Dynamic characteristics of transient responses

Network dynamics determine the autocrine and paracrine signaling functions of TNF

A hallmark of the inflammatory response to pathogen exposure is the production of tumor necrosis factor (TNF) that coordinates innate and adaptive immune responses by functioning in an autocrine or paracrine manner. Numerous molecular mechanisms contributing to TNF production have been identified, but how they function together in macrophages remains unclear. Here, we pursued an iterative systems biology approach to develop a quantitative understanding of the regulatory modules that control TNF mRNA synthesis and processing, mRNA half-life and translation, and protein processing and secretion. By linking the resulting model of TNF production to models of the TLR-, the TNFR-, and the NFκB signaling modules, we were able to study TNF's functions during the inflammatory response to diverse TLR agonists. Contrary to expectation, we predicted and then experimentally confirmed that in response to lipopolysaccaride, TNF does not have an autocrine function in amplifying the NFκB response, although it plays a potent paracrine role in neighboring cells. However, in response to CpG DNA, autocrine TNF extends the duration of NFκB activity and shapes CpG-induced gene expression programs. Our systems biology approach revealed that network dynamics of MyD88 and TRIF signaling and of cytokine production and response govern the stimulus-specific autocrine and paracrine functions of TNF.

A network characteristic that correlates environmental and genetic robustness

As scientific advances in perturbing biological systems and technological advances in data acquisition allow the large-scale quantitative analysis of biological function, the robustness of organisms to both transient environmental stresses and inter-generational genetic changes is a fundamental impediment to the identifiability of mathematical models of these functions. An approach to overcoming this impediment is to reduce the space of possible models to take into account both types of robustness. However, the relationship between the two is still controversial. This work uncovers a network characteristic, transient responsiveness, for a specific function that correlates environmental imperturbability and genetic robustness. We test this characteristic extensively for dynamic networks of ordinary differential equations ranging up to 30 interacting nodes and find that there is a power-law relating environmental imperturbability and genetic robustness that tends to linearity as the number of nodes increases. Using our methods, we refine the classification of known 3-node motifs in terms of their environmental and genetic robustness. We demonstrate our approach by applying it to the chemotaxis signaling network. In particular, we investigate plausible models for the role of CheV protein in biochemical adaptation via a phosphorylation pathway, testing modifications that could improve the robustness of the system to environmental and/or genetic perturbation.

Advances in the ways that living systems can be perturbed in order to study how they function and sharp reductions in the cost of computer resources have allowed the collection of large amounts of data. The aim of biological system modeling is to analyze this data in order to pin down the precise interactions of molecules that underlie the observed functions. This is made difficult due to two features of biological systems: (1) Living things do not show an appreciable loss of function across large ranges of environmental factors. (2) Their function is inherited from parent to child more or less unchanged in spite of random mutations in genetic sequences. We find that these two features are more correlated in a specific subset of networks and show how to use this observation to find networks in which these two features appear together. Working within this smaller space of networks may make it easier to find suitable underlying models from data.

Maintaining system homeostasis: the third law of Newtonian immunology

Because of the potent effector mechanisms of the immune system, the potential for self-destructive immune responses is especially high and many negative regulatory modalities exist to prevent excessive tissue damage. This Commentary places such regulatory mechanisms in the larger context of system organization on many scales. The sometimes counterintuitive nature of feedback control is discussed and a case is made for greater attention to quantitative spatiotemporal aspects of regulation, rather than limiting the discussion to the qualitative descriptions of pathways that dominate at present.

Temporal coding of insulin action through multiplexing of the AKT pathway

One of the unique characteristics of cellular signaling pathways is that a common signaling pathway can selectively regulate multiple cellular functions of a hormone; however, this selective downstream control through a common signaling pathway is poorly understood. Here we show that the insulin-dependent AKT pathway uses temporal patterns multiplexing for selective regulation of downstream molecules. Pulse and sustained insulin stimulations were simultaneously encoded into transient and sustained AKT phosphorylation, respectively. The downstream molecules, including ribosomal protein S6 kinase (S6K), glucose-6-phosphatase (G6Pase), and glycogen synthase kinase-3β (GSK3β) selectively decoded transient, sustained, and both transient and sustained AKT phosphorylation, respectively. Selective downstream decoding is mediated by the molecules' network structures and kinetics. Our results demonstrate that the AKT pathway can multiplex distinct patterns of blood insulin, such as pulse-like additional and sustained-like basal secretions, and the downstream molecules selectively decode secretion patterns of insulin.

A network of broadly expressed HLH genes regulates tissue-specific cell fates

Spatial and temporal expression of specific basic-helix-loop-helix (bHLH) transcription factors defines many types of cellular differentiation. We find that a distinct mechanism regulates the much broader expression of the heterodimer partners of these specific factors and impinges on differentiation. In Drosophila, a cross-interacting regulatory network links expression of the E protein Daughterless (Da), which heterodimerizes with bHLH proteins to activate them, with expression of the Id protein Extramacrochaetae (Emc), which antagonizes bHLH proteins. Coupled transcriptional feedback loops maintain the widespread Emc expression that restrains Da expression, opposing bHLH-dependent differentiation while enhancing growth and cell survival. Where extracellular signals repress emc, Da expression can increase. This defines regions of proneural ectoderm independently from the proneural bHLH genes. Similar regulation is found in multiple Drosophila tissues and in mammalian cells and therefore is likely to be a conserved general feature of developmental regulation by HLH proteins.

A possible role for long non-coding RNA in modulating signaling pathways

Signaling proteins often engage in multiple protein-protein interactions that are dependent upon cellular context. Little is known about how signaling proteins select their interacting targets. The Ras GTPase is an example of a protein that can activate a large number of distinct and interconnected downstream signaling pathways. Hyperactive forms of Ras are commonly found in a variety of different cancers, often due to somatic mutations within the RAS gene. Despite extensive studies to identify Ras-regulated pathways, it is still not known exactly which pathways might be activated by hyperactive Ras in a given cellular and disease context. Long non-coding RNAs (lncRNAs) are RNA transcripts longer than 200 bp exhibiting spatially and temporally-regulated expression patterns. LncRNAs have been shown to harbor biological activities but the functions of the great majority of lncRNAs are not known. We hypothesize that long non-coding RNAs serve as signaling modulators linking Ras and potentially other signaling proteins to their specific downstream targets and may therefore play a key role in how signals are propagated in a specific cellular environment. In support of our hypothesis we argue that lncRNAs have been shown to bind and regulate protein complexes targeting their enzymatic activity towards specific substrates. It has also been demonstrated that specific lncRNAs are expressed in particular types of cancers where they may influence tumor progression. Studies suggest that lncRNAs have evolved to help regulate complex biological processes that require the ability to stringently discriminate between a large number of potential effectors. If our hypothesis is correct, we envision that it will be possible to predict the target pathway of a mutant protein based on the lncRNA profile in a specific cancer. More generally, this will expand our understanding of how signal transduction networks are wired within a given biological context.

Electroconvulsive seizure increases phosphorylation of PKC substrates, including GAP-43, MARCKS, and neurogranin, in rat brain

Protein kinase C (PKC) has been suggested as a molecular target related to the pathogenetic and therapeutic mechanisms of mood disorders in which electroconvulsive seizure (ECS) is effective. However, the reports concerning the effects of ECS on PKC are anecdotal and need further clarification. In this study, we examined the effects of ECS treatment on the phosphorylation of PKC substrates, including GAP-43, MARCKS, and neurogranin. Immunoblot using anti-p-PKC substrate antibodies revealed that a single ECS treatment induced temporal changes in the phosphorylation level of PKC substrates in rat brain, reflecting the effects on PKC activity. Phosphorylation of GAP-43 and MARCKS, representative PKC substrates related to synaptic remodeling, increased from 5 to 30 min, after a transient decrease at 0 min immediately after ECS, and returned to basal levels at 60 min in rat frontal cortex, hippocampus, and cerebellum. Phosphorylation of neurogranin, another PKC substrate, showed a similar pattern of temporal changes in the frontal cortex and hippocampus. Immunohistochemical analysis revealed that p-GAP-43 and p-MARCKS were densely stained throughout the neuronal cells of the prefrontal cortex and hippocampus, and the Purkinje cells of cerebellum, after ECS treatment. Brief and transient activation of PKC may be translated into long-term biochemical changes, resulting in synaptic plasticity. Taken together, the acute effects of ECS on PKC activity, which could be an underpinning of long-term biochemical changes induced by ECS, may contribute to understand the molecular mechanism of ECS.

Low and nontoxic inorganic mercury burdens attenuate BCR-mediated signal transduction

The ubiquitous environmental heavy metal contaminant mercury (Hg) is a potent immunomodulator that has been implicated as a factor contributing to autoimmune disease. However, the mechanism(s) whereby Hg initiates or perpetuates autoimmune responses, especially at the biochemical/molecular level, remain poorly understood. Recent work has established a relationship between impaired B-cell receptor (BCR) signal strength and autoimmune disease. In previous studies, we have shown that in mouse WEHI-231 B cells, noncytotoxic concentrations of inorganic mercury (Hg(+2)) interfered with BCR-mediated growth control, suggesting that BCR signal strength was impaired by Hg(+2). Extracellular signal-regulated kinase (ERK) 1,2 mitogen-activated protein kinase (MAPK) is responsible for the activation of several transcription factors in B cells. Phosphorylation of ERK serves as an essential node of signal integration for the BCR. Thus, the magnitude of ERK activation serves as an operational metric for BCR signal strength. Using Western blotting and phospho-specific flow cytometry, we now show that the kinetics and magnitude of BCR-mediated activation of ERK-MAPK are markedly attenuated in WEHI-231 cells and splenic B cells that have been exposed to low and nontoxic burdens of Hg(+2). However, Hg(+2) does not seem to act directly on ERK-MAPK but rather on an upstream element or elements of the BCR signal transduction pathway, above the level of the key protein tyrosine kinase Syk. Our data suggest that the site of action of Hg(+2) may very well be localized on the plasma membrane. These findings support a connection between Hg(+2) and attenuated BCR signal strength in the etiology of autoimmune disease.

Spatiotemporal organization of Ras signaling: rasosomes and the galectin switch

1. Ras signaling and oncogenesis depend on the dynamic interplay of Ras with distinctive plasma membrane (PM) microdomains and various intracellular compartments. Such interaction is dictated by individual elements in the carboxy-terminal domain of the Ras proteins, including a farnesyl isoprenoid group, sequences in the hypervariable region (hvr)-linker, and palmitoyl groups in H/N-Ras isoforms. 2. The farnesyl group acts as a specific recognition unit that interacts with prenyl-binding pockets in galectin-1 (Gal-1), galectin-3 (Gal-3), and cGMP phosphodiesterase delta. This interaction appears to contribute to the prolongation of Ras signals in the PM, the determination of Ras effector usage, and perhaps also the transport of cytoplasmic Ras. Gal-1 promotes H-Ras signaling to Raf at the expense of phosphoinositide 3-kinase (PI3-K) and Ral guanine nucleotide exchange factor (RalGEF), while galectin-3 promotes K-Ras signaling to both Raf and PI3-K. 3. The hvr-linker and the palmitates of H-Ras and N-Ras determine the micro- and macro-localizations of these proteins in the PM and in the Golgi, as well as in 'rasosomes', randomly moving nanoparticles that carry palmitoylated Ras proteins and their signal through the cytoplasm.4. The dynamic compartmentalization of Ras proteins contributes to the spatial organization of Ras signaling, promotes redistribution of Ras, and provides an additional level of selectivity to the signal output of this regulatory GTPase.