Modeling Tissue Polarity in Context

Polarity is critical for development and tissue-specific function. However, the acquisition and maintenance of tissue polarity is context dependent. Thus, cell and tissue polarity depend on cell adhesion which is regulated by the cytoskeleton and influenced by the biochemical composition of the extracellular microenvironment and modified by biomechanical cues within the tissue. These biomechanical cues include fluid flow induced shear stresses, cell-density and confinement-mediated compression, and cellular actomyosin tension intrinsic to the tissue or induced in response to morphogens or extracellular matrix stiffness. Here, we discuss how extracellular matrix stiffness and fluid flow influence cell–cell and cell–extracellular matrix adhesion and alter cytoskeletal organization to modulate cell and tissue polarity. We describe model systems that when combined with state of the art molecular screens and high-resolution imaging can be used to investigate how force modulates cell and tissue polarity.     

Molecular mechanisms of cell-cell signaling by the Spemann-Mangold organizer

We review how studies on the first Spemann-Mangold organizer marker, the homeobox gene goosecoid, led to the discovery of secreted factors that pattern the vertebrate embryo. Microinjection of goosecoid mRNA formed secondary axes and recruited neighboring cells. These non-cell autonomous effects are mediated in part by the expression of secreted factors such as chordin, cerberus and Frzb-1. Unexpectedly, many of the molecules secreted by the Spemann-Mangold organizer turned out to be antagonists that bind growth factors in the extracellular space and prevent them from binding to their receptors. The case of chordin is reviewed in detail, for this molecule has provided biochemical insights into how patterning by Spemann's organizer can be regulated by diffusion and proteolytic control. The study of the BMP-binding repeats of Chordin, which are present in many extracellular proteins, may provide a new paradigm for how cell-cell signaling is regulated in the extracellular space not only in embryos, but also in adult tissues.     

Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications

Synthetic biologists use engineering principles to design and construct genetic circuits for programming cells with novel functions. A bottom-up approach is commonly used to design and construct genetic circuits by piecing together functional modules that are capable of reprogramming cells with novel behavior. While genetic circuits control cell operations through the tight regulation of gene expression, a diverse array of environmental factors within the extracellular space also has a significant impact on cell behavior. This extracellular space offers an addition route for synthetic biologists to apply their engineering principles to program cell-responsive modules within the extracellular space using biomaterials. In this review, we discuss how taking a bottom-up approach to build genetic circuits using DNA modules can be applied to biomaterials for controlling cell behavior from the extracellular milieu. We suggest that, by collectively controlling intrinsic and extrinsic signals in synthetic biology and biomaterials, tissue engineering outcomes can be improved.     

Modeling extracellular field potentials and the frequency-filtering properties of extracellular space

Extracellular local field potentials are usually modeled as arising from a set of current sources embedded in a homogeneous extracellular medium. Although this formalism can successfully model several properties of extracellular local field potentials, it does not account for their frequency-dependent attenuation with distance, a property essential to correctly model extracellular spikes. Here we derive expressions for the extracellular potential that include this frequency-dependent attenuation. We first show that, if the extracellular conductivity is nonhomogeneous, there is induction of nonhomogeneous charge densities that may result in a low-pass filter. We next derive a simplified model consisting of a punctual (or spherical) current source with spherically symmetric conductivity/permittivity gradients around the source. We analyze the effect of different radial profiles of conductivity and permittivity on the frequency-filtering behavior of this model. We show that this simple model generally displays low-pass filtering behavior, in which fast electrical events (such as Na(+)-mediated action potentials) attenuate very steeply with distance, whereas slower (K(+)-mediated) events propagate over larger distances in extracellular space, in qualitative agreement with experimental observations. This simple model can be used to obtain frequency-dependent extracellular field potentials without taking into account explicitly the complex folding of extracellular space.     

Syndecan transmembrane domain modulates intracellular signaling by regulating the oligomeric status of the cytoplasmic domain

Cell surface receptors must specifically recognize an extracellular ligand and then trigger an appropriate response within the cell. Their general structure enables this, as it comprises an extracellular domain that can bind an extracellular ligand, a cytoplasmic domain that can transduce a signal inside the cell to produce an appropriate response, and a transmembrane domain that links the two and is responsible for accurately delivering specific information on a binding event from the extracellular domain to the cytoplasmic domain, to trigger the proper response. A vast body of research has focused on elucidating the specific mechanisms responsible for regulating extracellular binding events and the subsequent interactions of the cytoplasmic domain with intracellular signaling. In contrast, far less work has focused on examining how the transmembrane domain links these domains and delivers the necessary information. In this review, we propose the importance of the transmembrane domain as a signal regulator. We highlight the cell adhesion receptor, syndecan, as a special case, and propose that the transmembrane domain-mediated oligomerization of the syndecan cytoplasmic domain is a unique regulatory mechanism in syndecan signaling.     

Effects of intermittent media replacement on the gene expression of differentiating neural progenitor cells

A culture medium provides the major environmental conditions for cells in vitro. Replenishment of a culture medium causes an abrupt change in the extracellular environment for maintaining cells in a certain state. As a primitive form of a complex system, a stem cell is likely to be influenced by culture conditions that can change the destination of development. To understand how the change in extracellular environment can influence a biological system, we studied the effect of culture media replacement on the gene expression of differentiating neural progenitor cells. From time-series microarray gene expression data of neural progenitor cells, we observed a periodic wave that was synchronized with intermittent culture media replacement. We identified three modes that mostly contribute to the periodic patterns in gene expression and investigated mode-related genes that are sensitive to the changes in the extracellular environment. The biological significance of the three modes was explored, such as progressive development and cell fate decision, extracellular matrix reassembly, and cell growth regulation in response to stress. In addition, we explored systemic influences of media replacement on differentiating neural progenitor cells. Intermittent culture media replacement interrupts expression of genes that participate in the major processes of differentiating neural progenitor cells. This study shows how the abrupt changes in the cell environment influence gene expression systematically.     

Tissue repair and the dynamics of the extracellular matrix

Repair of tissue after injury depends on the synthesis of a fibrous extracellular matrix to replace lost or damaged tissue. Newly deposited extracellular matrix is then re-modeled over time to emulate normal tissue. The extracellular matrix directs repair by regulating the behavior of the wide variety of cell types that are mobilized to the damaged area in order to rebuild the tissue. Acute inflammation, re-epithelialization, and contraction all depend on cell-extracellular matrix interactions and contribute to minimize infection and promote rapid wound closure. Matricellular proteins are up-regulated during wound healing where they modulate interactions between cells and the extracellular matrix to exert control over events that are essential for efficient tissue repair. Here, we discuss how the extracellular matrix changes during the stages of tissue repair, how matricellular proteins affect cell-extracellular matrix interactions, and how these proteins might be exploited for use therapeutically.     

Initiation and entrainment of multicellular automaticity via diffusion limited extracellular domains

Electrically excitable cells often spontaneously and synchronously depolarize in vitro and in vivo preparations. It remains unclear how cells entrain and autorhythmically activate above the intrinsic mean activation frequency of isolated cells with or without pacemaking mechanisms. Recent studies suggest that cyclic ion accumulation and depletion in diffusion-limited extracellular volumes modulate electrophysiology by ephaptic mechanisms (nongap junction or synaptic coupling). This report explores how potassium accumulation and depletion in a restricted extracellular domain induces spontaneous action potentials in two different computational models of excitable cells without gap junctional coupling: Hodgkin-Huxley and Luo-Rudy. Importantly, neither model will spontaneously activate on its own without external stimuli. Simulations demonstrate that cells sharing a diffusion-limited extracellular compartment can become autorhythmic and entrained despite intercellular electrical heterogeneity. Autorhythmic frequency is modulated by the cleft volume and potassium fluxes through the cleft. Additionally, inexcitable cells can suppress or induce autorhythmic activity in an excitable cell via a shared cleft. Diffusion-limited shared clefts can also entrain repolarization. Critically, this model predicts a mechanism by which diffusion-limited shared clefts can initiate, entrain, and modulate multicellular automaticity in the absence of gap junctions.     

Extracellular proteases and embryonic pattern formation

At least three genes that play crucial roles in dorsal-ventral patterning of the Drosophila embryo appear to encode extracellular proteases. These proteases are involved in the generation of localized extracellular ligands for membrane receptors. Because the sequences of these gene products closely resemble those of mammalian enzymes that have been studied in detail biochemically, it is possible to draw on the wealth of information on the biochemical mechanisms that regulate protease activity to make inferences about how proteases can be used to generate spatial asymmetries within fields of cells.     

Noise controlled synchronization in potassium coupled neural models

The paper applies biologically plausible models to investigate how noise input to small ensembles of neurons, coupled via the extracellular potassium concentration, can influence their firing patterns. Using the noise intensity and the volume of the extracellular space as control parameters, we show that potassium induced depolarization underlies the formation of noise-induced patterns such as delayed firing and synchronization. These phenomena are associated with the appearance of new time scales in the distribution of interspike intervals that may be significant for the spatio-temporal oscillations in neuronal ensembles.     

Structure and function of focal adhesions

Integrin-dependent cell adhesions come in different shapes and serve in different cell types for tasks ranging from cell-adhesion, migration, and the remodeling of the extracellular matrix to the formation and stabilization of immunological and chemical synapses. A major challenge consists in the identification of adhesion-specific as well as common regulatory mechanisms, motivating the need for a deeper analysis of protein-protein interactions in the context of intact focal adhesions. Specifically, it is critical to understand how small differences in binding of integrins to extracellular ligands and/or cytoplasmic adapter proteins affect the assembly and function of an entire focal adhesion. By using the talin-integrin pair as a starting point, I would like to discuss how specific protein-protein and protein-lipid interactions can control the behavior and function of focal adhesions. By responding to chemical and mechanical cues several allosterically regulated proteins create a dynamic multifunctional protein network that provides both adhesion to the extracellular matrix as well as intracellular signaling in response to mechanical changes in the cellular environment.     

The neutrophil in vascular inflammation

Here we focus on how neutrophils have a key regulatory role in vascular inflammation. Recent studies using advanced imaging techniques have yielded new insights into the mechanisms by which neutrophils contribute to defense against bacterial infections and also against sterile injury. In these settings, neutrophils are recruited by various mechanisms depending on the situation. We also describe how these processes may be disrupted in systemic infections, with a particular emphasis on mouse models of sepsis. Neutrophils are often immobilized in the lungs and liver during systemic infections, and this immobilization may be a mechanism through which bacteria can evade the innate immune response or allow neutrophils to form neutrophil extracellular traps that trap and kill bacteria in blood. The platelet is also an important player in sepsis, and we describe how it collaborates with neutrophils in the formation of neutrophil extracellular traps.     

Use of magnetic resonance to measure molecular diffusion within the brain extracellular space

Ion-selective microelectrode measurements of molecular diffusion have provided unique information about the structural characteristics of the extracellular compartment of brain tissue. Magnetic resonance (MR) techniques can also be used to perform diffusion measurements in living tissue in situ. In MR applications, the challenge to study a particular physiological compartment lies in achieving the appropriate specificity in the experimentally-observed MR signal, and many strategies have been used to provide measurements that reflect molecular diffusion within the extracellular space. This review describes how magnetic resonance and microelectrode diffusion measurements are performed, and applications using the MR technique are summarized. Comparisons of experimental results obtained from the two techniques indicate that their use in combination may further augment what is known about extracellular space structure.     

ARIA can be released from extracellular matrix through cleavage of a heparin-binding domain

ARIA, or acetylcholine receptor-inducing activity, is a polypeptide that stimulates the synthesis of acetylcholine receptors in skeletal muscle. Here we demonstrate that the ability of ARIA to induce phosphorylation of its receptor in muscle is blocked by highly charged glycosaminoglycans. ARIA constructs lacking the NH2-terminal portion, containing an immunoglobulin-like domain, are fully active and are not inhibited by glycosaminoglycans. Limited proteolysis of ARIA with subtilisin blocks the glycosaminoglycan interaction by degrading this NH2-terminal portion, but preserves the active, EGF-like domain. We also show that ARIA can be released from freshly dissociated cells from embryonic chick spinal cord and cerebellum by either heparin, high salt or limited proteolysis with subtilisin, suggesting that ARIA is bound to the extracellular matrix through charged interactions. We present a model of how ARIA may be stored in extracellular matrix at developing synapses and how its release may be mediated by local proteolysis.     

Extracellular ATP: an unexpected role as a signaler in plants

ATP and other nucleoside triphosphates not only drive energy-dependent reactions inside cells, but can also function outside the plasma membrane in the extracellular matrix, where they function as agonists that can induce diverse physiological responses without being hydrolyzed. This external role of ATP is well established in animal cells but only recently has it become apparent that extracellular ATP (eATP) can also function as a signaling agent in plants. Recent data have shown that eATP and other nucleotides can induce an increase in the cytosolic Ca(2+) concentration and diverse downstream changes that influence plant growth and defense responses. Ectoapyrase enzymes that regulate the eATP concentration also have an impact on plant growth. These results beg the question of whether there is a receptor that can bind to eATP and transduce this into signaling changes. Answering this will be key to understanding how eATP and ectoapyrases influence plant growth and development.     

A bistable membrane potential at low extracellular potassium concentration

In order to understand the electrochemical behavior of a living cell at a low extracellular potassium concentration, a model is constructed. The model involves only the ATP driven sodium-potassium pump, and the sodium and potassium channels. Predictions of the model fit the N-shape of the current-voltage characteristic at low extracellular potassium. The model can, furthermore, quantitatively account for the experimentally observed bistability of the membrane potential at low extracellular potassium concentration. A crucial role in the control of the transmembrane potential appears to be played by how the permeability of the inward rectifying potassium channels depends on the transmembrane potential and on the extracellular potassium concentration.     

Coupling of cell structure to cell metabolism and function

The fact that cells make directed decisions regarding how to use energy, i.e., where to direct intracellular particles or where to move, suggests that energy can be, and is, harnessed in specific ways. It is now well established that the chemical reactions of the cell do not occur in nonorganized soup, but rather in the context of ordered structure. The physical components that make up this ordered structure of the cell are part of the tissue matrix, which consists of the dynamic linkages between the skeletal networks of the nucleus (the nuclear matrix), the cytoplasm (the cytoskeleton), and the extracellular environment (the extracellular matrix). To understand gene function and how the energy of the cell is directed towards accomplishing the tasks directed by DNA (gene expression), a further understanding of how cell structure is tied to cellular energy and function is required. We propose that the structural components of the cell harness cellular energy to direct cell functions by providing a dynamic bridge between thermodynamics and gene expression. © 1994 Wiley-Liss, Inc.