Topological data analysis of molecule positions from super-resolution data to map molecular nano-environments in immune cell

Fluorescence microscopy is a vital and ubiquitous technique used throughout the life sciences and beyond. However, it suffers from a resolution limit of around 200 nm. In 2014, the Nobel Prize for Chemistry was awarded for the development of super-resolution microscopy which breaks this resolution barrier. At the forefront of these methods is single-molecule localisation microscopy (SMLM). Here, sample preparation and imaging are such that individual molecules can be localised with precisions around 20nm. This allows for mapping of the xy coordinates of all molecules of interest. This project is centred on developing analysis software for this type of imaging, including using topological analysis principles to analyse the nano-scale clustering of proteins on the cell surface.

By combining SMLM with environmentally sensitive fluorophores, which report on their local biophysical or biochemical environments through changes in their emission spectrum, we can probe properties of the cell membrane at each localisation. There are many such probes, but we are particularly interested in those that allow the visualisation of lipid packing in the cell membranes. We are now interested in further developing this technology - including establishing its use with other probes e.g. for viscosity, pH etc, and developing the topological analysis methodology to allow us to map cellular nano-environments for the first time. Biologically, we apply these to the study of T cells - white blood cells of the immune system. T cells survey other cells in the body for signs of infection and must activate when threats are detected - and avoid activation in response to the body's own proteins. This delicate balance is achieved through the nanoscale organisation of T cell proteins and, we hypothesise, via nano-environments including nanoscale membrane lipid domains which we aim to map.

In collaboration with Oxford Nanoimaging (the microscope hardware manufacturer), we aim to optimise the imaging process. We are also collaborating with Dr Maria Makarova, an expert in the genetic engineering of lipid metabolism, to be able to modify T cell nano-environments and thereby try to control immune cell function. This will afford us the opportunity to potentially apply the technology for therapeutic benefit. Finally, with the assistance of Prof. Iain Styles of the School of Computer Science, we are producing topological, machine learning and AI approaches to analysing the data. Ultimately, the biological applications of this project will provide insight and new understandings of how the immune system operates.

1. Our primary impact will be by supplying the UK knowledge economy with skilled multidisciplinary researchers, equipped with the technical and transferable skills to establish the UK as pre-eminent in topology-based future technologies. The training they receive will make them proficient in the demands of the translation of academic science (with a broad background in condensed matter physics, materials science and applied electromagnetics) to industry, with direct experience from internship and industry engagement days. With their exposure to both theoretical research (including modelling and big data-driven problems) and experimental practice, our graduates will be ideally equipped to tackle research challenges of the future and communicate to a broad audience, ready to lead teams made up of diverse specialised components. The potential impact of our researchers will be enhanced by a broad programme of transferable skills, focusing on innovation, entrepreneurship and responsible research. Beneficiaries here will include the students themselves as they embark on future careers intertwining academic research and industry, as well as the other sectors listed below.

2. The research undertaken by students in the CDT will have impact on the future direction of topological science. Related disciplines, including physics, materials science, mathematics, and information technology will benefit from the cross-disciplinary fertilisation it will enable. The CDT will not only provide an interface between research in physical sciences and engineering, but also provide a route for academia to interact effectively with industry. This will help organise researchers from different disciplines to collaborate around the needs of future technology to design materials based on topological properties.

3. Our research will enable industries to set the direction of topological research around the needs of commercial research and development, leading to wealth generation for the UK, and to influence the mindset of the next generation of future technologists. Specifically, topological design has the promise to revolutionise devices and materials relevant to communications, microwave and terahertz technologies, optical information processing, manufacturing, and cybersecurity. Through partnership with organisations from the wider knowledge sector, we will deepen the relationship between academic research and disciplines including IP law and scientific software development.

4. Our CDT will also have impact on the wider academic community. New specialist courses and training in transferable skills will be developed utilising cutting-edge multimedia technologies. Our international research collaborators, including prominent global laboratories, will benefit from placements and research visits of the CDT students. Our interdisciplinary research, combining the needs of academia and industry will be an exemplar of the effectiveness of the CDT model on an international stage.

5. The wider community will benefit from our organised public engagement activities. These will include direct interaction activities, such as demonstrating at the Birmingham Thinktank Science Centre, the Royal Society Summer Exhibition, local schools and community centres.