Cellular Signaling Systems Research Articles

Modeling biomolecular site dynamics in immunoreceptor signaling systems.

The immune system plays a central role in human health. The activities of immune cells, whether defending an organism from disease or triggering a pathological condition such as autoimmunity, are driven by the molecular machinery of cellular signaling systems. Decades of experimentation have elucidated many of the biomolecules and interactions involved in immune signaling and regulation, and recently developed technologies have led to new types of quantitative, systems-level data. To integrate such information and develop nontrivial insights into the immune system, computational modeling is needed, and it is essential for modeling methods to keep pace with experimental advances. In this chapter, we focus on the dynamic, site-specific, and context-dependent nature of interactions in immunoreceptor signaling (i.e., the biomolecular site dynamics of immunoreceptor signaling), the challenges associated with capturing these details in computational models, and how these challenges have been met through use of rule-based modeling approaches.

O-GlcNAcylation in cellular functions and human diseases

O-GlcNAcylation is dynamic and a ubiquitous post-translational modification. O-GlcNAcylated proteins influence fundamental functions of proteins such as protein-protein interactions, altering protein stability, and changing protein activity. Thus, aberrant regulation of O-GlcNAcylation contributes to the etiology of chronic diseases of aging, including cancer, cardiovascular disease, metabolic disorders, and Alzheimer's disease. Diverse cellular signaling systems are involved in pathogenesis of these diseases. O-GlcNAcylated proteins occur in many different tissues and cellular compartments and affect specific cell signaling. This review focuses on the O-GlcNAcylation in basic cellular functions and human diseases.

NO-dependent CaMKII activation during β-adrenergic stimulation of cardiac muscle

During β-adrenergic receptor (β-AR) stimulation, phosphorylation of cardiomyocyte ryanodine receptors by protein kinases may contribute to an increased diastolic Ca(2+) spark frequency. Regardless of prompt activation of protein kinase A during β-AR stimulation, this appears to rely more on activation of Ca(2+)/calmodulin-dependent protein kinase II (CaMKII), by a not yet identified signalling pathway. The goal of the present study was to identify and characterize the mechanisms which lead to CaMKII activation and elevated Ca(2+) spark frequencies during β-AR stimulation in single cardiomyocytes in diastolic conditions. Confocal imaging revealed that β-AR stimulation increases endogenous NO production in cardiomyocytes, resulting in NO-dependent activation of CaMKII and a subsequent increase in diastolic Ca(2+) spark frequency. These changes of spark frequency could be mimicked by exposure to the NO donor GSNO and were sensitive to the CaMKII inhibitors KN-93 and AIP. In vitro, CaMKII became nitrosated and its activity remained increased independent of Ca(2+) in the presence of GSNO, as assessed with biochemical assays. β-AR stimulation of cardiomyocytes may activate CaMKII by a novel direct pathway involving NO, without requiring Ca(2+) transients. This crosstalk between two established signalling pathways may contribute to arrhythmogenic diastolic Ca(2+) release and Ca(2+) waves during adrenergic stress, particularly in combination with cardiac diseases. In addition, NO-dependent activation of CaMKII is likely to have repercussions in many cellular signalling systems and cell types.

Targeting the sphingosine-1-phosphate axis in cancer, inflammation and beyond

The bioactive lipid sphingosine-1-phosphate (S1P) is involved in multiple cellular signalling systems and has a pivotal role in the control of immune cell trafficking. As such, S1P has been implicated in disorders such as cancer and inflammatory diseases. This Review discusses the ways in which S1P might be therapeutically targeted - for example, via the development of chemical inhibitors that target the generation, transport and degradation of S1P and via the development of specific S1P receptor agonists. We also highlight recent conflicting results observed in preclinical studies targeting S1P and discuss ongoing clinical trials in this field.

Dynamically reshaping signaling networks to program cell fate via genetic controllers.

Engineering of cell fate through synthetic gene circuits requires methods to precisely implement control around native decision-making pathways and offers the potential to direct cell processes. We demonstrate a class of genetic control systems, molecular network diverters, that interface with a native signaling pathway to route cells to divergent fates in response to environmental signals without modification of native genetic material. A method for identifying control points within natural networks is described that enables the construction of synthetic control systems that activate or attenuate native pathways to direct cell fate. We integrate opposing genetic programs by developing network architectures for reduced antagonism and demonstrate rational tuning of performance. Extension of these control strategies to mammalian systems should facilitate the engineering of complex cellular signaling systems.

Thermal analysis of injectable, cellular-scale optoelectronics with pulsed power

An ability to insert electronic/optoelectronic systems into precise locations of biological tissues provides powerful capabilities, especially in neuroscience such as optogenetics where light can activate/deactivate critical cellular signalling and neural systems. In such cases, engineered thermal management is essential, to avoid adverse effects of heating on normal biological processes. Here, an analytic model of heat conduction is developed for microscale, inorganic light-emitting diodes (μ-ILEDs) in a pulsed operation in biological tissues. The analytic solutions agree well with both three-dimensional finite-element analysis and experiments. A simple scaling law for the maximum temperature increase is presented in terms of material (e.g. thermal diffusivity), geometric (e.g. μ-ILED size) and loading parameters (e.g. pulsed peak power, duty cycle and frequency). These results provide useful design guidelines not only for injectable μ-ILED systems, but also for other similar classes of electronic and optoelectronic components.

Dual Delayed Feedback Provides Sensitivity and Robustness to the NF-κB Signaling Module

Many cellular stress-responsive signaling systems exhibit highly dynamic behavior with oscillatory features mediated by delayed negative feedback loops. What remains unclear is whether oscillatory behavior is the basis for a signaling code based on frequency modulation (FM) or whether the negative feedback control modules have evolved to fulfill other functional requirements. Here, we use experimentally calibrated computational models to interrogate the negative feedback loops that regulate the dynamic activity of the transcription factor NF-B. Linear stability analysis of the model shows that oscillatory frequency is a hard-wired feature of the primary negative feedback loop and not a function of the stimulus, thus arguing against an FM signaling code. Instead, our modeling studies suggest that the two feedback loops may be tuned to provide for rapid activation and inactivation capabilities for transient input signals of a wide range of durations; by minimizing late phase oscillations response durations may be fine-tuned in a graded rather than quantized manner. Further, in the presence of molecular noise the dual delayed negative feedback system minimizes stochastic excursions of the output to produce a robust NF-B response.

From data towards knowledge: revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data.

Genetic and pharmacological perturbation experiments, such as deleting a gene and monitoring gene expression responses, are powerful tools for studying cellular signal transduction pathways. However, it remains a challenge to automatically derive knowledge of a cellular signaling system at a conceptual level from systematic perturbation-response data. In this study, we explored a framework that unifies knowledge mining and data mining towards the goal. The framework consists of the following automated processes: 1) applying an ontology-driven knowledge mining approach to identify functional modules among the genes responding to a perturbation in order to reveal potential signals affected by the perturbation; 2) applying a graph-based data mining approach to search for perturbations that affect a common signal; and 3) revealing the architecture of a signaling system by organizing signaling units into a hierarchy based on their relationships. Applying this framework to a compendium of yeast perturbation-response data, we have successfully recovered many well-known signal transduction pathways; in addition, our analysis has led to many new hypotheses regarding the yeast signal transduction system; finally, our analysis automatically organized perturbed genes as a graph reflecting the architecture of the yeast signaling system. Importantly, this framework transformed molecular findings from a gene level to a conceptual level, which can be readily translated into computable knowledge in the form of rules regarding the yeast signaling system, such as “if genes involved in the MAPK signaling are perturbed, genes involved in pheromone responses will be differentially expressed.”

In situ visualization and detection of protein sulfenylation responses in living cells through a dimedone-based fluorescent probe

Sulfenylation is one of the reversible post-translational modifications, playing significant roles in cellular redox homeostasis and signaling systems. Herein, small fluorescent probe (CPD and CPDDM) based live-cell labelling technology for the visualization of protein sulfenylation responses in living cells has been developed. This approach enables the detection of protein sulfenylation without the need for cell lysis, fixation or purification, and permits the noninvasive study of protein sulfenylation in live cells through the direct fluorescent readout. This technology also can realize dynamic tracking of protein sulfenylation in situ with minimal perturbation to sulfenylated proteins and less interference with cellular function. Information on the global distribution and dynamic changes of endogenous protein sulfenylation has been obtained.

Self-organized node coordination scheme based on a biological inter-cell signaling system for wireless sensor networks

In this paper, we propose an energy efficient and delay guaranteed node coordination scheme inspired by biological systems, which have gained considerable attention as a computing and problem solving technique. With the identification of analogies between biological cellular signaling systems and WSN systems, we formulate a new mathematical model that considers the networking challenges of WSNs. The proposed bio-inspired scheme determines the state of the sensor node, as required by each mission-critical application and as determined by the local environmental conditions. A control analysis and simulation results show that the proposed bio-inspired scheme guarantees the system stability and provides significant energy savings, as well as reliable delay guarantees.

Age-related changes of gene expression in the neocortex: Preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas

The study of gene expression (i.e., the study of the transcriptome) in different cells and tissues allows us to understand the molecular mechanisms of their differentiation, development and functioning. In this article, we describe some studies of gene-expression profiling for the purposes of understanding developmental (age-related) changes in the brain using different technologies (e.g., DNA-Microarray) and the new and increasingly popular RNA-Seq. We focus on advancements in studies of gene expression in the human brain, which have provided data on the structure and age-related variability of the transcriptome in the brain. We present data on RNA-Seq of the transcriptome in three distinct areas of the neocortex from different ages: mature and elderly individuals. We report that most age-related transcriptional changes affect cellular signaling systems, and, as a result, the transmission of nerve impulses. In general, the results demonstrate the high potential of RNA-Seq for the study of distinctive features of gene expression among cortical areas and the changes in expression through normal and atypical development of the central nervous system.

Prediction of functional phosphorylation sites by incorporating evolutionary information

Protein phosphorylation is a ubiquitous protein post-translational modification, which plays an important role in cellular signaling systems underlying various physiological and pathological processes. Current in silico methods mainly focused on the prediction of phosphorylation sites, but rare methods considered whether a phosphorylation site is functional or not. Since functional phosphorylation sites are more valuable for further experimental research and a proportion of phosphorylation sites have no direct functional effects, the prediction of functional phosphorylation sites is quite necessary for this research area. Previous studies have shown that functional phosphorylation sites are more conserved than non-functional phosphorylation sites in evolution. Thus, in our method, we developed a web server by integrating existing phosphorylation site prediction methods, as well as both absolute and relative evolutionary conservation scores to predict the most likely functional phosphorylation sites. Using our method, we predicted the most likely functional sites of the human, rat and mouse proteomes and built a database for the predicted sites. By the analysis of overall prediction results, we demonstrated that protein phosphorylation plays an important role in all the enriched KEGG pathways. By the analysis of protein-specific prediction results, we demonstrated the usefulness of our method for individual protein studies. Our method would help to characterize the most likely functional phosphorylation sites for further studies in this research area.

Effects of salicylic and jasmonic acid on phospholipase D activity and the level of active oxygen species in soybean seedlings

Plant cell metabolism reactions upon biotic stress conditions are initiated via cellular signaling systems. At the same time, signaling pathways of phytohormonal mediators of biotic stress induction, salicylic acid and jasmonic acid, and their intracellular activities are implemented in cooperation with lipid-derived regulatory elements. In this work we have found that salicylic acid treatment evoke activation of phospholipase D responsible for the production of second messenger phosphatidic acid. Mediators of the defense reactions also affected the balance of active oxygen species and in particular induced accumulation of endogenous hydrogen peroxide and changes in the activities of antioxidant enzymes (catalase, peroxidases, and superoxide dismutase). Our results point out to the interactions between lipid signaling enzymes and cellular antioxidant systems required for realization of primary adaptation responses to biotic stress mediators in plants.

The regulatory circuits for hysteretic switching in cellular signal transduction pathways

Hysteresis can be found in many physical systems, and a hysteretic switch has been used for various mechanical and electrical systems. Such a hysteretic switch can be created by using a single positive feedback loop, as often used in engineering systems. It is, however, intriguing that various cellular signaling systems use coupled positive feedback loops to implement the hysteretic switch. A question then arises about the advantage of using coupled positive feedback loops instead of simple isolated positive feedback for an apparently equivalent hysteretic switch. Through mathematical simulations, we determined that cellular systems with coupled positive feedback loops show enhanced hysteretic switching, and can thereby make a more reliable decision under conditions of noisy signaling. As most intracellular processes are accompanied by intrinsic noise, important cellular decisions such as differentiation and apoptosis need to be highly robust to such noises. The coupled positive feedback loops might have been evolutionarily acquired to enable correct cell fate decisions to be made through enhanced hysteretic switching in noisy cellular environments.

Direct Response Analysis in cellular signalling networks

Direct Response Analysis is a general computational tool for quantifying direct functional interactions between components in cellular signalling systems from experimental perturbations and measurements alone. This paper aims to reveal the biological meaning of the direct response coefficients obtained upon applying DRA to simple Michaelis–Menten type proteomic and gene regulatory systems. These systems describe dimer formation and dissociation, protein preduction and decay, and transcription. We derive explicit formulae for the direct response coefficients in terms of biochemical reaction rates, and clarify the potential and limitations of the DRA method. We find that response coefficients are strongly asymmetric, and that they balance persistent characteristics of reactions (e.g. the ratios of on- and off rates) against the time-scales over which these reactions act; fast reactions give stronger response coefficients. The direct interactions between protein species, caused by dimer formation, are effectively negative. We illustrate our results with numerical simulations.

Signalling through the grapevine

The 5th Barossa Meeting on 'Cell Signalling and Molecular Medicine' was held in November 2011 in the Barossa Valley, South Australia. The combination of an inspirational environment and outstanding science led to a superb meeting that highlighted the versatility of cellular signalling systems and how they can be targeted by novel therapeutic approaches.

English

Today, mobile phones are used frequently and held close to the body. It is believed that microwaves may interfere with the cellular signaling systems, affecting the mechanisms by which the cells balance their functions. The objective of this work is the evaluation of the influence of different intensities of 950 MHz cell phone electromagnetic field (EMF) on the hematological parameters of male rabbits. This study was conducted on 54 male rabbits of average mass of 1400 to 1700 g. The exposure period of simulated mobile phone radiations (950 MHz, 3 and 6 W) was 2 h/day for 2 weeks. The blood from the heart was collected on ethylenediaminetetraacetic acid (EDTA) and was analyzed for hematological parameters, and was then compared with the control group. The results showed an increase (P < 0.05) in the white blood cells (WBC) counts in 6 W group when compared with both 3 W and control groups. Platelets (PLT) counts decreased in 3 W group but increased in 6 W group. Lymphocyte counts decreased in 3 and 6 W groups when compared with each other and control group. There were no differences in red blood cells (RBC) counts and related indices of any groups. In conclusions, mobile phone EMF disturb the constant number of some hematological parameters which may reflects from thermal or non-thermal effects of such radiations, but the exact reason for such discrepancies is not easy to identify.   Key words: Mobile phone 950 MHz radiations, hematological parameters, rabbits.

Knockdown of Ubiquitin Ligases in Glioblastoma Cancer Stem Cells Leads to Cell Death and Differentiation

The cancer stem cell (CSC) hypothesis proposes that a subpopulation of CSCs is frequently responsible for chemotherapy resistance and metastasis and is now a point of attack for research into the next generation of therapeutics. Although many of these agents are directed at inducing CSC apoptosis (as well as the bulk tumor), some agents may also decrease cell “stemness” possibly through induction of differentiation. Ubiquitin ligases, critical to virtually all cellular signaling systems, alter the degradation or trafficking of most proteins in the cell, and indeed broad perturbation of this system, through inhibition of the proteosome, is a successful cancer treatment. The authors examined several glioblastoma stem cell isolates pre- and postdifferentiation to elucidate the phenotypic effects following shRNA knockdown of ubiquitin ligases. The results were analyzed using high-content imaging (HCI) and identified ubiquitin ligases capable of inducing both CSC differentiation and apoptosis. Quite often these effects were specific to CSCs, as ubiquitin ligase knockdown in terminally differentiated progeny yielded markedly different results. The resolution of HCI at the subpopulation level makes it an excellent tool for the analysis of CSC phenotypic changes induced by shRNA knockdown and may suggest additional methods to target these cells for death or differentiation.

Development of Cures in the Era of Genomic Medicine

Cancer, in contrast to many other somatic disorders of mankind, is a semi-autonomous from its human host deregulation of cells where complex genetic, epigenetic and metabolic changes lead to a cancer phenotype- incessant growth, resistance to apoptosis, and perpetual mutations and clonal evolution. In depth understanding of biology of tumors has lead not only to spectacular cures and major advancements in the well-being of cancer patients, but it also propelled forward other fields of Medicine where similar pathological processes are at play. In fact, genetic and regulatory changes in cancer cells tend to involve pathways that are usually spared from germline alterations due to incompatibility with normal tissue and organ development [1]. Conversely, non-neoplastic disorders tend to affect genes and metabolic pathways that are more regulatory in nature and more peripheral to the life-sustaining pathways in mammalian cells [2]. Despite these differences, cancer medicine has been offering itself as a unique testing ground for manipulation of these core biological processes in humans. From perturbation of DNA replication with chemotherapy DNA poisons, the field of oncology moved on to develop a new class of anticancer agents targeting components of cellular signaling systems, usually a kinase of a cell surface receptor that are functionally upregulated or are products of an amplified gene. This approach is meeting with some success in specific tumor types: for example, trastuzumab against human epidermal growth factor receptor 2 (HER2) in breast cancer cells, bevacizumab against vascular endothelial growth factor (VEGF), cetuximab against epidermal growth factor receptor (EGFR), sorafenib against B-RAF. The lessons and challenges are instructive to other areas of drug development in several ways.

Differential patterns of whole-genome DNA methylation in institutionalized children and children raised by their biological parents

Previous studies with nonhuman species have shown that animals exposed to early adversity show differential DNA methylation relative to comparison animals. The current study examined differential methylation among 14 children raised since birth in institutional care and 14 comparison children raised by their biological parents. Blood samples were taken from children in middle childhood. Analysis of whole-genome methylation patterns was performed using the Infinium HumanMethylation27 BeadChip assay (Illumina), which contains 27,578 CpG sites, covering approximately 14,000 gene promoters. Group differences were registered, which were characterized primarily by greater methylation in the institutionalized group relative to the comparison group, with most of these differences in genes involved in the control of immune response and cellular signaling systems, including a number of crucial players important for neural communication and brain development and functioning. The findings suggest that patterns of differential methylation seen in nonhuman species with altered maternal care are also characteristic of children who experience early maternal separation.