Defining TILRR regulation of distinct IL-1RI responses using systems biology
Lead Research Organisation:
University of Sheffield
Department Name: Infection Immunity & Cardiovasc Disease
Abstract
The immune system is our defence against microorganisms such as bacteria. The immune/inflammatory system also controls repair, whether activated after microorganisms have been killing our cells, or induced because of physical damage such as cuts and wounds even if not accompanied by infection.
The immune/inflammatory system is organised for defence, white cells circulate in your blood "on patrol" constantly on alert for invaders with base depots called lymph nodes, where they can be marshalled in large numbers and sent out for attack. Some white cells produce antibodies and some produce substances that kill microorganisms directly. The immune/inflammatory system is divided into 2 parts, innate and adaptive. The adaptive part learns to recognise the invading microorganisms, and makes special antibodies tailored to each disease-producing microorganism. For a more rapid response a front line defence is needed. This is the innate immune/inflammatory system.
In so called inflammatory diseases, activators of these systems get produced without injury and infection and white cells are called into healthy tissue, and damage it. This occurs for example in heart disease and is the underlying mechanism inducing damage to joints in the disease called arthritis. To treat these diseases we need to find ways of shutting off the message to the activated cells. This project is the continuation of work we have been doing for many years on an inflammatory inducer called interleukin-1, which is particularly potent, and is known to contribute significantly to tissue damage.
In our earlier studies we have identified a novel regulator of the defence system, which significantly enhances activities induced by interleukin-1. We have demonstrated that this regulator is present in various types of inflammatory cells including those that can potentially damage healthy tissue. In addition, we have shown that in order to increase interleukin-1 activities the novel regulator binds to a so called "signalling receptor", which is located on the surface of the cell, and controls inflammatory activities through the cell.
In this project we are investigating how this new regulator interacts with the signalling receptor and how it changes its function. We are going to use this information to identify the events it triggers inside the cell, and which lead to changes in cell behaviour. This will improve our understanding of how signals by cytokines such as interleukin-1 are regulated, and how they increase activity in inflammatory cells. Such information will contribute to our knowledge of how these activities are controlled, how to moderate their effects, and ultimately how to develop specific treatments for inflammatory disease.
Specific intervention is very important in controlling these events, as we need to have a certain level of functioning inflammatory responses in case of bacterial infection and/or we are in need of tissue repair. By moderating the novel regulator, we have the possibility of leaving the main system intact and functioning normally. We have recently obtained detailed information about which parts of the regulator are particularly potent. In this project we will use this information to investigate the consequences of activating and blocking this regulator and determine what cellular functions will be disturbed through the different parts of the protein. This will make it possible to ultimately design specific treatments for diseases characterised by abnormalities in these functions.
State-of-the-art computational modelling will provide much clearer insights into the many processes involved in this very complex system, and predictions from the models will give us information, which we will use in future experimentation and drug development.
The immune/inflammatory system is organised for defence, white cells circulate in your blood "on patrol" constantly on alert for invaders with base depots called lymph nodes, where they can be marshalled in large numbers and sent out for attack. Some white cells produce antibodies and some produce substances that kill microorganisms directly. The immune/inflammatory system is divided into 2 parts, innate and adaptive. The adaptive part learns to recognise the invading microorganisms, and makes special antibodies tailored to each disease-producing microorganism. For a more rapid response a front line defence is needed. This is the innate immune/inflammatory system.
In so called inflammatory diseases, activators of these systems get produced without injury and infection and white cells are called into healthy tissue, and damage it. This occurs for example in heart disease and is the underlying mechanism inducing damage to joints in the disease called arthritis. To treat these diseases we need to find ways of shutting off the message to the activated cells. This project is the continuation of work we have been doing for many years on an inflammatory inducer called interleukin-1, which is particularly potent, and is known to contribute significantly to tissue damage.
In our earlier studies we have identified a novel regulator of the defence system, which significantly enhances activities induced by interleukin-1. We have demonstrated that this regulator is present in various types of inflammatory cells including those that can potentially damage healthy tissue. In addition, we have shown that in order to increase interleukin-1 activities the novel regulator binds to a so called "signalling receptor", which is located on the surface of the cell, and controls inflammatory activities through the cell.
In this project we are investigating how this new regulator interacts with the signalling receptor and how it changes its function. We are going to use this information to identify the events it triggers inside the cell, and which lead to changes in cell behaviour. This will improve our understanding of how signals by cytokines such as interleukin-1 are regulated, and how they increase activity in inflammatory cells. Such information will contribute to our knowledge of how these activities are controlled, how to moderate their effects, and ultimately how to develop specific treatments for inflammatory disease.
Specific intervention is very important in controlling these events, as we need to have a certain level of functioning inflammatory responses in case of bacterial infection and/or we are in need of tissue repair. By moderating the novel regulator, we have the possibility of leaving the main system intact and functioning normally. We have recently obtained detailed information about which parts of the regulator are particularly potent. In this project we will use this information to investigate the consequences of activating and blocking this regulator and determine what cellular functions will be disturbed through the different parts of the protein. This will make it possible to ultimately design specific treatments for diseases characterised by abnormalities in these functions.
State-of-the-art computational modelling will provide much clearer insights into the many processes involved in this very complex system, and predictions from the models will give us information, which we will use in future experimentation and drug development.
Technical Summary
Host defence responses are induced through the Toll-like and IL-1 receptors and activated by ligand binding and system-specific co-receptors. This project uses systems biology to analyse the function of the IL-1 receptor type I (IL-1RI), and its control by its co-receptor TILRR.
TILRR is a ubiquitously expressed spliced variant of FREM1, of the FRAS1 family, which is independently transcribed and translated. We have demonstrated that TILRR controls IL-1RI function and activation of NF-kB, and regulates inflammatory and anti-apoptotic responses by IL-1. Alanine-scanning mutagenesis identified mutants, which selectively control inflammation and survival signals through IL-1RI.
Here we will use these mutants to identify events at the level of the receptor complex, which selectively direct downstream activities. The data will be included in a computational model of receptor function, and predictions from this will inform design of experiments on signal transduction and gene regulation. We will use robotic screening to identify key intermediates involved, and characterise a subset of these in functional assays. The data will be incorporated in our NF-kB model, which we have demonstrated faithfully represents the biological system. Key regulators, predicted by the model, will be included in microarray experiments to identify relevant changes in gene activation profiles, and data analyzed using work-flow and included in the model. We will use FLAME, use super computers, to make possible expansion of the model to a level where we can link receptor function with signal transduction and gene activity. Predictions will be tested in relevant wet experiments and results will inform the model, in multiple iterations, to yield a comprehensive in silico representation of the biological system.
The results will provide a platform for future comprehensive investigations of cellular response and expand the use of agent based modelling and the FLAME framework.
TILRR is a ubiquitously expressed spliced variant of FREM1, of the FRAS1 family, which is independently transcribed and translated. We have demonstrated that TILRR controls IL-1RI function and activation of NF-kB, and regulates inflammatory and anti-apoptotic responses by IL-1. Alanine-scanning mutagenesis identified mutants, which selectively control inflammation and survival signals through IL-1RI.
Here we will use these mutants to identify events at the level of the receptor complex, which selectively direct downstream activities. The data will be included in a computational model of receptor function, and predictions from this will inform design of experiments on signal transduction and gene regulation. We will use robotic screening to identify key intermediates involved, and characterise a subset of these in functional assays. The data will be incorporated in our NF-kB model, which we have demonstrated faithfully represents the biological system. Key regulators, predicted by the model, will be included in microarray experiments to identify relevant changes in gene activation profiles, and data analyzed using work-flow and included in the model. We will use FLAME, use super computers, to make possible expansion of the model to a level where we can link receptor function with signal transduction and gene activity. Predictions will be tested in relevant wet experiments and results will inform the model, in multiple iterations, to yield a comprehensive in silico representation of the biological system.
The results will provide a platform for future comprehensive investigations of cellular response and expand the use of agent based modelling and the FLAME framework.
Planned Impact
Medicine and Biology
Background
We are investigating mechanisms driving cellular responses in the healthy organism. However, identification of events, which selectively perturb aspects of receptor function and response control, will improve our understanding of inflammatory dys-regulation, characterising disease as well as basic biological evens.
This field of work is fundamental to multi-factorial inflammatory conditions, widespread heath problems in the aging population of the developed world. Dys-regulation of inflammatory responses is a determining factor in prevalent and costly diseases including atherosclerosis, which costs the UK government £30.6 billion/year (NHS publication care quality commission, Sept 2009) and arthritis and related diseases which cost nearly £6 billion /year (Arthritis care sheet, 2007). It is also a major factor in organ failures and a highly significant parameter in the prognosis of cancer.
Host defence mechanisms are tightly controlled systems, activated through Toll-like and IL-1 receptors. Ligand binding and co-receptor recruitment determine the appropriate signal amplification and activation of downstream events. The potential for therapeutic targeting at the level of the receptor has been demonstrated by the major advances resulting from development of the anti-TNFs. Diseases such as arthritis and atherosclerosis contribute significantly to degradation of quality of life in the older population. The population as a whole and organisations such as the NHS will continue to benefit from advances in this area.
Benefits
1. Expanding the range of treatments for inflammatory diseases offers significant promise in reducing the period of morbidity in the last years of life. Greater specificity as is expected to result from targeting the functional sites in TILRR, will bring a number of benefits, such as potentially reducing side effects etc. In addition, selective blocking of anti-apoptotic responses is expected to increase the efficacy of chemotherapy while maintaining normal defence mechanisms against infection.
2. The innate immune defence is also critical to pathogen resistance in plants and animals, therefore, results from these studies may also have the potential to contribute to agricultural biotech - for example by GM strategies that derive disease resistant crops, without the need for agents, potentially hazardous to the environment. An example might be flax or rape engineered to express elevated levels of the TIR family Rust Resistance Protein.
Computer Science
Background
Successful detailed models of this system will be of great interest to researchers in systems biology because they will demonstrate the power of this approach, which can be used in any other types of system. The FLAME framework ensures that the model can be integrated with other related systems and is being used in labs worldwide.
Benefits
The models will be made public so that others can adapt and integrate them with their own systems. Companies such as Genesys, and epiGenesys, started by M. Holcombe, and others which develop software for a wide range applications, will benefit from expansion of the systems.
Biotechnology and systems biology, as applied to human health and innovation have been identified by the DTI as a growth R&D area in the UK because of the potential market for treatments. Given the stated aim of both the EU and organisations such as Yorkshire Forward to develop a Biotechnology Cluster in South Yorkshire, and the aims of the Treasury to foster Bioscience R&D in the UK as a whole, the potential commercial use for our work fits well strategically.
Background
We are investigating mechanisms driving cellular responses in the healthy organism. However, identification of events, which selectively perturb aspects of receptor function and response control, will improve our understanding of inflammatory dys-regulation, characterising disease as well as basic biological evens.
This field of work is fundamental to multi-factorial inflammatory conditions, widespread heath problems in the aging population of the developed world. Dys-regulation of inflammatory responses is a determining factor in prevalent and costly diseases including atherosclerosis, which costs the UK government £30.6 billion/year (NHS publication care quality commission, Sept 2009) and arthritis and related diseases which cost nearly £6 billion /year (Arthritis care sheet, 2007). It is also a major factor in organ failures and a highly significant parameter in the prognosis of cancer.
Host defence mechanisms are tightly controlled systems, activated through Toll-like and IL-1 receptors. Ligand binding and co-receptor recruitment determine the appropriate signal amplification and activation of downstream events. The potential for therapeutic targeting at the level of the receptor has been demonstrated by the major advances resulting from development of the anti-TNFs. Diseases such as arthritis and atherosclerosis contribute significantly to degradation of quality of life in the older population. The population as a whole and organisations such as the NHS will continue to benefit from advances in this area.
Benefits
1. Expanding the range of treatments for inflammatory diseases offers significant promise in reducing the period of morbidity in the last years of life. Greater specificity as is expected to result from targeting the functional sites in TILRR, will bring a number of benefits, such as potentially reducing side effects etc. In addition, selective blocking of anti-apoptotic responses is expected to increase the efficacy of chemotherapy while maintaining normal defence mechanisms against infection.
2. The innate immune defence is also critical to pathogen resistance in plants and animals, therefore, results from these studies may also have the potential to contribute to agricultural biotech - for example by GM strategies that derive disease resistant crops, without the need for agents, potentially hazardous to the environment. An example might be flax or rape engineered to express elevated levels of the TIR family Rust Resistance Protein.
Computer Science
Background
Successful detailed models of this system will be of great interest to researchers in systems biology because they will demonstrate the power of this approach, which can be used in any other types of system. The FLAME framework ensures that the model can be integrated with other related systems and is being used in labs worldwide.
Benefits
The models will be made public so that others can adapt and integrate them with their own systems. Companies such as Genesys, and epiGenesys, started by M. Holcombe, and others which develop software for a wide range applications, will benefit from expansion of the systems.
Biotechnology and systems biology, as applied to human health and innovation have been identified by the DTI as a growth R&D area in the UK because of the potential market for treatments. Given the stated aim of both the EU and organisations such as Yorkshire Forward to develop a Biotechnology Cluster in South Yorkshire, and the aims of the Treasury to foster Bioscience R&D in the UK as a whole, the potential commercial use for our work fits well strategically.
Organisations
- University of Sheffield (Lead Research Organisation)
- AstraZeneca (United Kingdom) (Collaboration)
- Cancer Research UK (Collaboration)
- Chinese Academy of Sciences (Collaboration)
- University of Sheffield (Collaboration)
- UNIVERSITY OF LEICESTER (Collaboration)
- MRC-Technology (Collaboration)
- University of Connecticut (Collaboration)
- UNIVERSITY OF YORK (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
Publications
Holcombe M
(2012)
Modelling complex biological systems using an agent-based approach.
in Integrative biology : quantitative biosciences from nano to macro
Hudson RC
(2012)
Bioinformatics Analysis of the FREM1 Gene-Evolutionary Development of the IL-1R1 Co-Receptor, TILRR.
in Biology
Kennelly TM
(2019)
Distinct Binding Interactions of a5ß1-Integrin and Proteoglycans with Fibronectin.
in Biophysical journal
Kennelly, T.M.
Characterisation of distinct binding interactions of fibronectin with proteoglycans and integrins using dynamic single molecule force microscopy.
in Biochemical Journal
| Description | Overview The focus of this project is regulation of the IL-1receptor system by the co-receptor TILRR. Our earlier studies identified TILRR as a novel regulator of inflammation and demonstrated that it significantly enhances activities induced by the cytokine interleukin-1. We demonstrated that in order to increase interleukin-1 activities TILRR, binds to a so called "signalling receptor", which is located on the surface of the cell, and controls activation of inflammatory signals and genes. This project focused on identifying the changes induced by TILRR, which underlie the dysregulated cell responses resulting from its association with the signalling IL-1 receptor. Our results show that TILRR binding to the IL-1 receptor imparts significant changes at several levels of system regulation. These include alterations within the receptor complex, and changes in regulation of signal transduction and in gene activity. The type of changes induced by an increase in TILRR expression and its association with the IL-1 receptor lead to aberrant cell responses such as those known to occur in disease. We find that expression of TILRR is very low to undetectable in healthy tissue but that it is highly upregulated at sites of disease. Using the results from our molecular studies we have identified highly sensitive functional sites within the TILRR protein sequence and have designed specific blocking anti-TILRR antibodies targeting these sites. We have demonstrated that these antibodies block aberrant cell signalling and further that they significantly reduce development of diseases such as vascular inflammation and lung fibrosis. As TILRR is only present in regions affected by disease, blocking its function is likely to have very little impact on healthy tissue. We therefore expect that inhibitors of TILRR will have minimal or no side effects and that blockers of TILRR, developed by pharmaceutical companies, will significantly improve treatments of disease. Further details Experiments on receptor function, have demonstrated the role of TILRR in adapter protein recruitment and signal co-ordination. The analysis has identified novel mechanisms controlling TIR receptor crosstalk, which will be examined in further detail using techniques optimized by our collaborators in Cambridge. We have used siRNA technology and TILRR knockout cells to determine the impact of TILRR expression on receptor function, inflammatory signalling and gene activation profiles. Results from both sets of experiments show effects IL-1 receptor expression, NF-?B regulation and gene activation profiles, central to control of inflammatory responses, and host defence mechanisms, and include alterations known to be significant in disease development. Proteomics was used to determine post-translational modifications affected by TILRR expression. The analysis identified a wide range of phosphorylation events correlating with changes in receptor complex composition and related to regulatory events known to be affected by changes in signal amplification. TILRR SNPs, recently identified by the 1000 Genomes Project, were selected based on predicted effects on TILRR/IL-1RI association and receptor conformation, using 3-D modelling, and impacts on signal amplification and gene activity tested in in vitro experiments. An ongoing collaborative study focuses on investigating the mechanisms controlling the interaction of the TILRR glycosaminoglycan chain with the extracellular matrix, and the impact of this interaction on signalling receptor function. We have successively expanded our agent based computational model to reproduce TILRR control including novel mechanisms and signalling intermediates, as well as structural components. As data from the in vitro experiments are confirmed, results are incorporated in the model, which is verified, and predictions tested in biological assays. We have demonstrated that the model accurately reproduces the biological system, and allows us to explore signal sensitive regulation of NF-?B and to consider the impact of crosstalk on IL-1-induced responses. In addition, the computational model has been used to identify a novel mechanism for structural control of the NF-?B pathway and to define a role for this process in pathway calibration. We have recent data using I?Ba mutants, which will be included in the agent-based model to further expand the comprehensive in silico representation of the NF-?B network and enable in depth analysis of mechanisms controlling signal amplification. Final Report 21.09.15 Delineating TILRR control of the IL-1RI system, using systems biology. BB/J009687/1. Regulation of receptor function: Experiments on receptor function have demonstrated the role of TILRR in regulatory cross talk. We have identified novel interactions at the level of the receptor complex, which are expected to contribute to signalling amplification and crosstalk. Specific tools are being developed to enable further analysis of these events, which will be carried out in collaboration with Prof N. Gay at the University of Cambridge. The project is expected to be completed spring 2016. We have employed 3-dimensional modelling to identify residues predicted to be located in the region of TILRR/IL-1RI binding. These data together with in vitro assays, was used to screen a series of TILRR SNPs recently identified by the 1000 Genomes Project. The selected SNPs include residue 448, which we identified earlier as a functional site using alanine scanning. Further, the screen includes both enhancers and inhibitors of TILRR amplification, as well as polymorphisms that selectively control the canonical and non-canonical NF-?B pathway, with similar effect as some functional mutants identified by our alanine scanning exercise. Effects have been confirmed at the level of gene activity as well as in relation to upstream regulators I?Ba and Akt phosphorylation, respectively. A series of experiments have used TILRR knockout cells to determine the impact receptor expression. These have demonstrated pronounced effects on IL-1 receptor expression levels, consistent with our published data showing reduced ligand binding in the presence of TILRR siRNA (Zhang et al., 2010). The data are currently being included in our agent-based model, to inform on long-term effects of TILRR expression on system control. Signalling and signalling crosstalk: We have assessed the involvement of signalling cross talk between IL-1 induced responses and regulators of cell attachment and structure. The experiments included 3-dimensional predictive modelling of I?Ba interaction with the cytoskeletal components actin and Spectrin, in vitro experimentation and agent based modelling of NF-?B regulation. The study identifies role for cytoskeletal sequestration and release of ??Ba during NF-?B activation, and predicts this to provide a rapid mechanism for calibration of signal activation in relation to input levels. Further, they show that the process is controlled by TILRR, and predicts the cytoskeletal involvement in NF-?B regulation to specifically impact inflammatory responses while anti-apoptotic signals are unaffected. Using alanine-scanning mutagenesis of conserved residues we have identified I?Ba regulatory sites, which control the cytoskeletal interaction and have created mutants with altered binding to the cytoskeletal component. A next set of studies is using the mutants together with the wt I?Ba to characterise the mechanisms controlling I?Ba/Spectrin interaction and further elucidate the impact of changes in this interaction on pathway control. Work on the impact of binding of the cell surface glycosaminoglycan/fibronectin interaction, have demonstrated significantly higher rupture forces for proteoglycans than measured for integrin /fibronectin binding, consistent with a distinct regulation of the two types of interactions. Further experiments have shown that fibronectin binding of the glycosaminoglycan at linked to GAG attachment site at residue 112, has pronounced effects on IL-1-induced signalling. Gene regulation profiles: We have demonstrated that alterations in TILRR expression have pronounced impacts on gene regulation profiles. The experiments have used TILRR siRNA transfection and in vitro assays. In addition, the analysis has taken advantage of TILRR knockout cells, and compared gene activation with profiles obtained using wild type cells, at the resting state and during an inflammatory response. Results show pronounced reductions in induction of inflammatory receptors and signalling intermediates, many of which are known to be key regulators in disease. Identification of novel intermediates: Our robotic screening of cDNA libraries has identified intermediates, which are activated by IL-1 only in the presence of TILRR. These include known regulators of the network as well as intermediates, which were not previously known to be induced by IL-1 and/or to control NF-?B activity. Dominant negative constructs of known intermediates of the pathway have been used in in vitro assays to determine the mechanism of activation and to identify relevant steps in pathway control. The project is expected to be completed spring 2016. Computational modelling: The agent based NF-?B model has been successively expanded through incorporation of in vitro and in vivo data and has been used to inform experimental design throughout the tenure of the grant. It now includes receptor systems, signalling intermediates, structural components and genes relevant to both the canonical and non-canonical NF-?B pathway. Using the model in interdisciplinary studies has had a marked impact on analysis of activation at the level of the receptor complex, signal transduction, specifically in relation to signalling crosstalk and gene activity in relation to signal amplification. Predictions at all levels have been tested in biological assays. In parallel with the interdisciplinary studies, we have determined limitations of the model in regards to simplifications and levels of complexity, in order to improve usability and increase speed. In addition, parts of the in silico work have been designed to compare the agent-based analysis with other modelling/analytical programmes, and to consider combining computational modelling with statistical approaches. Manuscripts in Revision and in Preparation In Revision Rhodes, D. M, Holcombe M., and Qwarnstrom E.E. Impact of varying complexity in Agent based modelling. BioSystems. (submitted after revision). Williams, R A, Timmis, J, and Qwarnstrom, E E. Statistical Techniques complement UML when modeling complex dynamical biosystems. PLOS One. (In revision). Published Smith S., Samokhin, A., Alfadi, M., Murphy, E., Rhodes, D, Holcombe MW. Vergani, VP, Storey, R., Kiss-Toth, E., Brown, N., Yee, S-P., Francis, SE. and Qwarnstrom E.E. The FREM1 isoform 2 (TILRR) controls aberrant NF-?B activation and dys-regulated inflammatory and anti-apoptotic responses in disease. Samokhin, A., Murphy, E., Smith, S., Rhodes, D.,Francis, SE., and Qwarnstrom E.E. Blocking IL-1RI co-receptor TILRR function reduces atherosclerosis and promotes development of stable plaques. In preparation Murphy, E.C., Smith S.A, Rhodes, D.M., Francis, S.E., Vergani, VP, Brown, N.J., and Qwarnstrom E.E. Elevated AKT phosphorylation in Ductal Carcinomas in Situ are controlled through the IL-1RI co-receptor TILRR. Smith, S, Samokhin, A., Alfadi, M., Murphy, E., Rhodes, D, Bowskill, S., Mistry, K., Holcombe MW, Vergani, VP., Kiss-Toth, E., Brown, N., Francis, SE., and Qwarnstrom E.E. Impaired receptor function, NF-?B activity and gene regulation - characterisation of the inflammatory phenotype of the TILRR KO mouse. Smith, S, Qwarnstrom EE. Ank 2 is a regulatory site for I?Ba/relA interaction and NF-?B control. Smith, S., Nichols A. and Qwarnstrom EE. Identification of functional SNPs in the TILRR core protein. Additional Information added, March 2018. The information gained about the molecular mechanism controlling the action of the co-receptor and the identification of the functional sites have been used to develop a series of blockers to aberrant cell responses, characteristic of disease conditions. One of the inhibitors has been used in disease models and has been demonstrated to have pronounce impact on progression of inflammatory vascular diseases, such as atherosclerosis. The data are published in Smith et al., 2017 JACCbst (Journal of American College of Cardiologists, basic to translational science) listed under "publications". |
| Exploitation Route | Background: Our earlier studies identified a novel regulatory component, which we demonstrated controls IL-1 receptor function and NF-kB activity, the IL1R1 co-receptor TILRR. The focus of the current project is to identify processes, which underlie TILRR-induced signal amplification resulting from its association with IL1R1. Key Findings: -TILRR association with IL1R1 leads to changes in receptor complex composition and increases in recruitment of the MyD88 adapter and PI3 kinase to the receptor complex. -TILRR is required for IL-1-induced activation of the Ras GTPase and consequent changes in the cytoskeleton. -The TILRR induced effects on the canonical and non-canonical pathway produce signalling patterns characteristic of dysregulated activation observed in disease. -In contrast to other components of the IL-1 receptor system, TILRR is present at low to undetectable levels in healthy tissue. However, it is highly upregulated in regions exhibiting aberrant activation of NF-kB and inflammatory responses such as the atherosclerotic plaque. -Genetic deletion of TILRR has marked effects on gene activation profiles. In particular, expression of regulators of immunity and inflammation, including receptors, ligands and signalling intermediates are significantly reduced. -Administration of a specific blocking TILRR antibody, which provides distinct inhibition of the NF-kB network, significantly reduces progression of atherosclerosis and lung fibrosis in well-established disease models. Because of the potential for obtaining site-specific inhibition, using TILRR as a therapeutic target is expected to reduce side effects known to be induced by inhibiting IL-1 and/or IL-1 receptor function. Our recent in vivo data is of particular interest to pharmaceutical companies and discussions are ongoing. We expect that, in the future, these blockers will be used in the clinic, and that they will provide marked benefits to the patients and impact policies. |
| Sectors | Digital/Communication/Information Technologies (including Software),Healthcare,Pharmaceuticals and Medical Biotechnology,Other |
| Description | The information obtained from the project has been used as the basis for development of anti-TILRR antibodies. Initial testing of the antibodies demonstrated pronounced reductions in amplified NF-kB activity, characteristic of diseases such as atherosclerosis. Published and ongoing studies using well established disease models demonstrate that TILRR antibody blocking causes significant reductions in disease development. One of the blocking antibodies has been demonstrated to have pronounced impact on progression atherosclerosis and also to reduce lung fibrosis. Unlike other components of the IL-1 system, TILRR is present at low/undetectable levels in healthy tissues. In contrast, it is highly expressed in regions affected by diseases with an underlying inflammatory component such as the atherosclerotic plaque and in fibrotic areas in the lung. Thus, providing an opportunity for specific targeting of affected areas. Because of the potential for obtaining selective and site-specific inhibition, using TILRR as a therapeutic target is expected to reduce or eliminate side effects, known to be induced by inhibiting IL-1 and/or IL-1 receptor function. We expect that, in the future, TILRR blockers will be used in the clinic, and that they will provide marked benefits to the patients and impact policies. |
| Description | BBSRC Sparking award |
| Amount | £20,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2014 |
| End | 04/2014 |
| Description | MRC Conficence in Concept |
| Amount | £70,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Department | MRC Confidence in Concept Scheme |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2014 |
| End | 09/2015 |
| Title | Agent based computational modelling of the NF-kB pathway |
| Description | This is a predictive modelling tool which uses the FLAM framework to enabled detailed analysis of large and complex biological systems. The predictive in silico representation of the NF-kB network faithfully represents the biological system and is used to direct development of wetlands experiments. Sourceforge. IL1R TILRR FlameGPU: Agent based model of IL1R1 signalling for FLAME GPU. Available at: https://sourceforge.net/projects/il1rtilrr-flamegpu/ |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | Not recorded |
| Title | New mouse imflammatory knockout |
| Description | Knockout mouse - Genetic deletion of the TILRR protein |
| Type Of Material | Model of mechanisms or symptoms - non-mammalian in vivo |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | Publications and data in vivo, in vitro and bioinformatics demonstrating the relevance of the novel protein in disease. |
| URL | https://doi.org/10.1016/j.jacbts.2017.03.014 |
| Title | knockout mouse |
| Description | TILRR knockout mouse |
| Type Of Material | Model of mechanisms or symptoms - non-mammalian in vivo |
| Provided To Others? | No |
| Impact | informative in investigations on inflammatory regulation and disease |
| Title | peptide antibody |
| Description | for use in cell biological and biochemical assays for detection of a novel regulatory protein. |
| Type Of Material | Antibody |
| Provided To Others? | No |
| Impact | Highly specific peptide antibody - improved signal/ noise in a range of assays |
| Title | receptor spectific siRNA |
| Description | specific siRNA for receptor regulatory component |
| Type Of Material | Technology assay or reagent |
| Provided To Others? | No |
| Impact | very efficient blocker of protein expression |
| Title | Agent based model of NF-kB regulation |
| Description | The agent based model was developed using the FLAME framework, a general agent-based modelling framework that can automatically produce software that runs on supercomputers. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | Agent based models and the FLAME framework are integrated with other related systems and is being used worldwide. |
| URL | https://sourceforge.net/projects/il1r-tilrr-flamegpu/ |
| Description | Analysis of novel receptor crosstalk on signal amplification |
| Organisation | University of Cambridge |
| Department | Department of Biochemistry |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Identification of novel regulators of receptor function |
| Collaborator Contribution | Expertise in Toll-like/IL-1 receptor function and signalling |
| Impact | The project focused on TIR signalling cross-talk. Techniques used by the Cambridge group were not required for completion of the project. |
| Start Year | 2012 |
| Description | Bioinformatics analysis to link TILRR effects on gene expression profiles and disease |
| Organisation | University of Sheffield |
| Department | Sheffield Institute for Translational Neuroscience (SITraN) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Identification of the regulatory protein, provided the relevant Knockout mice, provided financial support for the initial microarray analysis which was used as the basis for the bioinformatics analysis. |
| Collaborator Contribution | Bioinformatics analysis confirmed by wetlands experiments. Supervising of 2 students on the project. |
| Impact | An abstract has been submitted to a meeting, and a manuscript is in preparation. |
| Start Year | 2018 |
| Description | Computational evaluation of statistical approaches |
| Organisation | University of Leicester |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise in regulatory networks. |
| Collaborator Contribution | Expertise in computational modelling and analysis |
| Impact | 4 publications, 2 conference proceedings, 1 paper in preparation |
| Start Year | 2014 |
| Description | Computational modelling |
| Organisation | University of York |
| Department | Department of Electronics |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Data and expertise on cell signalling |
| Collaborator Contribution | Expertise in computational modelling of immune networks |
| Impact | This is a interdisciplinary collaboration including biology and computational modelling. The project has focused on agent based computational modelling of the NF-kB pathway and has included comparisons of different approaches in relation to statistics and predictions. In part the project has involved model development and testing which has benefited expansion of the in silico model of the NF-kB network. The collaboration has included co-supervision of one PhD student, now at a permanent faculty post. It has produced 6 publications, and abstracts and conference presentations. |
| Start Year | 2010 |
| Description | Control of Signal transduction through alterations in receptor complex composition |
| Organisation | Chinese Academy of Sciences |
| Department | Guangzhou Institute of Biomedicine and Health |
| Country | China |
| Sector | Public |
| PI Contribution | identification of novel regulatory components and complexes |
| Collaborator Contribution | The collaborators are creating cell specific knockouts and point mutations using CRISPR CAS9 |
| Impact | A collaborative project is expected to be completed in July 2017. The CRISPR knockouts have been characterised in the collaborators laboratory. The project has been expanded. |
| Start Year | 2016 |
| Description | Developing novel therapeutic targets |
| Organisation | AstraZeneca |
| Department | MedImmune |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Characterisation of potential targets |
| Collaborator Contribution | Expertise in antibody development and characterisation |
| Impact | None yet |
| Start Year | 2018 |
| Description | Developing novel therapeutic targets |
| Organisation | Cancer Research UK |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Characterisation of potential targets |
| Collaborator Contribution | Expertise in antibody development and characterisation |
| Impact | None yet |
| Start Year | 2018 |
| Description | Efficacy of chemotherapy |
| Organisation | University of Sheffield |
| Department | Department of Oncology and Metabolism |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Development of Akt blocking siRNAs and antibodies |
| Collaborator Contribution | Automatic screening of patient samples |
| Impact | None yet |
| Start Year | 2019 |
| Description | Genotyping |
| Organisation | University of Connecticut |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Identification of novel regulatory intermediates. |
| Collaborator Contribution | Technical expertise in genetic modification, CRISPR technology and disease models |
| Impact | Information on genetic modifications, has been included in the in silico model. Results from the collaboration are included in a manuscript published 2017 in JACCbts listed in "publications". |
| Start Year | 2015 |
| Description | Identification of post-translational networks using proteomics |
| Organisation | University of Sheffield |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise in Toll-like/IL-1 receptor function and signal transduction |
| Collaborator Contribution | The collaborators have expertise in quantitative mass spectrometry. |
| Impact | No publications yet. Initial experiments demonstrate the feasibility of using this technology to identify a wide range of phosphorylation changes affected by IL-1 receptor regulated signal amplification, and to investigate the global impact of the IL-1RI/TILRR complex on regulatory networks. Data have confirmed the impact of the TILRR co-receptor on signalling events identified through biochemical assays and predicted by in silico simulations. |
| Start Year | 2015 |
| Description | In vivo analysis to define the role of TILRR in cancer development |
| Organisation | University of Sheffield |
| Department | Department of Oncology and Metabolism |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | In vitro data demonstrating the significance of the TILRR protein in relevant signal transduction events. |
| Collaborator Contribution | Knowledge and experience with in vivo models of tumour growth and metastasis |
| Impact | No outputs yet |
| Start Year | 2018 |
| Description | Inflammatory responses in vascular disease |
| Organisation | University of Sheffield |
| Department | Department of Infection, Immunity and Cardiovascular Disease |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise in TIR receptor function and NF-kB signalling |
| Collaborator Contribution | Knowledge of in vivo models of disease and clinical expertise |
| Impact | This collaborative project establishes a central role for the IL-1RI co-receptor TILRR in development of atherosclerosis and lung fibrosis, and examines the potential of TILRR as a novel therapeutic target in vascular disease, using in vivo experimentation. A manuscript describing the findings has been published in JACCbts, 2017. In addition, the data have been published in 10 abstracts, proceedings and presented in invited talks. |
| Start Year | 2012 |
| Description | Integrative modelling of transcriptional networks |
| Organisation | University of Sheffield |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise in receptor function and in regulation of signal transduction networks. |
| Collaborator Contribution | The collaborators are experts in integrative modelling which will be used to identify transcriptional networks controlled by alterations in the IL-1 receptor complex. |
| Impact | No publications yet. An initial set of simulations using well established models have produced IL-1RI transcriptional networks diagrams and correlated with microarray data. |
| Start Year | 2015 |
| Description | Interdisciplinary studies on mechanisms of TILRR control of NF-kB regulated responses |
| Organisation | University of Sheffield |
| Department | Department of Computer Science |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Biological data focusing on characterisation of signal amplification |
| Collaborator Contribution | Developing a computational model using the biological data provided |
| Impact | Characterisation of the co-receptor TILRR is expected to be of interest to a range of scientists-- the interdisciplinary approach has allowed us to in great detail assess the impact of signal amplification at several levels of pathway activation. The projects have included co-supervision of 1 PhD student and 4 research associates. It has produced a comprehensive agent based computational model of the NF-kB pathway, 10 publications, one manuscript in preparation. |
| Description | NF-kB inhibition |
| Organisation | MRC-Technology |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Identification of novel regulatory component and knowledge of function |
| Collaborator Contribution | technical expertise, monoclonal antibody production |
| Impact | Production of monoclonal antibodies, targeting receptor induced amplification of NF-kB. |
| Start Year | 2013 |
| Description | NF-kB signalling and gene regulation in tumour development |
| Organisation | University of Sheffield |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise in NF-kB signal transduction and gene regulation |
| Collaborator Contribution | Expertise in in vitro and in vivo models and clinical oncology |
| Impact | The initial collaboration included co-supervision of a PhD student who graduated 2016. A manuscript describing the findings is in preparation. The collaboration has recently been expanded to include clinical oncolgists. An outline application was approved by CRUK, and a full proposal has been submitted and is currently in review. Experiments have included using TILRR KO cells and data has contributed to aspects of computational modelling of NF-kB. |
| Start Year | 2013 |
| Description | Regulation of cell signalling through membrane proteins /extracellular matrix binding |
| Organisation | University of Sheffield |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise in regulation of receptor function and signal transduction through the extracellular matrix and the cytoskeleton. |
| Collaborator Contribution | Expertise in Force Spectrometry and Atomic Force Microscopy (AMF). |
| Impact | This is an interdisciplinary project including the Departments of Physics. The study has identified differences in binding of specific cell surface proteins to extracellular matrix components, known to impact cell responses. A next set of studies will use this findings to design in vitro experiments to determine the impact of these extracellular interactions in control of signal transduction. A PhD student which has been co-supervised by the PIs is completing his thesis. The work has enable identification and measuring of forces controlling call matrix interactions under various conditions and has been presented at national meetings. It is expected that the work will be published in 3 collaborative papers. Student graduated in 2018. I conference proceedings paper has been published and one manuscript has been submitted. The data resulting from the collaboration constitute the basis for a collaborative grant application to the EPSRC |
| Start Year | 2013 |
| Description | University of Sheffield |
| Organisation | University of Sheffield |
| Department | Department of Journalism Studies |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | NF-kB signalling. |
| Collaborator Contribution | Map kinase signalling, robotic screening |
| Impact | 11 published papers |
| Description | Benaroya Research Institute, Seattle |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | followed by questions and discussion potential collaborations |
| Year(s) Of Engagement Activity | 2013 |
| Description | Integrated Biology Conference |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Member of conference organising committee |
| Year(s) Of Engagement Activity | 2016 |
| Description | International Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Organizing committee member Invited Conference talk |
| Year(s) Of Engagement Activity | 2016 |
| Description | Invited Talk University of Cambridge |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at Biochemistry Dept at University of Cambridge, to present recent findings and discuss collaborations |
| Year(s) Of Engagement Activity | 2015 |
| Description | Invited Talk at Guangzhou Institutes of Biomedicine and Health Chinese Academy of Science |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Invited Talk and continue collaborative work. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invited discussions at the University of Connecticut |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited to discuss recent projects and collaborations. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invited talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Conference in Paris |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Research Conference |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited talk at Virginia Commonwealth Unviersity |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invitation to give a talk to present recent data at the medical school and to discuss future collaborations with members of the faculty. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Krebs Institue Sheffield |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other academic audiences (collaborators, peers etc.) |
| Results and Impact | talk sparked questions and discussion initiation of a collaboration |
| Year(s) Of Engagement Activity | 2012 |
| Description | National scientific meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentations at the British Atherosclerosis society |
| Year(s) Of Engagement Activity | 2013,2014,2015 |
| Description | Royal Society International Seminar on Bridging the Gap between Experimental and Computational Immunology |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | exchanging knowledge and expertise on variety of systems Continued collaborations - new contacts |
| Year(s) Of Engagement Activity | 2012 |
| Description | University of Manchester |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | talk sparked questions and discussion started discussing potential collaboration which is ongoing |
| Year(s) Of Engagement Activity | 2011 |