Computational models of the NF-κB signalling pathway

In this review article, we discuss the current state of computational modelling of the nuclear factor-kappa B (NF-κB) signalling pathway. NF-κB is a transcription factor, which is ubiquitous within cells and controls a number of immune responses, including inflammation and apoptosis. The NF-κB signalling pathway is tightly regulated, commencing with activation at the cell membrane, signal transduction through various components within the cytoplasm, translocation of NF-κB into the nucleus and, finally, the transcription of various genes relating to the innate and adaptive immune responses. There have been a number of computational (mathematical) models developed of the signalling pathway over the past decade. This review describes how these approaches have helped advance our understanding of NF-κB control

The rise in computational systems biology approaches for understanding NF-κB signaling dynamics

A study by Cheng et al. in this issue of Science Signaling highlights the distinct single-cell signaling characteristics conferred by pathways mediated by the adaptor proteins MyD88 and TRIF in the TLR4-dependent activation of the transcription factor nuclear factor κB (NF-κB)

Towards a platform model of the IL-1 stimulated NF-kB signalling pathway using communicating stream X-machines

The Nuclear Factor-kappa B (NF-κB) signalling pathway is one of the key signalling pathways involved in the control and regulation of the immune system [3]. Activation of the NF-κB transcription factor is a tightly regulated event, with NF-κB normally sequestered in the cytosol of non-stimulated cells. Following activation of a cell membrane receptor and propagation of the signal via intracellular signalling to the IκB Kinase (IKK), phosphorylation-induced degradation of IκB inhibitors occurs to facilitate the release of NF-κB and its translocation to the nucleus. Dysregulation of the pathway is known to be involved in a large number of inflammatory diseases. Although considerable research has been performed since its discovery in 1986, we are still not in a position to control the signalling pathway, and thus limit the effects of NF-κB within promotion of inflammatory diseases. Through adherence to the CoSMoS framework, we are developing a computational model of the IL-1 stimulated NF-κB intracellular signalling pathway, to assist in promoting our understanding of the mechanistic behaviours within the signalling network, and therefore identify potential targets for therapeutic interventions. We have previously developed a separate domain model [4, 5] as advocated by the CoSMoS framework, which captures the essential processes and entities of the system under study using; in particular, the emergent behaviour, at an appropriate level of abstraction using a mixture of cartoon and UML diagrams, along with statistical techniques to define the temporal-spatial dynamics

Computational modelling of NF-κB activation by IL-1RI and its co-receptor TILRR, predicts a role for Cytoskeletal Sequestration of IκBα in inflammatory signalling.

The transcription factor NF-κB (nuclear factor kappa B) is activated by Toll-like receptors and controlled by mechanotransduction and changes in the cytoskeleton. In this study we combine 3-D predictive protein modelling and in vitro experiments with in silico simulations to determine the role of the cytoskeleton in regulation of NF-κB. Simulations used a comprehensive agent-based model of the NF-κB pathway, which includes the type 1 IL-1 receptor (IL-1R1) complex and signalling intermediates, as well as cytoskeletal components. Agent based modelling relies on in silico reproductions of systems through the interactions of its components, and provides a reliable tool in investigations of biological processes, which require spatial considerations and involve complex formation and translocation of regulatory components. We show that our model faithfully reproduces the multiple steps comprising the NF-κB pathway, and provides a framework from which we can explore novel aspects of the system. The analysis, using 3-D predictive protein modelling and in vitro assays, demonstrated that the NF-κB inhibitor, IκBα is sequestered to the actin/spectrin complex within the cytoskeleton of the resting cell, and released during IL-1 stimulation, through a process controlled by the IL-1RI co-receptor TILRR (Toll-like and IL-1 receptor regulator). In silico simulations using the agent-based model predict that the cytoskeletal pool of IκBα is released to adjust signal amplification in relation to input levels. The results suggest that the process provides a mechanism for signal calibration and enables efficient, activation-sensitive regulation of NF-κB and inflammatory responses

Mechanism of PP2A-mediated IKKβ dephosphorylation: a systems biological approach

BACKGROUND: Biological effects of nuclear factor-kappaB (NF kappaB) can differ tremendously depending on the cellular context. For example, NF kappaB induced by interleukin-1 (IL-1) is converted from an inhibitor of death receptor induced apoptosis into a promoter of ultraviolet-B radiation (UVB)-induced apoptosis. This conversion requires prolonged NF kappaB activation and is facilitated by IL-1 + UVB-induced abrogation of the negative feedback loop for NF kappaB, involving a lack of inhibitor of kappaB (I kappaB alpha) protein reappearance. Permanent activation of the upstream kinase IKK beta results from UVB-induced inhibition of the catalytic subunit of Ser-Thr phosphatase PP2A (PP2Ac), leading to immediate phosphorylation and degradation of newly synthesized I kappaB alpha. RESULTS: To investigate the mechanism underlying the general PP2A-mediated tuning of IKK beta phosphorylation upon IL-1 stimulation, we have developed a strictly reduced mathematical model based on ordinary differential equations which includes the essential processes concerning the IL-1 receptor, IKK beta and PP2A. Combining experimental and modelling approaches we demonstrate that constitutively active, but not post-stimulation activated PP2A, tunes out IKK beta phosphorylation thus allowing for I kappaB alpha resynthesis in response to IL-1. Identifiability analysis and determination of confidence intervals reveal that the model allows reliable predictions regarding the dynamics of PP2A deactivation and IKK beta phosphorylation. Additionally, scenario analysis is used to scrutinize several hypotheses regarding the mode of UVB-induced PP2Ac inhibition. The model suggests that down regulation of PP2Ac activity, which results in prevention of I kappaB alpha reappearance, is not a direct UVB action but requires instrumentality. CONCLUSION: The model developed here can be used as a reliable building block of larger NF kappa B models and offers comprehensive simplification potential for future modeling of NF kappa B signaling. It gives more insight into the newly discovered mechanisms for IKK deactivation and allows for substantiated predictions and investigation of different hypotheses. The evidence of constitutive activity of PP2Ac at the IKK complex provides new insights into the feedback regulation of NF kappa B, which is crucial for the development of new anti-cancer strategies

Statistical Techniques Complement UML When Developing Domain Models of Complex Dynamical Biosystems

Computational modelling and simulation is increasingly being used to complement traditional wet-lab techniques when investigating the mechanistic behaviours of complex biological systems. In order to ensure computational models are fit for purpose, it is essential that the abstracted view of biology captured in the computational model, is clearly and unambiguously defined within a conceptual model of the biological domain (a domain model), that acts to accurately represent the biological system and to document the functional requirements for the resultant computational model. We present a domain model of the IL-1 stimulated NF-κB signalling pathway, which unambiguously defines the spatial, temporal and stochastic requirements for our future computational model. Through the development of this model, we observe that, in isolation, UML is not sufficient for the purpose of creating a domain model, and that a number of descriptive and multivariate statistical techniques provide complementary perspectives, in particular when modelling the heterogeneity of dynamics at the single-cell level. We believe this approach of using UML to define the structure and interactions within a complex system, along with statistics to define the stochastic and dynamic nature of complex systems, is crucial for ensuring that conceptual models of complex dynamical biosystems, which are developed using UML, are fit for purpose, and unambiguously define the functional requirements for the resultant computational model

Distinct NF-kappa B regulation by shear stress through ras-dependent I kappa B alpha oscillations - Real-time analysis of flow-mediated activation in live cells

NF-{kappa}B, a transcription factor central to inflammatory regulation during development of atherosclerosis, is activated by soluble mediators and through biomechanical inputs such as flow-mediated shear- stress. To investigate the molecular mechanisms underlying shear stress mediated signal transduction in vascular cells we have developed a system that applies flow-mediated shear stress in a controlled manner, while inserted in a confocal microscope. In combination with GFP-based methods, this allows continuous monitoring of flow induced signal transduction in live cells and in real time. Flow-mediated shear stress, induced using the system, caused a successive increase in NF-{kappa}B-regulated gene activation. Experiments assessing the mechanisms underlying the NF-{kappa}B induced activity showed time and flow rate dependent effects on the inhibitor, I{kappa}B{alpha}, involving nuclear translocation characterized by a biphasic or cyclic pattern. The effect was observed in both endothelial- and smooth muscle cells, demonstrated to impact noncomplexed I{kappa}B{alpha}, and to involve mechanisms distinct from those mediating cytokine signals. In contrast, effects on the NF-{kappa}B subunit relA were similar to those observed during cytokine stimulation. Further experiments showed the flow induced inter-compartmental transport of I{kappa}B{alpha} to be regulated through the Ras GTP-ase, demonstrating a pronounced reduction in the effects following blocking of Ras activity. These studies show that flow-mediated shear stress, regulated by the Ras GTP-ase, uses distinct mechanisms of NF-{kappa}B control at the molecular level. The oscillatory pattern, reflecting inter-compartmental translocation of I{kappa}B{alpha}, is likely to have fundamental impact on pathway regulation and on development of shear stress-induced distinct vascular cell phenotypes

UML activity diagram.

<p>Full end-to-end UML activity diagram for the IL-1 stimulated NF-<i>κ</i>B signalling pathway using the concept of swim-lanes to convey sub-cellular location of components. Developed from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160834#pone.0160834.ref039" target="_blank">39</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160834#pone.0160834.ref056" target="_blank">56</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160834#pone.0160834.ref057" target="_blank">57</a>].</p