A systems biology approach to neural crest development: The role of noise in fate choice from bipotent precursors.

Lead Research Organisation: University of Surrey
Department Name: Microbial & Cellular Sciences

Abstract

All the body's different cell types derive from stem or other precursor cells. These precursors are multipotent, having the flexibility to develop into any one of many types of working cells (such as neurons, blood or skin cells). A major problem in developmental biology is to understand how these precursors maintain flexibility and are thus able to generate very different cell types, while at the same time, once the choice of cell-type to adopt has been initiated, they then develop into stable cells of that type. So far, trying to dissect the genetic and non-genetic components involved in this process, known as differentiation, has proven difficult. Despite many advances in the field, the mechanism allowing the fine balance between flexibility of the multipotent stem cell and stability of the differentiated state remains mysterious. In this project we adopt a Systems Biology approach to investigate this issue. Systems Biology approaches rely on the combination of mathematical modelling techniques and experiments, to make progress towards our understanding of the system under study. Within this framework, we plan to collect a variety of experimental data capable of informing detailed dynamical models, which will be used to make predictions to be tested experimentally, and then iteratively refined. In particular we hypothesize that, counter-intuitively, an important factor helping to create alternative fates in the stem cell is 'noise' - random fluctuations in biological processes. Noise originates in many aspects of the biology of gene expression, and of other cellular activities, and accounts for much of the variability that we see in all biological systems. While we imagine that the architecture of genetic components has evolved so as to minimize any negative impact of noise, and make biological systems robust despite its presence, recent theory suggests the unexpected hypothesis that noise is an important factor that is actually required to help drive fate choice. In the context of the cell differentiation process, we will investigate a system of two important pigment cells, black melanocytes and shiny iridophores, descending from a common progenitor cell, in zebrafish. The zebrafish is a very useful model system, because the embryo is transparent and readily allows a visual inspection by using microscope techniques, and because we can readily alter gene activity and see what effects this has on the pigment cells. We will use genetics to discern the key gene interactions underlying development of this pigment cell progenitor. Then we will make detailed measurements using state-of-the-art techniques of the different activities of the relevant genes at different time-points during differentiation. At the same time we will combine this information with a mathematical model of the gene interactions. The experimental studies and the modelling will be developed in parallel and with each informed by the results of the other, so as to reconstruct the gene regulatory network responsible for pigment cell choice from the progenitor. We will also measure the amount of noise affecting the components of this network, and from this information we will be able to develop a deeper understanding of the mechanisms leading to the choice of different fates and the stable differentiation into these two cell types. In particular, we will be able to assess for the first time in the living embryo, the degree to which noise in the system helps or hinders cell differentiation. Understanding these processes has implications well beyond the basic biology we are studying here. In particular, it is important in a medical context, in that this process of stem cells choosing between different cell-types, and the process of stabilisation of these cell-types, is of fundamental importance to understanding the healthy body and how it goes wrong in ageing and in disease. It thus will shed light on the mechanisms underlying congenital diseases and cancer.

Technical Summary

Noise originates in many aspects of the biology of gene expression and accounts for much of the variability that we see in all biological systems. The robustness of such systems, with discrete cell-types stably differentiated, indicates that the architecture of genetic components has evolved to minimize the impact of noise. Counter-intuitively, however, theory predicts that cells may also use dynamical noise to help drive fate specification and commitment processes i.e. understanding noise may be vital to understanding these cellular processes. Thus we propose a study to account for the effects of noise on the Waddington landscape of embryonic development. We will employ an iterative cycle of experimental genetics and quantitative mathematical modelling within a systems biology framework to begin to test this hypothesis in vivo. Our model system, zebrafish pigment cell differentiation, is ideal since this process is genetically well-characterised, easily manipulable, and shares many characteristics with mammals. We will investigate two pigment cell-types, black melanocytes and shiny iridophores, descending from a common progenitor cell, building directly on our recent breakthroughs in modelling the gene regulatory network (GRN) of melanocyte differentiation and in identifying key genetic mechanisms active in the common progenitor. We will identify the topology of the GRN of the common pigment cell progenitor. We will construct in an iterative manner both deterministic and stochastic models of this GRN, using key experimental data obtained in vivo to aid parameter fitting. Mathematical analysis will then allow us to assess the effects of intrinsic and extrinsic noise. This new approach will be widely applicable to understanding fate choice in other stem cell and developmental systems. The detailed understanding we will generate has important implications for lifelong health as the destabilisation of differentiation is strongly linked to aging and cancer.

Planned Impact

This research will contribute directly to the BBSRC's priority areas, including in the short term forming a pioneering in vivo exemplar of the BBSRC's priority areas Systems approach to biological research and Technology development for bioscience. In the medium to long-term, potential healthcare benefits (including improved diagnosis/personalised treatment) resulting from better understanding of basic biological processes are likely to contribute to Aging research and Economic and social impact. Finally, by developing quantitative models of differentiation, we expect to contribute to the priority of 3Rs in research using animals.

Due to its fundamental nature, this research is unlikely in the short term to have major direct benefits to human health or to the UK economy. However, it will be important for developing new techniques for systems biology of vertebrates, for developing in silico models of a medically-important cell-type, the melanocyte, and for understanding a highly medically-relevant process, fate choice in multipotent stem cells. The broader importance of our research lies principally in its interdisciplinary nature, exploring capabilities and limitations of in silico modelling in development. Thus, the most immediate impact will be via transfer of knowledge to other researchers. The most direct beneficiaries will be academic researchers in the zebrafish development and genetics, pigment cell biology, mathematical biology, biological physics and systems biology fields. Researchers in the commercial private sector, including research charities (e.g. CRUK) and the pharmaceuticals/regenerative medicine communities (e.g. Pfizer) will benefit from better understanding gene function in pigment cell development, phenotypic information, much expanded gene regulatory networks (GRNs), methodological advances regarding GRN development and testing and the use of dynamical systems and stochastic processes in development, as well as through secondary use of our data. This will have impact far beyond the immediate biological significance of our research. By reaching these groups of academic and biotechnology researchers, we will influence the quality of life of the UK public, by providing basic research informing our understanding of ageing and disease, and allowing safe and effective use of stem cells.

Policy-makers, including National Centre for 3Rs Research, will benefit in the longer term from developing improved methods for modelling in vivo GRNs; as these models become more sophisticated and quantitative, this will in time help to reduce the numbers of animals used in research.

In the commercial private sector, the data and models generated will be important to the pharmaceutical industry and research charities working on pigmentation disorders and melanoma. Our contribution will be indirect, by showing the value of the interdisciplinary approach we are pioneering, and also direct, towards understanding healthy melanocyte function. This research is vital to our better understanding of abnormal function and to the development of therapies against diseases such as melanoma and Waardenburg syndrome.

Within the public sector, and for the public themselves, our work will contribute to the public understanding of science, especially since pigment cell biology is so 'visual', and thus of interest to organisations such as the Bath Royal Literary and Scientific Institution. Our work could be used to explain the concepts of systems and mathematical biology, and differentiation in health and disease. Because of the relevance to melanoma, this topic could be of considerable interest to the public.

This project will have high impact on PDRA Training, in its combination and integration of innovative techniques in experimental in vivo biology and mathematical modelling. As such, the two PDRAs will obtain a superb training in this increasingly attractive area, making them highly employable in academe or in industry.

Publications

10 25 50
 
Description We have made excellent progress in understanding the problem of noise propagation in developmental GRNs. This has been aided by analysing simple models of stochastic gene expression. The solutions found show that noise-induced bifurcations can take place in the system, even though these happen in the case of bounded noise, but not in the case of Gaussian noise. A first paper has been now published (Aquino and Rocco, Mathematical Biosciences and Engineering, 2020), and we are now extending our findings to more complex GRNs. Together with our collaborators (group of Prof Robert Kelsh, Bath), our development of the dynamical model of the bipotent melano-iridophore pigment cell precursor has made excellent progress, with a core GRN well-defined genetically and a deterministic dynamic model developed. We have expanded our published core melanocyte GRN (Greenhill, Rocco, et al, Plos Genetics 2011) to include roles for Wnt signaling in both fate specification and ongoing differentiation, and have used iterative mathematical modelling to refine our understanding (Vibert, Aquino, et al, Pigment Cell & Melanoma Research, 2016). Likewise, we have been using that same iterative experimental genetics/mathematical modelling approach to reconstruct the GRN responsible for iridophore fate choice from neural crest cells (Petratou et al. Plos Genetics 2019). We have made progress on the multipotent melanocyte/iridophore GRN and have to date an advanced deterministic model that behaves well, and for which we have now developed a full pipeline for bifurcation analysis. Further to this, the analysis performed by our colleagues in Bath and by our collaborator V. Makeev (Moscow) provides the strongest in vivo evidence for a multipotent (as opposed to bipotent), but partially fate-restricted progenitor in zebrafish, a MIXGN cell (Nikaido, Subkhankulova et al., in prep.). Guided by these findings, we are expanding the GRN obtained for the melano-iridophore precursor to incorporate the MIXGN finding, and adapt accordingly our bifurcation analysis pipeline.
Exploitation Route Our findings are being disseminated to the academic community, and we will continue to do so while our results are published. Outputs to date include multiple papers and book chapters published; a Modeling, Noise and Development workshop held between 18-19th May 2017; and 18 posters/talks/invited seminars to date. Our key target audience for this grant is the academic community, so these are listed in full in the Impacts section. Academics from the biosciences community are direct beneficiaries of our research, but also, given the highly interdisciplinary nature of our research, so are those belonging to the mathematics and physics communities. In order to maximise the impact of our research, we held a workshop on "Modeling, Noise and Development" at the University of Bath, with 3 international speakers (see for instance http://www.surrey.ac.uk/mathematical-biology-of-cell-differentiation/modelling-noise-and-development-workshop/ and http://www.bath.ac.uk/events/modeling-noise-and-development/). This was a great success, with several groups encouraging us to organise a follow-on meeting, which we hope to do, given successful bids for funding. We will continue to reach the broader public by using the extensive experience that both the University of Bath and the University of Surrey have in communicating success stories to the media. We will make sure that each publication is accompanied by a press release which will emphasise its importance for the broader public. Our research is very fundamental in its nature, and as such it will probably not have an immediate impact in the close future. However pharmaceutical industries and biotechnological companies (and more in general the private sector) will benefit from the deeper understanding of developmental processes gained with our approach, and from the lessons learned by the successful interdisciplinary combination of quantitative and experimental approaches.
Sectors Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL https://www.surrey.ac.uk/systems-biology-stem-cell-differentiation
 
Description 10th Zebrafish European Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact 10th Zebrafish European Meeting, 3-7 July 2017 Budapest, Hungary, T Subkhankulova, M. Nikaido, A. Kasianov, G. Aquino, H. Schwetlick, T. Sauka-Spengler, A Rocco, V. Makeev and RN Kelsh, Single cell expression profiling of neural crest-derived cells identifies partially-restricted intermediate progenitor cell.
Year(s) Of Engagement Activity 2017
 
Description 12th International Conference on Zebrafish Development and Genetics 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Talk given by K. Petratou: K. Petratou, T. Subhankulova, G. Aquino, H. Schwetlick, A. Rocco, R.N. Kelsh, Constructing gene regulatory networks underlying fate specification of multipotent progenitors in the neural crest. Strong interest manifested by academic colleagues.
Year(s) Of Engagement Activity 2016
 
Description 22nd International Congress of Zoology & The 87th Meeting of The Zoological Society of Japan 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Robert Kelsh gives a talk: K. Petratou, T. Subkhankulova, G. Aquino, J. Lister, H. Schwetlick, A. Rocco, R.N. Kelsh, Constructing gene regulatory networks underlying fate specification of multipotent progenitors in the zebrafish neural crest.Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2016
 
Description 5th European Zebrafish Principal Investigators Meeting, Trento, Italy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Robert N. Kelsh, Tatiana Subkhankulova, Masataka Nikaido, Artem Kasianov, Leonid Uroshlev, Gerardo Aquino, Hartmut Schwetlick, Tatjana Sauker-Spengler, Andrea Rocco, Vsevolod Makeev, Single cell expression profiling identifies pigment cell differentiation trajectories from partially-restricted intermediate pigment progenitor cell
Year(s) Of Engagement Activity 2018
 
Description BGRS\SB-2016, 10th anniversary International Multiconference "Bioinformatics of Genome Regulation and Structure\ Systems Biology" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Tatiana Subkhankulova gives the talk: T. Subkhankulova, G. Aquino, A. Rocco, H. Schwetlick and R.N. Kelsh, Single cell expression profiling of neural crest-derived cells. Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2016
 
Description BSDB Meeting, Warwick 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact T Subkhankulova, M Nikaido, A Kasianov, L Uroshlev, G Aquino, H Schwetlick, T Sauka-Spengler, A Rocco, V Makeev, RN Kelsh, Single cell expression profiling identifies pigment cell differentiation trajectories from unexpectedly multipotent intermediate pigment progenitor cell
Year(s) Of Engagement Activity 2018
 
Description Bath Workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Modeling, Noise, and Development Workshop, University of Bath, 18-19 May 2017, Gerardo Aquino, Nicole Salvatori, Tatiana Subkhankulova, Kleio Petratou, Hartmut Schwetlick, Robert N. Kelsh, Andrea Rocco, On the dynamical role of gene expression noise in cell differentiation. Poster contribution. Extensive discussion with colleagues at the Workshop.
Year(s) Of Engagement Activity 2017
 
Description Denver, IPCC (Robert Kelsh) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Subkhankulova, T., Nikaido, M., Kasianov, A., Uroshlev, L., Aquino, G., Schwetlick, H., Sauker-Spengler, T., Rocco, A., Makeev, V. and Kelsh, R.N. Single cell expression profiling of neural crest-derived cells identifies pigment cell differentiation trajectories from partially-restricted intermediate pigment progenitor cell. International Pigment Cell Conference 2017, Denver, USA, Aug 2017
Year(s) Of Engagement Activity 2017
 
Description EMBL-EBI-Wellcome Trust workshop on In Silico Systems Biology, 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact EMBL-EBI-Wellcome Trust workshop on In Silico Systems Biology, 2015: K. Petratou, T. Subkhankulova, A. Rocco, H. Schwetlick, R.N. Kelsh: A Systems Biology Approach for Constructing Gene Regulatory Networks Underlying Fate Segregation in the Neural Crest. Poster contribution.
Year(s) Of Engagement Activity 2015
 
Description Festival of Research 2016, FHMS, University of Surrey 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Poster presented by G. Aquino: : L. Vibert, G. Aquino, A. Rocco and R.N. Kelsh, An ongoing role for Wnt signalling in differentiating melanocytes in vivo.
Year(s) Of Engagement Activity 2016
 
Description Festival of Research, University of Surrey, 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Festival of Research 2015, University of Surrey: Finn Gubay, Tatiana Subkhankulova, Hartmut Schwetlick, Robert Kelsh, and Andrea Rocco, Noise-Induced Multistability in Developmental Gene Networks. Poster contribution.
Year(s) Of Engagement Activity 2015
 
Description Gordon Research Conference "Neural Crest & Cranial Placodes 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Kleio Petratou presents the poster: K. Petratou, T. Subkhankulova, H. Schwetlick, J. Lister, G. Aquino, A. Rocco and R.N. Kelsh, Constructing gene regulatory networks underlying fate specification of multipotent progenitors in the zebrafish neural crest. Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2017
 
Description Gordon Research Conference "Neural Crest & Cranial Placodes" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Robert Kelsh presents the poster: T. Subkhankulova, M. Nikaido, G. Aquino, H. Schwetlick, T. Sauker-Spengler, A. Rocco and R.N. Kelsh, Single cell expression profiling of neural crest-derived cells identifies partially-restricted intermediate pigment progenitor cell. Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2017
 
Description Gordon Research Conference "Stochastic Physics in Biology" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Gerardo Aquino presents the poster: G. Aquino, T. Subkhankulova, K. Petratou, H. Schwetlick, R.N. Kelsh, A. Rocco, A theoretical framework for intrinsic-noise induced transitions in biochemical reaction networks with time scale separation. Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2017
 
Description Gordon Research Conference "Stochastic Physics in Biology" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Andrea Rocco presents the poster: G. Aquino, T. Subkhankulova, K. Petratou, H. Schwetlick, R.N. Kelsh, A. Rocco, On the dynamical role of gene expression noise in cell differentiation. Poster awarded with the Excellent Poster Presentation Prize of the conference. Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2017
 
Description Gordon Research Conferences, Neural Crest & Cranial Placodes, 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Gordon Research Conferences, Neural Crest & Cranial Placodes , Bentley University, Waltham, MA
T Subkhankulova, K Petratou, FSLM Rodrigues, F Gubay, H Schwetlick, J Lister,A Rocco and RN Kelsh, A core gene regulatory network for zebrafish pigment cells. Poster contribution. Strong interest manifested by academic colleagues.
Year(s) Of Engagement Activity 2015
 
Description ICSB2016, International Conference in Systems Biology, Barcelona, Spain 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Gerardo Aquino presents the poster: G. Aquino, T. Subkhankulova, K. Petratou, H. Schwetlick, R.N. Kelsh, A. Rocco, A theoretical framework for intrinsic-noise induced transitions in biochemical reaction networks with time scale separation. Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2016
 
Description ICSB2016, International Conference in Systems Biology, Barcelona, Spain 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Andrea Rocco presents the poster: G. Aquino, T. Subkhankulova, K. Petratou, H. Schwetlick, R.N. Kelsh, A. Rocco, On the dynamical role of gene expression noise in cell differentiation. Poster shortlisted for "Best poster presentation prize". Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2016
 
Description ICSB2016, International Conference in Systems Biology, Barcelona, Spain 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Robert Kelsh presents the poster: T Subkhankulova, G Aquino, H. Schwetlick, T. Sauker-Spengler, A Rocco and RN Kelsh, Single cell expression profiling of neural crest-derived cells identifies partially-restricted intermediate progenitor cells. Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2016
 
Description ICSB2016, International Conference in Systems Biology, Barcelona, Spain 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Hartmut Schwetlick gives the talk: Kleio Petratou, Gerardo Aquino, Tatiana Subkhankulova, Andrea Rocco, Robert N. Kelsh, Hartmut Schwetlick,
Applying randomised search strategies for the model selection of developmental gene regulatory networks.
Year(s) Of Engagement Activity 2016
 
Description INRIA Seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact INRIA, InriaBCD Seminar, Lyon, France, 2 May 2017: A. Rocco, On the dynamical role of stochastic fluctuations in cell differentiation. Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2017
 
Description Invited seminar University of Nagoya (Robert Kelsh) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Seminar to target academic audience, interesting discussion and interest from academic colleagues in applying similar approach in due course to their studies.
Year(s) Of Engagement Activity 2016
 
Description Mathematical Sciences, University of Southampton, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Andrea Rocco gives the talk: From dynamic gene expression noise to static heterogeneities: The role of stochastic effects in Molecular Biology. Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2016
 
Description Seminar Bristol (Maths) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact University of Bristol, Faculty of Engineering, Applied Nonlinear Mathematics Seminar, 26 May 2017: A. Rocco, On the dynamical role of stochastic fluctuations in cell differentiation. Interesting discussion afterwards with academic colleagues.
Year(s) Of Engagement Activity 2017
 
Description Stem Cell Symposium, CITER, Cardiff, 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Stem Cell Symposium, CITER, Cardiff, 2016, Petratou K., Subhankulova T., Aquino G., Schwetlick H., Rocco A., Kelsh R.,
Constructing gene regulatory networks underlying fate specification of multipotent stem cells in the vertebrate neural crest. Oral presentation. Strong interest manifested by academic colleagues.
Year(s) Of Engagement Activity 2016