Summary Influenza A virus (IAV) is a lytic virus in primary cultures of many cell types and in vivo. We report that the kinase RIPK3 is essential for IAV-induced lysis of mammalian fibroblasts and lung epithelial cells. Replicating IAV drives assembly of a RIPK3-containing complex that includes the kinase RIPK1, the pseudokinase MLKL, and the adaptor protein FADD, and forms independently of signaling by RNA-sensing innate immune receptors (RLRs, TLRs, PKR), or the cytokines type I interferons and TNF-α. Downstream of RIPK3, IAV activates parallel pathways of MLKL-driven necroptosis and FADD-mediated apoptosis, with the former reliant on RIPK3 kinase activity and neither on RIPK1 activity. Mice deficient in RIPK3 or doubly-deficient in MLKL and FADD, but not MLKL alone, are more susceptible to IAV than their wild-type counterparts, revealing an important role for RIPK3-mediated apoptosis in antiviral immunity. Collectively, these results outline RIPK3-activated cytolytic mechanisms essential for controlling respiratory IAV infection.

One-sentence summary: Analysis of the ERK circuitry suggests the most effective targets in the pathway for inhibition, which may aid in drug development Editor's Summary: Biological Circuits Inform Drug Development The mitogen-activated protein kinase (MAPK) pathway involves a three-tiered kinase module, which amplifies the signal. Many cells also have negative feedback loops from the last kinase in the module back to various points upstream in the pathway. Sturm et al. show that the MAPK module with negative feedback loops results in a system like that of a negative feedback amplifier (NFA), which is an engineering design that smoothens the output to changes in input and makes a system robust to change. These NFA-like properties may explain why some cells are sensitive to inhibition of the second kinase in the cascade (they lack the feedback loops); whereas other cells are resistant to inhibition at this point (their feedback loops are intact). These results also have implications for drug development, because inhibitors that target components that are outside the NFA are more effective at inhibiting the pathway. Abstract Three-tiered kinase modules, such as the Raf-MEK-ERK mitogen-activated protein kinase pathway, are widespread in biology suggesting that this structure conveys evolutionary advantageous properties. Here, we show that the three-tiered kinase amplifier module combined with negative feedback recapitulates the design principles of a negative feedback amplifier (NFA), which is used in electronic circuits to convey robustness, output stabilization, and linearization of nonlinear signal amplification. With mathematical modelling and experimental validation, we demonstrated that the ERK pathway has properties of a NFA that (i) converts intrinsic switch-like activation kinetics into graded linear responses; (ii) conveys robustness to changes in rates of reactions within the NFA module; and (iii) stabilizes outputs in response to drug-induced perturbations of the amplifier. These properties determine biological behavior, including activation kinetics and the response to drugs.

The MAPK (mitogen-activated protein kinase) pathway is one of the most important and intensively studied signalling pathways. It is at the heart of a molecular-signalling network that governs the growth, proliferation, differentiation and survival of many, if not all, cell types. It is de-regulated in various diseases, ranging from cancer to immunological, inflammatory and degenerative syndromes, and thus represents an important drug target. Over recent years, the computational or mathematical modelling of biological systems has become increasingly valuable, and there is now a wide variety of mathematical models of the MAPK pathway which have led to some novel insights and predictions as to how this system functions. In the present review we give an overview of the processes involved in modelling a biological system using the popular approach of ordinary differential equations. Focusing on the MAPK pathway, we introduce the features and functions of the pathway itself before comparing the available models and describing what new biological insights they have led to.

Summary The role of Apoptosis inducing factor (AIF) in promoting cell death versus survival remains controversial. We report that loss of AIF in fibroblasts led to mitochondrial electron transport chain (ETC) defects and loss of proliferation that could be restored by ectopic expression of the yeast NADH dehydrogenase Ndi1. Aif-deletion in T cells impacted the numbers of peripheral T cells and their ability to undergo homeostatic proliferation, while not affecting their thymic development. However, Aif-deficient B cells developed and functioned normally. The difference in the dependency of T cells versus B cells on AIF for function and survival correlated with their metabolic requirements. Expression of Ndi1 rescued homeostatic proliferation of Aif-deficient T cells. Despite its reported roles in cell death, fibroblasts, thymocytes and B cells lacking AIF undergo normal death. These studies suggest that the primary role of AIF relates to complex I function, differentially affecting T and B cells.

BackgroundThe Epidermal Growth Factor Receptor (EGFR) activated Extracellular-signal Regulated Kinase (ERK) pathway is a critical cell signalling pathway that relays the signal for a cell to proliferate from the plasma membrane to the nucleus. Deregulation of the EGFR/ERK pathway due to alterations affecting the expression or function of a number of pathway components has long been associated with numerous forms of cancer. Under normal conditions, Epidermal Growth Factor (EGF) stimulates a rapid but transient activation of ERK as the signal is rapidly shutdown. Whereas, under cancerous mutation conditions the ERK signal cannot be shutdown and is sustained resulting in the constitutive activation of ERK and continual cell proliferation. In this study, we have used computational modelling techniques to investigate what effects various cancerous alterations have on the signalling flow through the ERK pathway.ResultsWe have generated a new model of the EGFR activated ERK pathway, which was verified by our own experimental data. We then altered our model to represent various cancerous situations such as Ras, B-Raf and EGFR mutations, as well as EGFR overexpression. Analysis of the models showed that different cancerous situations resulted in different signalling patterns through the ERK pathway, especially when compared to the normal EGF signal pattern. Our model predicts that cancerous EGFR mutation and overexpression signals almost exclusively via the Rap1 pathway, predicting that this pathway is the best target for drugs. Furthermore, our model also highlights the importance of receptor degradation in normal and cancerous EGFR signalling, and suggests that receptor degradation is a key difference between the signalling from the EGF and Nerve Growth Factor (NGF) receptors.ConclusionOur results suggest that different routes to ERK activation are being utilised in different cancerous situations which therefore has interesting implications for drug selection strategies. We also conducted a comparison of the critical differences between signalling from different growth factor receptors (namely EGFR, mutated EGFR, NGF, and Insulin) with our results suggesting the difference between the systems are large scale and can be attributed to the presence/absence of entire pathways rather than subtle difference in individual rate constants between the systems.

The epidermal growth factor receptor (EGFR) activated extracellular-signal regulated kinase (ERK) pathway is a central cell signalling pathway that mediates many biological responses including cell proliferation, transformation, survival and motility. Deregulation of the pathway either through mutation of components or overexpression of EGFRs is associated with several forms of cancer. Under normal conditions, EGF stimulates a rapid but transient activation of ERK as the signal is rapidly shutdown, whereas under cancerous conditions, the ERK signal cannot be shutdown and is sustained. Computational modelling techniques have been used to investigate the signalling dynamics of the EGFR/ERK pathway, focusing on identifying the key processes involved in signal termination and what role the ERK to son of sevenless (SOS) negative feedback loop plays in generating a transient response. This model predicts that this negative feedback loop is not needed to achieve a transient activation of ERK as the process of receptor degradation alone is enough to terminate the signal. Importantly, the behaviour and predictions of this model are verified with laboratory data, as is essential for modern systems biology approaches. Further analysis showed that the feedback loop and receptor degradation were both redundant processes, as each could compensate for the absence of the other. This led to the prediction that in the case of a receptor which is not degraded, such as the insulin receptor, the negative feedback loop to SOS will actually be essential for a transient response to be achieved. Overall, the results shed new light on the role of negative feedback in EGF receptor signalling and suggest that different receptors are dependent on different features within the ERK pathway when relaying their signals.

Purpose: Sexual function is crucial for the quality of life and can be highly affected by preoperative therapy and surgery. The aim of this study was to identify potential risk factors for poor sexual function and quality of life. Methods: Female patients were asked to complete the Female Sexual Function Index (FSFI-6). Male patients were demanded to answer the International Index of Erectile Function (IIEF-5). Results: In total, 79 patients filled in the questionary, yielding a response rate of 41.57%. The proportion of women was represented by 32.91%, and the median age was 76.0 years (66.0–81.0). Sexual dysfunction appeared in 88.46% of female patients. Severe erectile dysfunction occurred in 52.83% of male patients. Univariate analysis showed female patients (OR: 0.17, 95%CI: 0.05–0.64, p = 0.01), older age (OR: 0.34, 95%CI 0.11–1.01, p = 0.05), tumor localization under 6cm from the anal verge (OR: 4.43, 95%CI: 1.44–13.67, p = 0.01) and extension of operation (APR and ISR) (OR: 0.13, 95%CI: 0.03–0.59, p = 0.01) as significant risk factors for poor outcome. Female patients (OR: 0.12, 95%CI: 0.03–0.62, p = 0.01) and tumors below 6 cm from the anal verge (OR: 4.64, 95%CI: 1.18–18.29, p = 0.03) were shown to be independent risk factors for sexual dysfunction after multimodal therapy in the multivariate analysis. Quality of life was only affected in the case of extensive surgery (p = 0.02). Conclusion: Higher Age, female sex, distal tumors and extensive surgery (APR, ISR) are revealed risk factors for SD in this study. Quality of life was only affected in the case of APR or ISR.

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