Harnessing the power of T-cell responses to control future pandemics

一些病毒科能够引起突然爆发，根据定义，对于新出现的病毒，没有疫苗。与抗体不同，t细胞反应通常在病原体之间交叉反应。因此，选择病毒的保守区域作为靶疫苗抗原，为在病毒出现之前制造出具有一定效力的疫苗提供了一种策略。然而，在此之前，必须确定这些保护区域，并提供其保护能力的证据。该项目将重点关注与医学相关的两个RNA病毒家族：黄病毒和冠状病毒，特别是SARS-CoV-2。黄病毒包括登革热病毒、寨卡病毒、西尼罗河病毒等。该项目的目标是开发新的方法，为与全球健康有关的疾病选择疫苗抗原，最终目的是预防未来的疾病爆发。黄病毒已经引起了引人注目的疫情，比如2015年的寨卡疫情。尽管有疫苗和抗病毒药物，但SARS-CoV-2仍在引起许多感染。本项目将使用来自几个地方和国家研究的样本，包括我们团队开发的寨卡疫苗的I期临床试验，研究CD8+ t细胞在自然感染和疫苗接种后的表型。学生将学习t细胞表位定位技术，评估t细胞功能的几种方法（一级导师），以及识别病毒之间t细胞表位保护的生物信息学（二级导师）。他们将研究已发表的和实验确定的表位。生物信息学分析将检查这些表位与蛋白质功能的关系，以及在一个家族中不同病毒之间的保存。接下来，将合成变异表位并进行实验测试，以检验蛋白质功能、保守性和t细胞反应的交叉反应性之间的关系。将测试针对交叉反应性表位的反应的快速性和功能，以确保它们是高质量的，并有望提供保护。抗原特异性细胞将使用四聚体/五聚体进行单细胞rna测序，以确定受体使用或转录谱是否驱动交叉反应性。然后，学生将使用来自人类实验医学研究的样本来测试异源黄病毒暴露，并使用感染性疫苗直接测试（黄病毒）在引物和随后的人类异源感染之间的哪些表位交叉反应。还有机会测试利物浦设计的针对SARS-CoV-2和MERS-CoV的疫苗在现实世界中的反应。上述工作将揭示表位选择的基本原则。最后，这些表位将通过合成包膜mrna进行抗原呈递试验来测试，以确保它们可以被人类t细胞处理、呈递和识别，使用抗原扩增的短期t细胞培养（我们实验室中已经建立的方法）。学生将受益于广泛的人体免疫学和生物信息学培训，使他们能够发展良好的跨学科技能。他们还将从人类研究的样品中受益，因此他们将学习如何在GCP的实验室中工作，以及早期产品开发的治理和监管方面。将有机会学习R编程，并将这些和其他新获得的生物信息学技能应用于使用主要导师实验室正在开发的管道处理免疫学数据。

Several virus families are capable of causing sudden outbreaks, and by definition, for newly emerging viruses, vaccines are not available. Unlike antibodies, T-cell responses are often cross-reactive between pathogens. Therefore, choosing conserved regions of viruses as target vaccine antigens offers a strategy for making vaccines that have some efficacy before a virus has emerged. However, before this can be done, these conserved regions must be identified, and evidence for their protective capacity must be provided. This project will focus on two RNA virus families that are medically relevant: flaviviruses and coronaviruses, specifically SARS-CoV-2. Flaviviruses include dengue, Zika, West Nile and others. The project will aim to develop novel approaches to selecting vaccine antigens for diseases relevant to global health, with the ultimate aim of prevention of future outbreaks.Flaviviruses have caused notable outbreaks such as the 2015 Zika epidemic. SARS-CoV-2 continues to cause many infections despite the availability of vaccines and antivirals. Using samples from several local and national studies, including a phase I clinical trial of a Zika vaccine developed by our team, this project will investigate the phenotype of CD8+ T-cells that develop after both natural infection and vaccination.The student will learn techniques in T-cell epitope mapping, several methods for assessing the T-cell functions (primary supervisor), and bioinformatics (secondary supervisor) to identify T-cell epitope conservation between viruses. They will work on published and experimentally determined epitopes. Bioinformatic analyses will examine where these epitopes are found in relation to protein function, and conservation across different viruses within a family.Next, variant epitopes will be synthesised and tested experimentally to examine this relationship between protein function, conservation, and cross-reactivity of the T-cell response. The avidity and function of responses against cross-reactive epitopes will be tested to ensure they are high quality and expected to provide protection. Antigen specific cells will be sorted for single cell RNA-seq using tetramers/pentamers, to address whether receptor usage or transcriptional profile drives cross-reactivity. The student will then use samples from human experimental medicine studies testing heterologous flavivirus exposure, and directly test (for flaviviruses) which eptiopes cross-react between priming and subsequent heterologous infection in humans, using infectious vaccines. There will also be the opportunity to test real-world responses against a vaccine designed in Liverpool to target both SARS-CoV-2 and MERS-CoV.The above work will uncover the underpinning principles of epitope selection. Finally, these epitopes will be tested by synthesising enveloped mRNAs for antigen presentation assays, to ensure that they can be processed, presented and recognised by human T-cells, using antigen expanded short term T-cell cultures (a well-established method in our lab).The student will benefit from a broad range of training in human immunology and bioinformatics, allowing them to develop good interdisciplinary skills. They will also benefit from working on samples from human studies, so they will learn how to work in a laboratory at GCP, and the governance and regulatory aspects of early phase product development. There will be opportunities to learn programming in R, and to apply both these and other newly acquired bioinformatics skills to the processing of immunological data using pipelines under development in the lab of the primary supervisor.