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Systems-level characterization of mammalian cell cycle transitions

Reference	BB/M00354X/1
Principal Investigator / Supervisor	Professor Bela Novak
Co-Investigators / Co-Supervisors	Professor Chris Bakal, Professor Francis Barr, Professor Ulrike Gruneberg, Dr Helfrid Hochegger
Institution	University of Oxford
Department	Biochemistry
Funding type	Research
Value (£)	3,012,573
Status	Completed
Type	Research Grant
Start date	01/12/2014
End date	31/01/2020
Duration	62 months

Abstract

One way of propelling eukaryotic cells from birth through chromosome replication and segregation into cell division is generated by irreversible cell cycle transitions (Restriction Point, G1/S, G2/M, meta/anaphase and mitotic exit/cytokinesis). These transitions are controlled by mutual antagonism of phase specific cell cycle inhibitors and activators, which embody a complex regulatory network. Although the pair-wise interactions of cell cycle activators and inhibitors in human cells have been identified, the systems-level (physiological) significance of these interactions is not understood for a number of reasons. Most experimental data is neither quantitative nor time-resolved and therefore unsuitable for mathematical description. To overcome these shortcomings we are bringing together modellers, biochemists and cell biologists to apply an iterative cycle of mathematical modelling and experimental testing/verification. The aim of this proposal is to understand the dynamic characteristics of the major cell cycle transitions in human cells by combining mathematical modelling with live-cell imaging and biochemistry. With model building at the heart of this strategy, we will be able to predict the requirements for cell cycle regulators, analyse them using biochemistry, and test their functional role using cell-based and in vitro assays. We want to uncover the functionally relevant network motifs at four specific transitions of the human cell cycle. We are particularly interested in positive and double-negative feedback loops which can create irreversible switch-like transitions, but other network motifs (negative feedback and feed-forward loops) will not escape our attention. By disrupting, these network motifs both in silico and in vivo the robustness of the cell cycle transitions will be analysed as well.

Summary

During human development and growth, cells must proliferate in an ordered and controlled manner to form the adult body. The cell cycle is a series of events that results in two cells forming from one parent cell. Importantly each daughter cell must be identical to the parent cell, thus successful completion of the cell cycle requires the precise copying and distribution of genetic information contained within DNA. Cell cycle events are orchestrated by a large array of proteins that interact and function together to ensure the cell cycle is precisely controlled. Molecular biologists have uncovered many of these cell cycle proteins. Remarkably, these proteins and how they interact are highly conserved from yeasts to humans. However because the system is very complex, it is not obvious how all these proteins work together to drive the cell cycle forward. In order to use this hard-won information about the mechanisms controlling the cell cycle, computational tools are necessary to reliably simulate the integrated behaviour of the system. Mathematical models of relatively simple, cell-cycle control systems in yeasts and early embryos revealed that the cell cycle control network has the property of a "switch-like" system. These effects make the transitions between cell cycle states abrupt (switch-like), unidirectional (irreversible) and controllable (sensitive to error-detection mechanisms). When the cell detects a problem with the execution of a particular process, it can block the transition to the next cell cycle stage by inhibiting the switch. This switch-like behaviour has been demonstrated experimentally for all cell cycle transitions in single-celled organisms (e.g. yeasts). However it is still unknown whether these principles are also manifested in the cell cycle control of more complex cells (e.g. in humans). Therefore in this hypothesis-driven research programme, we propose to test the design principles of more complex cell cycle control network of human cells. We will use a combination of high-tech experimental and theoretical tools to tackle this problem. In order to achieve this goal, an interdisciplinary team of biochemists, cell biologists and modellers will be assembled. Understanding the principles of cell cycle controls in mammalian cells is vital to the understanding of human disease. For example, in cancer, cells lose control of the cell cycle and replicate repeatedly, forming a tumour. By understanding how the cell cycle is controlled, we can develop new ways to restore cell cycle control to cancer cells and stop them replicating out of control. In contrast, if the cellular reproduction of stem cells in the body is compromised, renewal of differentiated cells is retarded which is one of the reasons underlying the ageing process. Since many emerging stem cell therapies rely on the precise control of cell replication this field will also benefit from our research. Therefore our research proposal addresses two fundamental Strategic Priorities of BBSRC: "Systems Approaches to the Biosciences" and "Ageing across life-course".

Impact Summary

The aim of this proposal is to provide a quantitative characterization of the major cell cycle transitions of mammalian cells by combining mathematical modelling with live-cell imaging and biochemistry. The cell division cycle is intimately involved in the growth, development, reproduction and ageing of all biological organisms, therefore gaining insight into cell cycle controls is a fundamental quest in both biology and medicine. Our work will lead to reliable models of cell cycle transitions which will create new ways to address crucial questions about cell proliferation. The potential beneficiary groups of this research include the followings: - Academic researchers studying cell cycle, cancer, systems biology and age-related diseases. - Industrial organizations devising therapies to control cell proliferation. - Public benefits by improving the quality of life Academic Researchers By high profile publications and presentations at professional meetings, our research will have an immediate academic impact. Our systems biology approach will provide a template for how to bridge cell physiology to its underlying biochemical machinery. The potential of such an approach is far-reaching, not only in understanding the cell cycle but also more generally in pioneering novel ways to study complex genetic regulatory systems. Such system biology tools will be extremely useful to rationally define targets in the initial stages of drug discovery and biotechnological invention, thereby decreasing the need for extensive experimental screening, and saving much expense and unnecessary animal testing. Commercial Private Sector Beneficiaries A better understanding of mammalian cell cycle controls has significant potential to change medical treatments of cancer cells that have escaped the normal controls on growth and division in multicellular animals. Therefore the objectives of the proposal are of interest to pharmaceutical and biotechnological companies working on cell cycle'drugs' (inhibitors of kinases and phosphatases). Quantitative description of cell transitions represents an important step towards an in silico model of the human cell cycle. A validated computer model could be very useful to identify the rate limiting steps in cell cycle transitions which are the optimal targets for cell cycle inhibitors. Therefore the project outlined could potentially lead to the development of both single and combinatorial therapeutic targets to block cell cycle progression by industrial organizations. Applications of knowledge about cell cycle controls are also important for investigating development, aging and chronic diseases. The regeneration of tissues that normally have only limited capacity for repair may be achievable by genetic manipulation of cell cycle control pathways in vivo or genetic engineering of artificial tissues in vitro. The potential benefits for the commercial sector will be realized almost immediately after completion of this research (5-10 years). Our institutions are well equipped to protect any Intellectual Property generated by this project and to pursue this IP in terms of commercial exploitation (e.g. ISIS Innovation at OU). Public sector A better understanding of cell reproduction in mammals may lead to more rational and effective strategies for stopping malignancies, fibroses and other proliferative disorders. By providing novel insights into the regulation of cell cycle regulation this research could potentially lead to therapies and treatments which could dramatically improve the well-being, health, and creative output of the British economy. An appreciation of subtle differences in the molecular regulation of cell division in mammals and protists may suggest new drugs for combating infectious diseases and thus improve the quality of life an ageing population. Potential benefits to the health of the public sector would be realized over a longer period (10-15 years).

Committee	Research Committee C (Genes, development and STEM approaches to biology)
Research Topics	Pharmaceuticals, Systems Biology
Research Priority	X – Research Priority information not available
Research Initiative	Longer and Larger Grants (LoLas) [2007-2015]
Funding Scheme	X – not Funded via a specific Funding Scheme

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