Dynamics and Function of the NF-kB Signalling System
Lead Research Organisation:
University of Warwick
Department Name: Warwick Systems Biology Centre
Abstract
A major challenge in biology is to understand how cells recognize external signals and give appropriate responses. Now that the sequence of the human genome is complete, it is important to assign functions to each gene and to identify the corresponding proteins that control key cellular functions. White and colleagues pioneered the development of microscopy-based methods for the visualization and timelapse measurement of biological processes in single living cells. We have used natural light-emitting proteins from fireflies, jelly fish and fluorescent corals. Synthesis (expression) of these proteins causes mammalian cells to become luminescent (light emitting in the dark) or fluorescent (change the colour of light). By placing the gene that codes for a luminescent protein next to a promoter that controls a gene of interest, we can use luminescence from living cells as a way of measuring when the gene of interest is normally switched on and off. Fluorescent proteins have also been used to genetically label proteins of interest, so that the movement of the protein can be visualized in a living cell. White and colleagues previously used timelapse fluorescence and luminescence microscopy coupled to computer simulations to investigate cell decision making. We discovered that a set of important signalling proteins, called NF-kappaB, move repeatedly into and out of the nucleus of the cell, suggesting that cells may use proteins as timers to encode complex messages (like Morse Code). This was a surprise since the original NF-kappaB protein, p65, was discovered 20 years ago and was thought to act as a simple switch that moves into the nucleus once to activate genes. Only timelapse measurements in single living cells were able to see this. The NF-kappaB system is widely recognised as crucial to the control of important cellular processes including both cell division and cell death. It is implicated as being involved in a variety of diseases, such as cancer and inflammatory disease. We will now develop a substantial systems biology project to study all of the components of this complex system. While the previous work has provided major insights, we now need a far broader range of integrated experimental tools to study it. Also the use of mathematical models to make computer predictions will be critical to help us to visualize how this system works. We will make accurate measurements of the (much larger) set of proteins that are involved in NF-kappaB signalling and the genes that are controlled by these signals. The (very experienced) project team includes bioinformaticians, cell biologists, computer scientists, mathematicians, molecular biologists, microscopists and protein chemists. The project will be managed in a structured and organized way, so that the mathematical modelling can be used to predict and design the biological experiments. A central team of experimental officers will be responsible for coordinating the experiments, data and model storage and communication of information between team members. We will study the numbers of molecules of each of the NF-kappaB proteins in the cell, their stability, chemical states and interactions with each other and with other proteins. We will also study in detail which genes that they bind to and control. We will also aim to understand how single protein molecules acting at single genes can act to control decisions of cell life and death. This multidisciplinary approach is essential in order to understand this complex system. A further aim of the project is to provide training for post-docs and students. In this respect, we will benefit from sponsorship of training courses and symposia by the instrumentation companies Carl Zeiss, Hamamatsu Photonics, Coherent and Nano Imaging Devices. The project will also benefit from ongoing collaborations with Genetix and AstraZeneca
Technical Summary
We will develop an integrated systems biology programme to analyse the dynamic and physiological function of the NF-kappaB signalling system. We previously applied iterative real-time imaging and mathematical modelling approaches to show that the NF-kappaB system is oscillatory and uses delayed negative feedback to direct nuclear to cytoplasmic cycling of transcription factor(s) that regulate gene expression. Our recent work has made clear how little is currently understood about even the core parts of the NF-kappaB system and only included a small subset of the NF-?B proteins and feedback loops. We will develop and apply a set of quantitative experimental tools coupled to an intensive theoretical analysis to properly analyse the dynamic function of the system. A key question is how cells achieve appropriate cell fate decisions in response to time-varying signals. Our team includes the expertise to measure and simulate the important processes involved in the core NF-?B network and is supported by leading technology companies.. The experimental work (involving network perturbations) will integrate dynamic cell and single molecule imaging, quantitative proteomics (for measurement of absolute protein and phosphoprotein levels and rates of turnover), chromatin immunoprecipitation (ChIP) analysis (for the dynamics of NF-kappaB binding to target promoters) and RT-PCR and DNA microarray analysis (for measurement of endogenous gene expression). The theoretical work will develop: 1) new data analysis tools to interpret and direct experimental strategy, 2) deterministic and 3) stochastic mathematical models of the system. The computer simulations will develop new experimentally testable hypotheses. Our goal is complete understanding of this complex and non-linear system. We will determine how the set of complex feedback loops controls NF-kappaB dynamics and controls downstream gene expression in the nucleus and how it operates at the single molecule/gene level.
Publications
Adamson A
(2016)
Signal transduction controls heterogeneous NF-?B dynamics and target gene expression through cytokine-specific refractory states.
in Nature communications
Domijan M
(2015)
Using constraints and their value for optimization of large ODE systems.
in Journal of the Royal Society, Interface
Domijan M
(2016)
PeTTSy: a computational tool for perturbation analysis of complex systems biology models.
in BMC bioinformatics
Dunham LSS
(2017)
Asymmetry between Activation and Deactivation during a Transcriptional Pulse.
in Cell systems
Feillet C
(2015)
Coupling between the Circadian Clock and Cell Cycle Oscillators: Implication for Healthy Cells and Malignant Growth.
in Frontiers in neurology
Feillet C
(2014)
Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle.
in Proceedings of the National Academy of Sciences of the United States of America
Feillet Celine
(2015)
Coupling between the circadian clock and cell cycle oscillators: implication for healthy cells and malignant growth
in FRONTIERS IN NEUROLOGY
Finkenstädt B
(2013)
Quantifying intrinsic and extrinsic noise in gene transcription using the linear noise approximation: An application to single cell data
in The Annals of Applied Statistics
Finkenstädt B
(2008)
Reconstruction of transcriptional dynamics from gene reporter data using differential equations.
in Bioinformatics (Oxford, England)
Description | This grant was joint with Manchester and other universities. The project PI is Professor Mike White (Manchester) and the Key Findings Report has been uploaded with his report on this grant. |
Exploitation Route | See above |
Sectors | Healthcare,Pharmaceuticals and Medical Biotechnology |
URL | http://www.davidrand.co.uk |
Description | This grant was joint with Manchester and other universities. The project PI is Professor Mike White (Manchester) and the Narrative Impact has been uploaded with his report on this grant. |
Sector | Healthcare,Pharmaceuticals and Medical Biotechnology |
Description | BBSRC Grouped |
Amount | £246,768 (GBP) |
Funding ID | BB/I004521/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2010 |
End | 06/2013 |
Description | BBSRC Grouped |
Amount | £654,256 (GBP) |
Funding ID | BB/G005699/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 10/2008 |
End | 02/2012 |
Description | BBSRC Grouped CCCC |
Amount | £246,768 (GBP) |
Funding ID | BB/I004521/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2010 |
End | 06/2013 |
Description | EPSRC Responsive Mode |
Amount | £356,217 (GBP) |
Funding ID | EP/P019811/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 04/2017 |
End | 04/2020 |
Description | Wellcome Trust, The |
Amount | £177,880 (GBP) |
Funding ID | 091688/D/10/Z |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 09/2010 |
End | 09/2015 |
Title | PeTTSy (Perturbation Theory Toolbox for Systems) |
Description | This is a GUI based Matlab toolbox which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation based models. |
Type Of Technology | Webtool/Application |
Year Produced | 2015 |
Impact | Has enabled analysis of complex dynamics of big systems that was not possible before. |
URL | http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/ |
Title | ReTrOS: Reconstructing Transcription Open Software |
Description | Matlab based software to reconstruct transcription profiles e.g. from time-course (LUC-, GFP- etc) imaging data. Written in Matlab 2009b, and distributed with test data. A paper on this has now been published: 123. Giorgos Minas, Hiroshi Momiji, Dafyd J Jenkins, Maria J Costa, David A Rand and Bärbel Finkenstädt. ReTrOS: A MATLAB Toolbox for Reconstructing Transcriptional Activity from Gene and Protein Expression Data. BMC Bioinformatics (2017) 18:316 DOI 10.1186/s12859-017-1695-8. |
Type Of Technology | Webtool/Application |
Year Produced | 2010 |
Impact | Mainly used by biological community. |
URL | http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/ |
Title | Spectrum Resampler |
Description | A period fitting algorithm with a graphical front end for Matlab, which imports periodic time series data from Microsoft Excel xls files. This work was produced in collaboration with the Universities of Liverpool and Edinburgh, as part of the ROBuST project, funded by BBSRC and EPSRC under the SABR initiative. |
Type Of Technology | Webtool/Application |
Year Produced | 2014 |
Impact | Enables calculation of period with rigorous error estimates. Used within biological and biomedical communities studying circadian oscillations. |
URL | http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/ |
Description | BIOMS Symposium 2018 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Keynote Lecture. BIOMS Symposium 2018, BioQuant, University of Heidelberg, October, 2018. Title: Multiplexing information flow through dynamic signalling systems |
Year(s) Of Engagement Activity | 2018 |
Description | Invited Lecture, Modelling signalling systems. British Toxicology Society Annual Congress, Solihull, UK, April 2015. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | British Toxicology Society Annual Congress. Toxicity is a major concern for Pharma and this talk enabled me to make contact with a wide range of people from Pharma and related areas. |
Year(s) Of Engagement Activity | 2015 |
Description | Invited Lecture, Oberwolfach Meeting June, 2017. |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | Invited Lecture, Oberwolfach Meeting on Reaction Networks and Population Dynamics, June, 2017. |
Year(s) Of Engagement Activity | 2017 |
Description | Invited Spring School Lectures at CompSysBio Spring School. Aussois, France. March 2017 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Two Invited Spring School Lectures. Information and Decision-Making in Dynamic Cell Signalling. |
Year(s) Of Engagement Activity | 2017 |
URL | https://project.inria.fr/compsysbio2017/ |
Description | Keynote Lecture. 2016 Information and Decision-Making in Dynamic Cell Signaling. IEEE International Conference on Bioinformatics and Biomedicine, Shenzhen, China. December, 2016. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Enabled contact/collaboration with professional/industry keen to collaborate in the bioinformatics are and enabled me to get over to them the new opportunites that recent mathematical developments allow. |
Year(s) Of Engagement Activity | 2016 |
Description | Lecture to UK Plant and Algal Clocks workshop, 16-17 April 2018 Edinburgh |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Lecture to UK Plant and Algal Clocks workshop, 16-17 April 2018 Edinburgh. Title: Modelling & measuring the stochasticity in circadian clocks: information theory, new methodology & measuring clock function |
Year(s) Of Engagement Activity | 2018 |
Description | Mini-symposium on Multi-scale Mathematical Models in Endocrinology. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited Lecture, ECMTB 2018 Stochastic transcriptional dynamics and spatial signalling for the prolactin gene in single cells and tissue. Mini-symposium on Multi-scale Mathematical Models in Endocrinology. |
Year(s) Of Engagement Activity | 2018 |
Description | Open Evening panel discussion and questions: "Did you know chemotherapy can be less toxic based on the time of day it's delivered?" |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Organised as part of our recent international scientific meeting "Medicine in the 4th Dimension" July 2016. Chaired by a scientific journalist panel contained oncologists, scientists, patients, psychologist. I was a panel member. A local charitable donor who has supported us attended. |
Year(s) Of Engagement Activity | 2016 |
Description | Plenary Lecture, International Conference on Systems Biology (ICSB14), Melbourne, September 2014. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Primed collaborations with biologists and clinicians (particularly oncologists). Enabled communication with patients groups. |
Year(s) Of Engagement Activity | 2014 |
Description | Plenary Lecture, Probing the cell's dynamic regulators and their coupling: clocks, signals and the cell cycle. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | European Conference on Mathematical and Theoretical Biology (ECMTP), Gothenburg, Sweden, June 2014. |
Year(s) Of Engagement Activity | 2014 |
Description | SysmedIBD Satellite Symposium |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | SysmedIBD Satellite Symposium in IBD took place at the premises of ECI Congress in Vienna on 5-6 September 2015. |
Year(s) Of Engagement Activity | 2015 |
URL | https://www.sysmedibd.eu/home/index267c.html?L=2998 |
Description | SysmedIBD Spring School |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | The SysmedIBD Spring School was organized at Palazzo Pesaro-Papafava in Venice, Italy on 7-11 March 2016. |
Year(s) Of Engagement Activity | 2016 |
URL | https://www.sysmedibd.eu/home/index267c.html?L=2998 |