses are regulated by complex signalling networks that mediate specific and dynamic plant responses upon activation by various types of exogenous and endogenous signal. In this review, we focus on the latest published work on jasmonate (JA) signalling components and new regulatory nodes in the transcriptional network that regulates a number of diverse plant responses to developmental and environmental cues. Not surprisingly, the majority of the key revelations in the field have been made in Arabidopsis thaliana. However, for comparative reasons, we integrate information on Arabidopsis with recent reports for other plant species (when available). Recent findings on the regulation of plant responses to pathogens by JAs, as well as new evidence implicating JAs in the regulation of senescence, suggest a common mechanism of JA action in these responses via distinct groups of transcription factors. Moreover, a significant increase in the amount of evidence has allowed placing of specific mitogen-activated protein kinases (MAPKs) as crucial regulatory nodes in the defence signalling network. In addition, we report on new physiological scenarios for JA signalling, such as organogenesis of nitrogen-fixing nodules and anticancer therapy.

Expression of the human beta3 integrin subunit in mouse smooth muscle cells enhances IGF-I-stimulated signaling and proliferation

Optimal stimulation of signal transduction and biological functions by IGF-I in porcine smooth muscle cells (pSMC) requires ligand occupancy of the alphaVbeta3 integrin. Binding of heparin-binding domain (HBD) of vitronectin (VN) to the cysteine loop (C-loop) region of beta3 is required for pSMC to respond optimally to IGF-I stimulation. Mouse smooth muscle cells (mSMC), which express a form of beta3 whose sequence within the C-loop region is different than porcine or human beta3, do not respond optimally to IGF-I, and IGF-I stimulated beta3 and SHPS-1 phosphorylation which are necessary for optimal IGF-I signaling were undetectable. VN also had no effect on IGF-I stimulated the cell proliferation. In contrast, when human beta3 (hbeta3) was introduced into mSMC, there was an enhanced VN binding in spite of an equivalent amount of total beta3 expression, and IGF-I-dependent beta3, and SHPS-1 phosphorylation were detected. In addition, there was enhanced IGF-I-stimulated Shc association with SHPS-1, Shc tyrosine phosphorylation, Shc and Grb2 association, and MAP kinase activation leading to increased cell proliferation. These enhancements could be further augmented by adding a peptide containing the HBD of VN. To determine if these changes were mediated by the C-loop region of beta3, an antibody that reacts with that region of beta3 was utilized. The addition of the hbeta3 C-loop antibody abolished VN-induced enhancement of IGF-I signaling and IGF-I-stimulated cell proliferation. These results strongly support the conclusion that optimal SMC responsiveness to IGF-I requires ligand interaction with the C-loop domain of hbeta3.

Elastin receptor (spliced galactosidase) occupancy by elastin peptides counteracts proinflammatory cytokine expression in lipopolysaccharide-stimulated human monocytes through NF-kappaB down-regulation

In inflammatory diseases, strong release of elastinolytic proteases results in elastin fiber degradation generating elastin peptides (EPs). Chemotactic activity for inflammatory cells was, among wide range of properties, the former identified biological activity exerted by EPs. Recently, we demonstrated the ability of EPs to favor a Th1 cytokine (IL-2, IFN-gamma) cell response in lymphocytes and to regulate IL-1beta expression in melanoma cells. We hypothesized that EPs might also influence inflammatory cell properties by regulating cytokine expression by these cells. Therefore, we investigated the influence of EPs on inflammatory cytokine synthesis by human monocytes. We evidenced that EPs down-regulated both at the mRNA and protein levels the proinflammatory TNF-alpha, IL-1beta, and IL-6 expression in LPS-activated monocytes. Such negative feedback loop could be accounted solely for EP-mediated effects on proinflammatory cytokine production because EPs did not affect anti-inflammatory IL-10 or TGF-beta secretion by LPS-activated monocytes. Furthermore, we demonstrated that EP effect on proinflammatory cytokine expression by LPS-stimulated monocytes could not be due either to a decrease of LPS receptor expression or to an alteration of LPS binding to its receptor. The inhibitory effects of EPs on cytokine expression were found to be mediated by receptor (spliced galactosidase) occupancy, as being suppressed by lactose, and to be associated with the decrease of NF-kappaB-DNA complex formation. As a whole, these results demonstrated that EP/spliced galactosidase interaction on human monocytes down-regulated NF-kappaB-dependent proinflammatory cytokine expression and pointed out the critical role of EPs in the regulation of inflammatory response.

Mathematical classification of regulatory logics for compound environmental changes

This paper is concerned with biological regulatory mechanisms in response to the simultaneous occurrence of a huge number of environmental changes. The restricted resources of cells strictly limit the number of their regulatory methods; hence, cells must adopt, as compensation, special mechanisms to deal with the simultaneous occurrence of environmental changes. We hypothesize that cells use various control logics to integrate information about independent environmental changes related to a cell task and represent the resulting effects of the different ways of integration by logical functions. Using the notion of equivalence classes in set theory, we describe the mathematical classification of the effects into biologically unequivalent ones realized by different control logics. Our purely mathematical and systematic classification of logical functions reveals three elementary control logics with different biological relevance. To better understand their biological significance, we consider examples of biological systems that use these elementary control logics.

Cellular impedance biosensors for drug screening and toxin detection

Cell-based impedance biosensing is an emerging technology that can be used to non-invasively and instantaneously detect and analyze cell responses to chemical and biological agents. This article highlights the fabrication and measurement technologies of cell impedance sensors, and their application in toxin detection and anti-cancer drug screening. We start with an introduction that describes the capability and advantages of cell-based sensors over conventional sensing technology, followed by a discussion of the influence of cell adhesion, spreading and viability during cell patterning on the subsequent impedance measurements and sensing applications. We then present an electronic circuit that models the cell-electrode system, by which the cellular changes can be detected in terms of impedance changes of the circuit. Finally, we discuss the current status on using cell impedance sensors for toxin detection and anti-cancer drug screening.

EGFR plays a pivotal role in the regulation of polyamine-dependent apoptosis in intestinal epithelial cells

Intracellular polyamine synthesis is regulated by the enzyme ornithine decarboxylase (ODC), and its inhibition by alpha-difluromethylornithine (DFMO), confers resistance to apoptosis. We have previously shown that DFMO leads to the inhibition of de novo polyamine synthesis, which in turn rapidly activates Src, STAT3 and NF-kappaB via integrin beta3 in intestinal epithelial cells. One mechanism to explain these effects involves the activation of upstream growth factor receptors, such as the epidermal growth factor receptor (EGFR). We therefore hypothesized that EGFR phosphorylation regulates the early response to polyamine depletion. DFMO increased EGFR phosphorylation on tyrosine residues 1173 (pY1173) and 845 (pY845) within 5 min. Phosphorylation declined after 10 min and was prevented by the addition of exogenous putrescine to DFMO containing medium. Phosphorylation of EGFR was concomitant with the activation of ERK1/2. Pretreatment with either DFMO or EGF for 1 h protected cells from TNF-alpha/CHX-induced apoptosis. Exogenous addition of polyamines prevented the protective effect of DFMO. In addition, inhibition of integrin beta3 activity (with RGDS), Src activity (with PP2), or EGFR kinase activity (with AG1478), increased basal apoptosis and prevented protection conferred by either DFMO or EGF. Polyamine depletion failed to protect B82L fibroblasts lacking the EGFR (PRN) and PRN cells expressing either a kinase dead EGFR (K721A) or an EGFR (Y845F) mutant lacking the Src phosphorylation site. Conversely, expression of WT-EGFR (WT) restored the protective effect of polyamine depletion. Fibronectin activated the EGFR, Src, ERKs and protected cells from apoptosis. Taken together, our data indicate an essential role of EGFR kinase activity in MEK/ERK-mediated protection, which synergizes with integrin beta3 leading to Src-mediated protective responses in polyamine depleted cells.

Epidermal Growth Factor Signaling for Matrix-Dependent Cell Proliferation and Differentiation in Primary Cultured Hepatocytes

Understanding hepatocellular signaling occurring in biomaterial systems is important for successful hepatic tissue engineering. Toward this end, we employed synthetic glycopolymers, as artificial matrices, to examine integrin-mediated epidermal growth factor (EGF) signaling in primary hepatocyte cultures. We dispersed hepatocytes on a collagen matrix or on a synthetic glycopolymer matrix and subsequently stimulated them with EGF. Only hepatocytes cultured on collagen proliferated, and we observed significant expression of cyclin B1 in these cells. Pharmacological agents, LY294004 (a phosphatidylinositol [PI] 3-kinase inhibitor) and AG1478 (an EGF kinase receptor inhibitor), blocked hepatocyte proliferation and cyclin B1 expression. In addition, EGF-stimulated hepatocytes formed spheroids, exhibited membrane ruffling, and increased tryptophan 2,3-oxygenase (TO) expression when cultured on glycopolymer matrices. Interestingly, PI 3-kinase inhibition suppressed membrane ruffling, spheroid formation, and TO expression. Taken together, this data suggests PI 3-kinase plays an important role in mediating cross talk between integrin and the EGF signaling pathways in primary hepatocyte cultures.

Mathematical models of specificity in cell signaling

Cellular signaling pathways transduce extracellular signals into appropriate responses. These pathways are typically interconnected to form networks, often with different pathways sharing similar or identical components. A consequence of this connectedness is the potential for cross talk, some of which may be undesirable. Indeed, experimental evidence indicates that cells have evolved insulating mechanisms to partially suppress "leaking" between pathways. Here we characterize mathematical models of simple signaling networks and obtain exact analytical expressions for two measures of cross talk called specificity and fidelity. The performance of several insulating mechanisms--combinatorial signaling, compartmentalization, the inhibition of one pathway by another, and the selective activation of scaffold proteins--is evaluated with respect to the trade-off between the specificity they provide and the constraints they place on the network. The effects of noise are also examined. The insights gained from this analysis are applied to understanding specificity in the yeast mating and invasive growth MAP kinase signaling network.