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Pathway diagrams describing the regulation of Interferon-beta and the Major Immediate Early Promotor (MIE) of human Cytomegalovirus, obtained from a review of the published literature as part of the project work for our MSc in Genomics and Pathway Biology. The pathways are presented in SBGN notation. This document has not been peer reviewed.

Pathway diagrams describing the regulation of Interferon Regulatory Factor-1 (IRF1), Interleukin-12 (IL12) and Human Papilloma Virus-18 (proteins E6 and E7, HPV-18 E6, E7), obtained from a review of the published literature as part of the project work for our MSc in Genomics and Pathway Biology. The pathways are presented in SBGN notation. This document has not been peer reviewed.

Pathway diagrams describing the regulation of Interferon-gamma, SV40 and Adenovirus, obtained from a review of the published literature as part of the project work for our MSc in Genomics and Pathway Biology. The pathways are presented in SBGN notation. This document has not been peer reviewed.

Pathway diagrams describing the regulation of activation for Interleukin-8 (IL-1b) and Human Immunodeficiency Virus Type 1 long terminal repeat (HIV-1 LTR), obtained from a review of the published literature as part of the project work for our MSc in Genomics and Pathway Biology. The pathways are presented in SBGN notation. This document has not been peer reviewed.

Pathway diagrams describing the regulation of Interferon-beta and the Major Immediate Early Promotor (MIE) of human Cytomegalovirus, obtained from a review of the published literature as part of the project work for our MSc in Genomics and Pathway Biology. The pathways are presented in SBGN notation. This document has not been peer reviewed.

Pathway diagrams describing the regulation of Interferon-beta and the Major Immediate Early Promotor (MIE) of human Cytomegalovirus, obtained from a review of the published literature as part of the project work for our MSc in Genomics and Pathway Biology. The pathways are presented in SBGN notation. This document has not been peer reviewed.

A report produced as part of the MSc in Genomics and Pathway Biology course at the Division of Pathway Medicine, University of Edinburgh. (http://www.ed.ac.uk/schools-departments/pathway-medicine). Note, that this has not been peer-reviewed.

A pathway diagram describing the regulation of oxysterol metabolim, obtained from a review of the published literature as part of the project work for our MSc in Genomics and Pathway Biology. The pathway is presented in SBGN notation. This pathway diagram has not been peer reviewed.

Little is known about the role of viral genes in modulating host cytokine responses. Here we report a new functional role of the viral encoded IE1 protein of the murine cytomegalovirus in sculpting the inflammatory response in an acute infection. In time course experiments of infected primary macrophages (MΦs) measuring cytokine production levels, genetic ablation of the immediate-early 1 (ie1) gene results in a significant increase in TNFα production. Intracellular staining for cytokine production and viral early gene expression shows that TNFα production is highly associated with the productively infected MΦ population of cells. The ie1- dependent phenotype of enhanced MΦ TNFα production occurs at both protein and RNA levels. Noticeably, we show in a series of in vivo infection experiments that in multiple organs the presence of ie1 potently inhibits the pro-inflammatory cytokine response. From these experiments, levels of TNFα, and to a lesser extent IFNβ, but not the anti-inflammatory cytokine IL10, are moderated in the presence of ie1. The ie1- mediated inhibition of TNFα production has a similar quantitative phenotype profile in infection of susceptible (BALB/c) and resistant (C57BL/6) mouse strains as well as in a severe immuno-ablative model of infection. In vitro experiments with infected macrophages reveal that deletion of ie1 results in increased sensitivity of viral replication to TNFα inhibition. However, in vivo infection studies show that genetic ablation of TNFα or TNFRp55 receptor is not sufficient to rescue the restricted replication phenotype of the ie1 mutant virus. These results provide, for the first time, evidence for a role of IE1 as a regulator of the pro-inflammatory response and demonstrate a specific pathogen gene capable of moderating the host production of TNFα in vivo., Author Summary The suppression of the production rather than the blockage of action of the potent inflammatory mediator TNFα is a particular hallmark of anti-TNFα mechanisms associated with microbial and parasitic infections. Whether this mode of counter-regulation is an important feature of infection by viruses is not clear. Also, it remains to be determined whether a specific pathogen gene in the context of an infection in vivo is capable of modulating levels of TNFα production. In this study we disclose a virus-mediated moderation of TNFα production, dependent on the ie1 gene of murine cytomegalovirus (MCMV). The ie1 gene product IE1 is a well-characterized nuclear protein capable of altering levels of host and viral gene expression although its biological role in the context of a natural infection is to date unknown. We provide evidence showing that ie1 is associated with a moderated pro-inflammatory cytokine response, in particular with TNFα production. Further, we show that the viral moderation of this cytokine is not only readily apparent in vitro but also in the natural host. The identification of a viral gene responsible for this mode of regulation in vivo may have therapeutic potential in the future in both anti-viral and anti-inflammatory strategies.

A pathway diagram describing the synthesis of vitamin D3 and its relationship to the cholesterol synthesis pathway, obtained from a review of the published literature as part of the project work for our MSc in Genomics and Pathway Biology. The pathway is presented in SBGN notation. This pathway diagram has not been peer reviewed.

A pathway diagram describing the synthesis of androgens and estrogens from cholesterol, obtained from a review of the published literature as part of the project work for our MSc in Genomics and Pathway Biology. The pathway is presented in SBGN notation. This pathway diagram has not been peer reviewed.

A report produced as part of the MSc in Genomics and Pathway Biology course at the Division of Pathway Medicine, University of Edinburgh. (http://www.ed.ac.uk/schools-departments/pathway-medicine). Note, that this has not been peer-reviewed.

A pathway diagram describing the regulation of HMGCR and its impact on the cholesterol synthesis pathway, obtained from a review of the published literature as part of the project work for our MSc in Genomics and Pathway Biology. The pathway is presented in SBGN notation. This pathway diagram has not been peer reviewed.

Upon infection, our immune cells produce a small protein called interferon, which in turn signals a protective response through a series of biochemical reactions that involves lowering the cells' ability to make cholesterol by targeting a gene essential for controlling the pathway for cholesterol metabolism., Little is known about the protective role of inflammatory processes in modulating lipid metabolism in infection. Here we report an intimate link between the innate immune response to infection and regulation of the sterol metabolic network characterized by down-regulation of sterol biosynthesis by an interferon regulatory loop mechanism. In time-series experiments profiling genome-wide lipid-associated gene expression of macrophages, we show a selective and coordinated negative regulation of the complete sterol pathway upon viral infection or cytokine treatment with IFNγ or β but not TNF, IL1β, or IL6. Quantitative analysis at the protein level of selected sterol metabolic enzymes upon infection shows a similar level of suppression. Experimental testing of sterol metabolite levels using lipidomic-based measurements shows a reduction in metabolic output. On the basis of pharmacologic and RNAi inhibition of the sterol pathway we show augmented protection against viral infection, and in combination with metabolite rescue experiments, we identify the requirement of the mevalonate-isoprenoid branch of the sterol metabolic network in the protective response upon statin or IFNβ treatment. Conditioned media experiments from infected cells support an involvement of secreted type 1 interferon(s) to be sufficient for reducing the sterol pathway upon infection. Moreover, we show that infection of primary macrophages containing a genetic knockout of the major type I interferon, IFNβ, leads to only a partial suppression of the sterol pathway, while genetic knockout of the receptor for all type I interferon family members, ifnar1, or associated signaling component, tyk2, completely abolishes the reduction of the sterol biosynthetic activity upon infection. Levels of the proteolytically cleaved nuclear forms of SREBP2, a key transcriptional regulator of sterol biosynthesis, are reduced upon infection and IFNβ treatment at both the protein and de novo transcription level. The reduction in srebf2 gene transcription upon infection and IFN treatment is also found to be strictly dependent on ifnar1. Altogether these results show that type 1 IFN signaling is both necessary and sufficient for reducing the sterol metabolic network activity upon infection, thereby linking the regulation of the sterol pathway with interferon anti-viral defense responses. These findings bring a new link between sterol metabolism and interferon antiviral response and support the idea of using host metabolic modifiers of innate immunity as a potential antiviral strategy., Author Summary Currently, little is known about the crosstalk between the body's immune and metabolic systems that occurs after viral infection. This work uncovers a previously unappreciated physiological role for the cholesterol-metabolic pathway in protecting against infection that involves a molecular link with the protein interferon, which is made by immune cells and known to “interfere” with viral replication. We used a clinically relevant model based on mouse cytomegalovirus (CMV) infection of bone-marrow-derived cells. Upon infection these cells produce high levels of interferon as part of the innate-immune response, which we show in turn signals through the interferon receptor resulting in lowering enzyme levels on the cholesterol pathway. We observed this effect with a range of other viruses, and in each case it leads to a notable drop in the metabolites involved in the cholesterol pathway. We found that the control mechanism involves regulation by interferon of an essential transcription factor, named SREBP-2, which coordinates the gene activity of the cholesterol pathway. This mechanism may explain clinical observations of reduced cholesterol levels in patients receiving interferon treatment. Our initial investigation into how lowered cholesterol might protect against viral infection reveals that the protection is not due to a requirement of the virus for cholesterol itself but instead involves a particular side-branch of the pathway that chemically links lipids to proteins. Drugs such as statins and small interfering RNAs that block this part of the pathway are also shown to protect against CMV infection of cells in culture and in mice. This provides the first example of targeting a host metabolic pathway in order to protect against an acute infection.

One of the most famous cytokines, tumor necrosis factor (TNF), shows a vast spectrum of bioactivities influencing majority of cell types. Produced mostly by macrophages, it is considered to be a major mediator of inflammation and cellular immune response. Although infection with several viruses has been shown to induce production of TNF, indicating its importance in successful viral clearance, it seems that not many viruses have learned how to control this potent cytokine. However, considering their reputation as masters of disguise, it does not come as a surprise that both human and murine cytomegaloviruses (MCMV) have developed means to avoid TNF-induced response (caspase dependent and independent apoptosis and expression of TNF-induced genes). Here it is shown that the MCMV ie1 gene product acts as a negative regulator of TNF expression in vitro and in vivo at both transcriptional and translational level, thus revealing yet another immunoevasive strategy employed by MCMV. Mice infected with MCMVdie1 show lower viral titers, but higher levels of TNF when compared to mice infected with MCMVdie1-rev or wt virus and this effect is not strain dependant. NK cell depletion didn’t rescue the virus from its attenuated phenotype, indicating that this immunoevasion strategy is directed mostly at macrophages, which in addition of being the main producers of TNF, are also a major site of viral replication, dissemination and establishment of latency. Interestingly, despite the attenuated phenotype, growth kinetics of MCMVdie1 showed reactivation around 30th day PI in spleen, liver, kidney and, most prominently, in salivary gland.

Summary The modelling of biological intra-cellular pathways requires the systematic capture and representation of interactions between components that are biologically correct and computationally rigorous. The challenge is two fold, to verify and extend our understanding of such pathways by comparing in silico models to experiments; and to ensure that such models are understandable by biologists and for checking biological validity. In this report we present a graphical notation, the Edinburgh Pathway Notation (EPN), which satisfies the central biologically driven requirements while providing a strict formal framework for analysis. The EPN emphasises the use of a logical representation of pathways, which is particularly suited to pathways were some mechanisms are not known in detail.

The present invention provides a method for detecting a target analyte in a sample, using a pro-macromolecular structure switch which has an analyte binding site for binding the analyte to form together, a macromolecular switch, with an ion coordination site, and arms flippable between discretely different conformations corresponding to different ion binding conditions. The different conformations provide, with an output signal reading system, characteristic output signals. The pro-switch is contacted with sample and an external input signal applied to the input device to change ion binding conditions to flip switch conformations, and changes in output signal are read out. The invention also provides a pro-macromolecular structure switch.

Workshop on molecular mechanisms of immune modulation: lessons from viruses