https://www.cell.com/cell/pdf/S0092-8674(15)00010-0.pdf

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

The tumor suppressor PTEN was originally identified as a negative regulator of the phosphoinositide 3-kinase (PI3K) signaling, a main regulator of cell growth, metabolism and survival. Yet this function of PTEN is extremely relevant for its tumor-suppressive ability, albeit the recent characterization of many PI3K-independent tumor-suppressive activities. PI3K-mediated PIP(3) production leads to the activation of the canonical AKT-mTORC1 pathway. The implications of this signaling cascade in health and disease have been underscored by the high number of regulators within the pathway whose alterations give rise to different malignancies, including familiar syndromes, metabolic dysfunctions and cancer. Moreover, PI3K is tightly buffered at multiple levels by downstream components, which have turned this signaling pathway literally upside down. PI3K and its downstream components in turn cross-talk with a number of other pathways, thereby leading to a complex network of signals that may have dramatic consequences when perturbed. Here, we review the current status of the PTEN-PI3K signaling pathway with special emphasis on the most recent data on targets and regulation of the PTEN-PI3K axis. This provides novel provocative therapeutic implications based on the targeted modulation of PI3K-cross-talking signals.

The PTEN–PI3K pathway: of feedbacks and cross-talks

http://cvri.ucsf.edu/~weiner/papers/21.houk.cell.2012.pdf

Membrane tension maintains cell polarity by confining signals to the leading edge during neutrophil migration

Neurons are among the most highly polarized cell types in the body, and the polarization of axon and dendrites underlies the ability of neurons to integrate and transmit information in the brain. Significant progress has been made in the identification of the cellular and molecular mechanisms underlying the establishment of neuronal polarity using primarily in vitro approaches such as dissociated culture of rodent hippocampal and cortical neurons. This model has led to the predominant view suggesting that neuronal polarization is specified largely by stochastic, asymmetric activation of intracellular signaling pathways. Recent evidence shows that extracellular cues can play an instructive role during neuronal polarization in vitro and in vivo. In this review, we synthesize the recent data supporting an integrative model whereby extracellular cues orchestrate the intracellular signaling underlying the initial break of neuronal symmetry leading to axon-dendrite polarization.

Establishment of axon-dendrite polarity in developing neurons

Conserved proteins of the partitioning defective (PAR), Scribble and Crumbs complexes guide the establishment of cell polarity in various organisms. Small GTPases have also been implicated in cell polarization. How do the polarity complexes and the small GTPases coordinate cellular polarization in different cell types?

Crosstalk between small GTPases and polarity proteins in cell polarization.

When cells are exposed to death ligands such as TRAIL, a fraction undergoes apoptosis and a fraction survives; if surviving cells are re-exposed to TRAIL, fractional killing is once again observed. Therapeutic antibodies directed against TRAIL receptors also cause fractional killing, even at saturating concentrations, limiting their effectiveness. Fractional killing arises from cell-to-cell fluctuations in protein levels (extrinsic noise), but how this results in a clean bifurcation between life and death remains unclear. In this paper, we identify a threshold in the rate and timing of initiator caspase activation that distinguishes cells that live from those that die; by mapping this threshold, we can predict fractional killing of cells exposed to natural and synthetic agonists alone or in combination with sensitizing drugs such as bortezomib. A phenomenological model of the threshold also quantifies the contributions of two resistance genes (c-FLIP and Bcl-2), providing new insight into the control of cell fate by opposing pro-death and pro-survival proteins and suggesting new criteria for evaluating the efficacy of therapeutic TRAIL receptor agonists.

/pdf/fractional-killing-arises-from-cell-to-cell-variability-in-1vsdtomby9.pdf

Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold

Differential equation models that describe the dynamic changes of biochemical signaling states are important tools to understand cellular behavior. An essential task in building such representations is to infer the affinities, rate constants, and other parameters of a model from actual measurement data. However, intuitive measurement protocols often fail to generate data that restrict the range of possible parameter values. Here we utilized a numerical method to iteratively design optimal live-cell fluorescence microscopy experiments in order to reveal pharmacological and kinetic parameters of a phosphatidylinositol 3,4,5-trisphosphate (PIP3) second messenger signaling process that is deregulated in many tumors. The experimental approach included the activation of endogenous phosphoinositide 3-kinase (PI3K) by chemically induced recruitment of a regulatory peptide, reversible inhibition of PI3K using a kinase inhibitor, and monitoring of the PI3K-mediated production of PIP3 lipids using the pleckstrin homology (PH) domain of Akt. We found that an intuitively planned and established experimental protocol did not yield data from which relevant parameters could be inferred. Starting from a set of poorly defined model parameters derived from the intuitively planned experiment, we calculated concentration-time profiles for both the inducing and the inhibitory compound that would minimize the predicted uncertainty of parameter estimates. Two cycles of optimization and experimentation were sufficient to narrowly confine the model parameters, with the mean variance of estimates dropping more than sixty-fold. Thus, optimal experimental design proved to be a powerful strategy to minimize the number of experiments needed to infer biological parameters from a cell signaling assay.

/pdf/optimal-experimental-design-for-parameter-estimation-of-a-11ix1ztiwh.pdf

Optimal experimental design for parameter estimation of a cell signaling model.

https://www.cell.com/current-biology/pdf/S0960-9822(07)02336-6.pdf

Robust Neuronal Symmetry Breaking by Ras-Triggered Local Positive Feedback

Assigning molecular functions and revealing dynamic connections between large numbers of partially characterized proteins in regulatory networks are challenges in systems biology We showed that functions of signaling proteins can be discovered with a differential equations model of the underlying signaling process to extract specific molecular parameter values from single-cell, time-course measurements By analyzing the effects of 250 small interfering RNAs on Ca(2+) signals in single cells over time, we identified parameters that were specifically altered in the Ca(2+) regulatory system Analysis of the screen confirmed known functions of the Ca(2+) sensors STIM1 (stromal interaction molecule 1) and calmodulin and of Ca(2+) channels and pumps localized in the endoplasmic reticulum (ER) or plasma membrane Furthermore, we showed that the Alzheimer's disease-linked protein presenilin-2 and the channel protein ORAI2 prevented overload of ER Ca(2+) and that feedback from Ca(2+) to phosphatidylinositol 4-kinase and PLCδ (phospholipase Cδ) may regulate the abundance of the plasma membrane lipid PI(4,5)P2 (phosphatidylinositol 4,5-bisphosphate) to control Ca(2+) extrusion Thus, functions of signaling proteins and dynamic regulatory connections can be identified by extracting molecular parameter values from single-cell, time-course data

/pdf/regulators-of-calcium-homeostasis-identified-by-inference-of-42tkgp8bkc.pdf

Regulators of calcium homeostasis identified by inference of kinetic model parameters from live single cells perturbed by siRNA.

Our brains contain a vast network of many billions of cells that communicate with, and are connected to, each other. Each brain cell, or neuron, can form connections with as many as 10,000 other neurons—and signals pass from one neuron to the next at sites known as synapses. A neuron's surface has numerous finger-like protrusions known as filopodia that are important for sensing the environment around the cells. Filopodia are highly changeable and constantly extend and retract as the filaments that support them—which are made up of a protein called actin—grow and shrink back. Neurons use their filopodia to explore and seek out other neurons in the brain, and when they make contact with the right neuron, it leads to the formation of a synapse. However, how filopodial extensions begin to grow—and what stops a neuron from forming too many filopodia—is not fully understood. Galic et al. now show that a protein called ArhGAP44 limits the formation of new filopodia in neurons. The ArhGAP44 protein is recruited to patches of the surface membrane that have a lot of actin and that curve inwards. ArhGAP44 then locally inhibits other proteins that are normally required to extend the actin filaments and drive the growth of filopodia out from the surface of the cell. Galic et al. also show that more ArhGAP44 is produced with age—levels are low in embryos and high in adults—and this increase in the amount of protein correlates with a decrease in the number of filopodia formed. When Galic et al. engineered rat neurons to produce more of the ArhGAP44 protein, fewer filopodia formed on the surface of the neurons. Decreasing the amount of this protein had the opposite effect. Moreover, ArhGAP44 was shown to mainly stop new filopodia from forming and had little effect on existing filopodia. Together, these findings suggest that ArhGAP44 may help neurons transition from a dynamic exploratory mode to a mature, more static, state; this is a characteristic of the development of the nervous system.

/pdf/dynamic-recruitment-of-the-curvature-sensitive-protein-4asec0dtnz.pdf

Samuel Bandara

Papers

Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold

Optimal experimental design for parameter estimation of a cell signaling model.

Robust Neuronal Symmetry Breaking by Ras-Triggered Local Positive Feedback

Regulators of calcium homeostasis identified by inference of kinetic model parameters from live single cells perturbed by siRNA.

Dynamic recruitment of the curvature-sensitive protein ArhGAP44 to nanoscale membrane deformations limits exploratory filopodia initiation in neurons