Stem Cell Dynamics: Exploration of the Stem Cell attractor Landscape

Lead Research Organisation: University of Sheffield
Department Name: Automatic Control and Systems Eng

Abstract

Stem cells have the unique ability to transform into any cell to make every type of tissue in the human body.
The growth and transformation of an embryo into a human body is an amazing self-assembling process in which stem cells are not only building blocks but also builders. The blueprint of the final edifice is inscribed in every single cell. Each cell has to read and interpret this blueprint, according to its positional information and environmental signals. As a result the cell may decide to keep its options open, self-renew and proliferate or become a mature cell and assume a specific role as a neuron, liver or heart cell for example.
In recent years no other field of science has captured our imagination more than stem cell research. The possibility to use both adult and embryonic stem cells to engineer and regenerate tissues and organs, develop therapies for degenerative conditions such as Alzheimer?s and Parkinson?s disease, multiple sclerosis, retinal degeneration, diabetes and ischemic heard disease represents probably the most significant and exciting advance in medical science that society has ever seen.
The biggest challenge in pursuit of this vision is to understand the mechanisms and factors that influence the decision of a stem cell to differentiate into a specific cell type i.e. liver cell, neuron etc.
Stem cells have been isolated from different sources and are currently grown and maintained in vitro.
However,the lack of a quantitative understanding of
the complex processes underlying cell fate determination means that it has been difficult to engineer robust and specific lineages from stem cells grown in vitro. In order to use in vitro differentiated ES cells for human stem cell therapies, it is imperative to derive mathematical models of stem cells that will aid the understanding of their behaviour and will allow the development of effective strategies to manipulate stem cell fate.
This project aims to apply mathematical modelling and analysis techniques, which are routinely used by systems engineers, to study the behaviour of embryonic stem cells in order to understand the mechanisms that control the ability of stem cells to choose between self renewal and differentiation.

Technical Summary

Cultures of human embryonic stem cells are typically heterogeneous including both the undifferentiated stem cells and their spontaneously differentiated derivatives. It has also become apparent that the undifferentiated stem cells themselves may exist in a number of interchangeable substates comprising the stem cell compartment. The underlying hypothesis of the project is that the behaviour of human ES cell populations depends upon stochastic events relating the interconversion of undifferentiated stem cells between a number of metastable states as well as positive and negative signalling arising both from ES cells in those different substates and their differentiated derivatives. The project proposes to apply qualitative and quantitative modeling and analysis techniques, developed for nonlinear dynamical systems, to identify criteria to identify the different stem cell substates, to investigate the underlying mechanism responsible for the observed heterogeneity in undifferentiated stem cell cultures and to monitor both the stochastic interconversions of cells between those substates and their propensity to differentiate along distinct lineages.

Publications

10 25 50
 
Description Using time-lapse imaging, modelling and analysis we have identified an characterised a series of bottlenecks that restrict growth of early-passage human embryonic stem cells (hESCs). These bottlenecks also explain why hESCs develop abnormal characteristics during prolonged culture rendering these unsafe for therapy.
Characterisation of barriers that drive the appearance of abnormal hESCs is pivotal for optimizing their maintenance conditions and minimizing the opportunity for expansion of mutated clones that could compromise safety and efficacy for applications in regenerative medicine.
Exploitation Route We have shown that all three bottlenecks to survival of hESCs during passaging can be overcome by using a certain inhibitor which suggests a possible way to overcoming these bottlenecks involving signaling associated with the cytoskeleton. Our findings could be exploited to design culture conditions that minimize the selective advantages of particular mutations and so reduce the occurrence of variant cells during prolonged culture and scale-up.
Sectors Healthcare

URL http://www.cell.com/stem-cell-reports/fulltext/S2213-6711(14)00147-7
 
Description Capital bid
Amount £47,000 (GBP)
Funding ID EP/J013714/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 12/2013 
End 12/2015
 
Description Program Grant
Amount $900,000 (USD)
Funding ID RGP0001/2012 
Organisation Human Frontier Science Program (HFSP) 
Sector Charity/Non Profit
Country France
Start 06/2012 
End 06/2015
 
Title Modelling cell heterogeneity tool 
Description Modelling tool for characterising dynamical mechanisms which underpin heterogeneity of cell populations. It allows inferring a dynamical model based on sequences of distribution functions generated using Fluorescence Activated Flow Cytometry. 
Type Of Material Model of mechanisms or symptoms - human 
Year Produced 2013 
Provided To Others? Yes  
Impact Identification of substates within the stem cell compartment. 
 
Title Motility Analysis 
Description We developed a framework for characterizing quantitatively different cell lines in terms of their motility and colony-forming properties using individual cell trajectories extracted from time-lapse microscopy images. 
Type Of Material Data analysis technique 
Provided To Others? No  
Impact No major impact yet. We have started to apply this framework to characterize motility of polycystic kidney cells under the the influence of different drugs. 
 
Title New algorithms for image segementation and tracking 
Description New algorithms for image segmentation and tracking based on geometric active contours and information theoretic criteria were developed and used to process images obtained from time-lapse experiments and generate data automatically. Previously, because the existing commercial/open source software available did not work well with the phase contrast images generated by the time-lapse experiments carried out in the lab, the imaging data used to be sent to a group in Germany for analysis. 
Type Of Material Improvements to research infrastructure 
Year Produced 2010 
Provided To Others? Yes  
Impact The new algorithms were used to analyse time-lapse images of normal and adapted hESC colonies providing information about the movement type (random difussion, directed diffusion etc) and interactions (number and duration of contacts with other cells) of individual stem cells in vitro. A journal paper which will incorpoare rhe results of these studies is currently in preparation. 
 
Description Centre for Stem Cell Biology 
Organisation University of Sheffield
Department Department of Biomedical Science
Country United Kingdom 
Sector Academic/University 
PI Contribution Developed software for image segmentation and tracking of stem cells in time-lapse experiments. Analysed raw experimental data from a range of experiments. Developed quantitative models that were used for hypothesis testing. Proposed and carried out new experiments
Collaborator Contribution Provided accees to lab facilities and equipment: cell culture facilities, flow citometry equipment, cell imaging/microscopy equipment. Provided embryonic stem cell lines for experiments. Provided training in basic stem cell biology, cell culture, immunochemistry, PCR and the use of laboratory equipment.
Impact All outputs for this discipline hopping fellowship project have resulted from this collaboration. This is a multidsicplinary collaboration between a control engineer and a stem cell biologist.
Start Year 2009
 
Description Stem Cell Australia 
Organisation University of Melbourne
Department Centre for Neuroscience Research
Country Australia 
Sector Academic/University 
PI Contribution Modelling and analysis of experimental data
Collaborator Contribution Single cell QPCR data Microdiscetion and subfractionation experiments
Impact Multidisciplinary collaboration funded by a HFSP program grant started in June 2012 We presented new research results at the 2013 Awardees Meeting in Strasbourg
Start Year 2012
 
Description Modelling Culture Adaptation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Public event organized at the end of the final ESTOOLS annual meeting.

Unknown
Year(s) Of Engagement Activity 2010
 
Description Talk UKACC2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Keynote talk at the 12th UKACC International Conference on Contro.l The scope of the conference is intended to be broad with coverage of theory and applications of control and systems engineering. The talk highlighted how existing methods and tools in control, nonlinear systems and information theory, including system identification, higher-order frequency response and rate-distortion analysis, can be combined with remarkable experimental approaches to elucidate gain adaptation mechanisms and the role of nonlinearity in early visual processing.
Year(s) Of Engagement Activity 2018
URL https://control2018.group.shef.ac.uk/plenary-speakers/daniel-coca/