Quantification of dynamic biological systems: formation, function and stability of ensemble behaviour

Lead Research Organisation: Swansea University
Department Name: School of Engineering

Abstract

The main focus of this project is to experimentally investigate and mathematically describe emergent properties of a large cellular system. A large cellular population is a complex dynamical system far from equilibrium, where macro-dynamics are driven by interactions and heterogeneity at the systems micro- or cell-level. Understanding exactly how microstate properties instigate and perpetuate emergent macroscopic phenomena is one of the fundamental challenges facing contemporary biology today.

Quantifying such symbiotic relationships is at the heart of many scientific research endeavours. This broad scientific area covers an equally matched myriad of length scales, ranging from spontaneous symmetry breaking at the sub-atomic level through to galactic cluster formation at the cosmic scale. For the most part, formations of emergent configurations in these systems are intrinsically linked to non-linear interactions between the individual components that together constitute the complex system. It has been established that many of the confounding features of such systems can be adequately described through the application of statistical mechanics. The mathematical methodology can encapsulate and link macroscopic descriptions of the system to that of the microstate, allowing emergent ensemble behaviours to be quantified.

Large cellular populations fulfil all necessary criteria to be considered a complex system (i.e. the cell being the systems microstate); constituent cells are vast number; cells are heterogeneous in physical, biological function; cell-cell and cell-environment interactions are inherently nonlinear. Adherence of the microstates to these criteria promotes the formation of emergent behaviour at the cellular population level; significant examples include embryo development, tissue regeneration during wound healing and the proliferation of metastatic diseases.

However, application of statistical mechanics to describe and predict large-scale cellular systems have been hampered due to the fact that (i) such systems are in a state of non-equilibrium exhibiting vast heterogeneity across constituent microstates, simply averaging over ensemble variability results in distorted macroscopic system view and (ii) the ability to identify, track and quantify significant numbers of individuals within a cellular population to assess and account for microstate variability has been hindered by the availability of high-throughput microscopy platforms. Together these issues have obstructed application of statistical mechanics methods to elucidate upon the formation, function and stability of ensemble behaviour of a complex cellular system.

The work presented as part of this EPSRC first grant application will address this current shortfall in scientific application and understanding. Recent advances in high-throughput microscopy present an opportunity to collate detailed information of microstate behaviour and allow development of mathematical models to describe the system. This interdisciplinary proposal seeks to unify contemporary biology, advanced imaging and statistical mathematics in order to measure and track the evolving interactions, dynamics and fate of >100,000 individual cells over extended periods. This databank will provide invaluable information, detailing microstate quantities such as morphology, biological function and spatial correlation and will further allow realisation of stochastic and master equation descriptions of the large-scale cellular system in question. Furthermore, this will ensure system variability is incorporated within models at the outset, providing robust linkage between the systems micro- to macro-levels and allowing sources of emergent phenomena to be more accurately described and predicted.

Planned Impact

Who will benefit from this research?

One of the major challenges that contemporary biology faces today is to go beyond identifying life's basic elements and explain the formation, function and stability of emergent biological organization across length scales. In order to tackle this behemoth task a pragmatic approach must be adopted by breaking down and focusing investigations at the cellular scale. Emergent behaviour at this level dictates the function and structure of tissues, organs and ultimately us. Projects such as this are the only way we can hope to unravel the complex physics of life. The methodology presented statistically quantifies the final determined state of the system (tissue/organ) and analyses the biophysical route taken by constituent cells in its formation. Principles beneficiaries of the project in the medium to long-term will be patients (in the UK mainly NHS patients), suffering from the tissue or organ malfunction. These include patients suffering from metastatic disease, currently a major cause of morbidity and mortality in our aging Western society, patients suffering from respiratory disorders (responsible for 68,000 deaths in 2010 alone), such as pulmonary fibrosis or emphysema. The mechanical behaviour of lung tissue in the latter emerges as a macroscopic phenomenon from the interactions of its microscopic components; however the mechanism is neither intuitive nor easily understood.

The data and models developed will be employed to:
1) Assess cellular movement and identify highly motile sub-factions that have higher propensity for adjacent tissue invasion
2) Aid prognosis, treatment and drug design to combat the onset and spread of these diseases.

Other benefactors include those needing skin grafts; fundamental concepts of the grant are directly related to tissue regeneration during wound healing and cicatrisation. Treatment of patients with these diseases represents a serious healthcare issue and is currently a significant financial burden to the NHS. Embryogenesis is the exemplar of coordinated or emergent behaviour at the cellular level directly reflecting the main theme of the proposal. It is envisaged that the work undertaken by the project will enhance understanding of the dominant intracellular interactions this will aid treatment and therapies for early fetal dysfunction.

How will they benefit from this research?

In addition to the benefit to patients from improved tests and hence better treatments, a principal benefit would be to their clinicians who would obtain more reliable, timely information regarding responses to on-going treatment or disease progression (better information, better care). Companies in the medical device technologies sector will also benefit. Significant commercial opportunities exist for the production of commercially available forms of new tests for the aforementioned disease, both within hospital settings and more widely as the basis for point of care testing in GP surgeries, clinics or, eventually, the homes of outpatients. The opportunities are global due to demographic change and the increasing incidence of tissue abnormalities linked to the acquisition of westernised life-style and diets.

The impact this area of the applicant's research has already been demonstrated at GE Healthcare, where he was approached by GE Healthcare to disseminate details of his current research at the 2012 Cellular Technologies Symposium in Albany, New York and the inaugural European Cell Technologies Symposium (Cardiff 2013). Through these interactions the applicant was requested to highlight and identifying important research areas that GE Healthcare should target in the next decade. The applicant has been given £13,500 in-kind to further his research in conjunction with GE Healthcare.

Publications

10 25 50
 
Description We have developed new biological and imaging protocols to robustly characterise to evolution of large cellular systems (the necessary intimidate step between cell and tissue). Additionally, we have developed a suite of numerical analysis that is able to acquire information from the vast datasets and configure appropriate mathematical models of the cellular system under controlled (ideal) and perturbed (pharmacologically perturbed) constraints.
Exploitation Route First and foremost we have developed imaging and biological protocols that allow robust access to large cellular systems at a temporal resolution that can capture important biological checkpoints. Additionally, we are (in conjunction with project partners) disseminating this knowledge to the wider community. Furthermore, we are developing mathematical models that are able to imitate and predict emergent properties of the control and perturbed cellular systems.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description Blood Diagnostics
Amount £999,726 (GBP)
Funding ID EP/N013506/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 02/2016 
End 01/2021
 
Description EPSRC First Grant Collaborators 
Organisation Broad Institute
Department Imaging Platform
Country United States 
Sector Charity/Non Profit 
PI Contribution We have driven both the imaging and mathematical development of the project. The imaging was challenging in this project; we were seeking to contiguously image a large cellular population (~100000 individual cells) at a frequency of 30 minutes for up to 5-7 days. We had to re-address the timescale of the project to compensate for significant set backs in the imaging fidelity (we asked for a 3 month extension to the project, which was granted). We are currently writing a series of papers to disseminate the project outcomes.
Collaborator Contribution GE Healthcare and Cardiff University were key collaborators in the acquisition and maintenance/health of the cellular system. Together we have developed new biological and imaging protocols to ensure high-throughput, large-scale imaging can be achieved. Collaborators at both Oxford and Eotvos have been instrumental in helping develop mathematical models of our cellular system. We are in the process of writing a suite of papers to disseminate to the scientific community.
Impact Multidisciplinary - reference to all project partners CYTO 2015 Presentations Examining Inheritance during Mitosis, in U-2OS cells, using Quantum Dot Labelled Vesicles. Characterising the Heterogeneity of Inheritance Across Mitosis
Start Year 2014
 
Description EPSRC First Grant Collaborators 
Organisation Cardiff University
Department School of Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution We have driven both the imaging and mathematical development of the project. The imaging was challenging in this project; we were seeking to contiguously image a large cellular population (~100000 individual cells) at a frequency of 30 minutes for up to 5-7 days. We had to re-address the timescale of the project to compensate for significant set backs in the imaging fidelity (we asked for a 3 month extension to the project, which was granted). We are currently writing a series of papers to disseminate the project outcomes.
Collaborator Contribution GE Healthcare and Cardiff University were key collaborators in the acquisition and maintenance/health of the cellular system. Together we have developed new biological and imaging protocols to ensure high-throughput, large-scale imaging can be achieved. Collaborators at both Oxford and Eotvos have been instrumental in helping develop mathematical models of our cellular system. We are in the process of writing a suite of papers to disseminate to the scientific community.
Impact Multidisciplinary - reference to all project partners CYTO 2015 Presentations Examining Inheritance during Mitosis, in U-2OS cells, using Quantum Dot Labelled Vesicles. Characterising the Heterogeneity of Inheritance Across Mitosis
Start Year 2014
 
Description EPSRC First Grant Collaborators 
Organisation Eotvos Lorand University
Country Hungary 
Sector Academic/University 
PI Contribution We have driven both the imaging and mathematical development of the project. The imaging was challenging in this project; we were seeking to contiguously image a large cellular population (~100000 individual cells) at a frequency of 30 minutes for up to 5-7 days. We had to re-address the timescale of the project to compensate for significant set backs in the imaging fidelity (we asked for a 3 month extension to the project, which was granted). We are currently writing a series of papers to disseminate the project outcomes.
Collaborator Contribution GE Healthcare and Cardiff University were key collaborators in the acquisition and maintenance/health of the cellular system. Together we have developed new biological and imaging protocols to ensure high-throughput, large-scale imaging can be achieved. Collaborators at both Oxford and Eotvos have been instrumental in helping develop mathematical models of our cellular system. We are in the process of writing a suite of papers to disseminate to the scientific community.
Impact Multidisciplinary - reference to all project partners CYTO 2015 Presentations Examining Inheritance during Mitosis, in U-2OS cells, using Quantum Dot Labelled Vesicles. Characterising the Heterogeneity of Inheritance Across Mitosis
Start Year 2014
 
Description EPSRC First Grant Collaborators 
Organisation GE Healthcare Limited
Country United Kingdom 
Sector Private 
PI Contribution We have driven both the imaging and mathematical development of the project. The imaging was challenging in this project; we were seeking to contiguously image a large cellular population (~100000 individual cells) at a frequency of 30 minutes for up to 5-7 days. We had to re-address the timescale of the project to compensate for significant set backs in the imaging fidelity (we asked for a 3 month extension to the project, which was granted). We are currently writing a series of papers to disseminate the project outcomes.
Collaborator Contribution GE Healthcare and Cardiff University were key collaborators in the acquisition and maintenance/health of the cellular system. Together we have developed new biological and imaging protocols to ensure high-throughput, large-scale imaging can be achieved. Collaborators at both Oxford and Eotvos have been instrumental in helping develop mathematical models of our cellular system. We are in the process of writing a suite of papers to disseminate to the scientific community.
Impact Multidisciplinary - reference to all project partners CYTO 2015 Presentations Examining Inheritance during Mitosis, in U-2OS cells, using Quantum Dot Labelled Vesicles. Characterising the Heterogeneity of Inheritance Across Mitosis
Start Year 2014
 
Description EPSRC First Grant Collaborators 
Organisation University of Oxford
Department Mathematical Institute Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution We have driven both the imaging and mathematical development of the project. The imaging was challenging in this project; we were seeking to contiguously image a large cellular population (~100000 individual cells) at a frequency of 30 minutes for up to 5-7 days. We had to re-address the timescale of the project to compensate for significant set backs in the imaging fidelity (we asked for a 3 month extension to the project, which was granted). We are currently writing a series of papers to disseminate the project outcomes.
Collaborator Contribution GE Healthcare and Cardiff University were key collaborators in the acquisition and maintenance/health of the cellular system. Together we have developed new biological and imaging protocols to ensure high-throughput, large-scale imaging can be achieved. Collaborators at both Oxford and Eotvos have been instrumental in helping develop mathematical models of our cellular system. We are in the process of writing a suite of papers to disseminate to the scientific community.
Impact Multidisciplinary - reference to all project partners CYTO 2015 Presentations Examining Inheritance during Mitosis, in U-2OS cells, using Quantum Dot Labelled Vesicles. Characterising the Heterogeneity of Inheritance Across Mitosis
Start Year 2014
 
Company Name Cellometry 
Description Provides bespoke analysis from high-throughput imaging platforms, i.e. flow cytometry, image cytometry and microscopy 
Year Established 2014 
Impact None so far
 
Description CYTO 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact to fill in
Year(s) Of Engagement Activity 2015
URL http://cytoconference.org/2015/Home.aspx
 
Description Pharmaceutical Flow Cytometry and Imaging Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact to fill in
Year(s) Of Engagement Activity 2014
URL http://www.elrig.org