Mapping antibody class switch mechanisms and function

Antibodies are produced by a specialised immune cell (B cell) and act as important immune mediators, bridging between pathogens and effector cells to protect us from infection. Antibody molecules can also exist bound to the B cell surface where they act as receptor for detecting target molecules (antigens). Their versatility is immense, they are used to make diagnostics, research tools and therapeutics. One part of the antibody (variable region) is responsible for binding to the antigen, the other end of the molecule is responsible for activating/mediating different functions in the immune system. Uniquely, the antibody variable region can evolve within the organism within a short timescale, in response to infection or vaccination, to improve its binding to the antigen. The constant region does not evolve, but it can be changed to one of 9 different classes or subclasses in order to change the function of the antibody in a genetic process known as Class Switch Recombination (CSR). The (sub)classes of antibody are arranged in the genome in this order: IgM-IgD-IgG3-IgG1-IgA1-IgG2-IgG4-IgE-IgA2; a B cell starts life with IgM and IgD and after activation switches to another (sub)class. Until very recently it was thought that CSR had no effect on the binding abilities of the Variable region. Recent research in different areas (Ageing, Ebola, HIV infection, Cancer) indicates that we don't fully understand the processes that control which (sub)class will be used, the difference that CSR between subclasses makes to the outcome of an immune response or the exact molecular effects that CSR might have on the variable region binding properties. Therapeutic antibodies are a critical pharmaceutical resource, being the fastest growing class of pharmaceuticals, with thousands now in the development pipeline. Current products with regulatory approval/undergoing regulatory review are mostly IgG1 whilst none are IgA or IgE. As we understand more about the functions of these classes, we may find that the potential utility of antibodies can be increased, such as IgE in skin cancers or IgA in gut-related disorders. In this programme we propose to harness the unique expertise of a team of bioinformaticians and immunologists to determine what factors, both outside the cell and inside the cell, control CSR. We will monitor how CSR progresses with time on a daily basis for a fortnight after challenge with the flu vaccine and we will use computer modelling of antibody structures to investigate how changing one side of the antibody molecule may affect the other. Each of these three main objectives will produce a range of results, some of which will help to understand the work in the other objectives, although would not be critical for their success. All parts of the programme require input from all the team to varying levels. The methods we will use and develop are ground-breaking, in our preliminary data, we show pathways of class switching to different types of antibody in cell culture on a single cell basis. We will alter the conditions of these experiments, note the resulting changes and map the protein-protein and gene interactions to deduce what molecules are controlling CSR. These methods will be applicable in all cellular Bioscience disciplines and will transform cell biology research. The mapping of human CSR and the molecular modelling of antibody structure will also result in new tools for others to use, we have successfully done this before and have large global user groups in several areas. The interdisciplinary nature of our team means that we have insight into how to design tools that are user friendly and flexible, all data and tools will be made publicly available in a collective resource "BHive". We will also run our programme in such a way as to maximise the interdisciplinary familiarisation across all our teams and ensure our ECRs have a springboard into their future careers.