DBP4: Spatiotemporal modeling of T-cell Signaling
PI: Christoph Wülfing, PhD, Professor of Immunology, School of Cellular and Molecular Medicine, University of Bristol
Funding Source(s): ERC PCIG11-GA-2012-321554, The spatiotemporal organization of T cell signaling as a regulator of T cell function, European Research Council (Wülfing), 8/1/12-7/31/16; 102387/Z/13/Z, Characterising the disruption of signalling dynamics at the immune synapse interface of tumour infiltrating lymphocytes, Wellcome Trust (Wülfing), 8/1/14-9/30/17; 201254/Z/16/Z, Ability of Tumour Infiltrating Lymphocytes (TILs) to Mediate Tumour Killing, Wellcome Trust (Wülfing), 5/1/16-4/30/19; GW4 BioMed DTP, Defining Mechanisms of T Cell Suppression in the Tumour Microenvironment, Medical Research Council (Wülfing), 9/1/16-8/31/19
How DBP acts as a driver of test bed:
The project is essential to the creation of CellOrganizer functions for aligning and comparing spatiotemporal distributions of multiple molecules and creating causal models
Understanding how cellular function is regulated in complex signalling networks with dozens of interacting proteins is a critical challenge in current biomedical science. A critical component of signalling complexity is that proteins are rarely evenly distributed throughout cells but enrich at particular locations at particular times. Co-localisation of two proteins enhances their interaction efficiency. At the systems scale, spatiotemporal organization thus determines how regulatory information flows through signalling networks both in time and space. Approaches to harness this regulatory information encoded in systems scale spatiotemporal distributions, because they address signalling as it occurs in real time inside live cells, are essential if we are to understand the complex regulation of cell function.
We investigate the activation of primary T cells by antigen presenting cells with systems scale live cell imaging (> 50 sensors) to comprehensively understand roles of spatiotemporal signalling distributions and to efficiently exploit such organization to discover mechanisms in the regulation of cellular function. As one of our key projects we address the tyrosine kinase Itk. We have already established Itk as a critical regulator of the spatiotemporal organization of T cell signaling and can now relate such organization to roles of Itk in cytokine secretion and primary immunodeficiency, as functionally corroborated by manipulation of the spatiotemporal features of Itk-dependent signaling.
The key strength of systems scale imaging data and the central challenge in their analysis is the abundance of information. For example, our current data set contains more than 10,000 three-dimensional time-lapse videos of individual T cells undergoing activation. Moreover, already for each individual T cell, at each individual time point during its activation, the imaging data provide thousands of data points, the amount of a signalling sensor at each resolved position inside the T cell, i.e. a three-dimensional map of the local concentrations of the signalling sensor. The more of these maps can be efficiently analysed, the more one can understand how proteins are poised to interact inside live primary cells in the regulation of their activation. Advanced image analysis approaches that maximize the extraction and processing of the quantitative data contained in large image data sets are thus of great relevance.
In collaboration with TR&D2 and TR&D3 we pursue two aims.
- To construct models of the relationship between the spatiotemporal distributions of potential signaling molecules
- Quantifying the spatiotemporal organization of signaling under different T cell activation conditions, e.g. in T cells that do or do not express Itk, we can thus discover how signaling relations change as a powerful tool to generate testable hypotheses about how signaling governs cellular function.
- To construct biochemical cell simulations that capture the sequence of events involved in T cell signaling
- Cell simulations based on the actual local concentrations of signaling intermediates inside a live cell will help to understand how biochemically defined protein interactions occur during cellular activation and thus regulate cell function.
Publications resulting from this work:
- Roybal KT, Sinai P, Verkade P, Murphy RF, Wuelfing C (2013) The actin-driven spatiotemporal organization of T-cell signaling at the system scale Immunol Rev 256: 133-47 PMID: 24117818.
- Roybal*, K.T.; T. E. Buck*, X. Ruan*, B. H. Cho, D. J. Clark, R. Ambler, H. M. Tunbridge, J. Zhang, P. Verkade, C. Wuelfing, and R. F. Murphy (2016) Computational spatiotemporal analysis identifies WAVE2 and Cofilin as joint regulators of costimulation-mediated T cell actin dynamics. Science Signaling 9: rs3 [*co-first authors].
- Ambler*, JE, X. Ruan*, R. F. Murphy†, and C. Wülfing† (2017) Systems Imaging of the Immune Synapse . Methods in Molecular Biology, vol. 1584 (C. T. Baldari and M. L. Dustin, eds.), in press [*co-first authors, †co-senior authors].