Mapping antibody class switch mechanisms and function

抗体是由一种特殊的免疫细胞（B细胞）产生的，作为重要的免疫介质，在病原体和效应细胞之间架起桥梁，保护我们免受感染。抗体分子也可以结合在B细胞表面，充当检测靶分子（抗原）的受体。它们的多功能性是巨大的，它们被用来制造诊断、研究工具和治疗方法。抗体的一部分（可变区）负责与抗原结合，分子的另一端负责激活/介导免疫系统中的不同功能。独特的是，抗体可变区可以在生物体内短时间内进化，以响应感染或疫苗接种，以改善其与抗原的结合。恒定区不会进化，但它可以被改变为9个不同的类或亚类之一，以便在称为类开关重组（CSR）的遗传过程中改变抗体的功能。（亚）类抗体在基因组中的排列顺序为：IgM-IgD-IgG3-IgG1-IgA1-IgG2-IgG4-IgE-IgA2；B细胞一开始具有IgM和IgD，激活后转换为另一（亚）类。直到最近，人们才认为CSR对可变区域的结合能力没有影响。最近在不同领域（衰老、埃博拉、艾滋病毒感染、癌症）的研究表明，我们并不完全了解控制将使用哪个（亚）类的过程，亚类之间CSR对免疫反应结果的差异，或者CSR可能对可变区域结合特性产生的确切分子效应。治疗性抗体是一种重要的药物资源，是增长最快的一类药物，目前有数千种正在开发中。目前获得监管机构批准或正在接受监管审查的产品主要是IgG1，而没有IgA或IgE。随着我们对这些类别的功能了解的越来越多，我们可能会发现抗体的潜在效用可以增加，例如皮肤癌中的IgE或肠道相关疾病中的IgA。在这个项目中，我们建议利用一个由生物信息学家和免疫学家组成的团队的独特专业知识，确定细胞内外的哪些因素控制了CSR。我们将在接种流感疫苗后的两周内每天监测CSR如何随时间发展，我们将使用抗体结构的计算机建模来研究改变抗体分子的一侧如何影响另一侧。这三个主要目标中的每一个都将产生一系列结果，其中一些结果将有助于理解其他目标中的工作，尽管对它们的成功不是至关重要的。该计划的所有部分都需要所有团队在不同层面上的投入。我们将使用和开发的方法是开创性的，在我们的初步数据中，我们展示了在单细胞基础上在细胞培养中切换到不同类型抗体的途径。我们将改变这些实验的条件，记录由此产生的变化，并绘制蛋白质-蛋白质和基因相互作用图，以推断哪些分子控制CSR。这些方法将适用于所有细胞生物科学学科，并将改变细胞生物学研究。人类CSR的制图和抗体结构的分子建模也将为其他人提供新的工具，我们之前已经成功地做到了这一点，并在几个领域拥有庞大的全球用户群。我们团队的跨学科性质意味着我们对如何设计用户友好和灵活的工具有深入的了解，所有的数据和工具将在一个集体资源“BHive”中公开提供。我们还将以这样一种方式来运行我们的项目，即最大限度地提高我们所有团队的跨学科熟悉程度，并确保我们的ecr有一个进入未来职业生涯的跳板。

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.