Immune cell dynamics predictive of vaccine protection in Atlantic salmon

鲑鱼养殖是英国重要的食品行业，2019年生产超过20万吨鱼，是英国最大的食品出口。该部门每年提供18亿英镑的经济贡献，并负责提供约8，000个工作岗位，主要集中在苏格兰农村地区。鲑鱼产业有着雄心勃勃的增长目标，旨在到2030年将其对经济和就业市场的贡献翻一番。传染病对鱼类福利和环境造成的负面影响阻碍了这一目标，一系列病毒性疾病是当前的主要问题。为了帮助该行业实现可持续发展，需要在科学创新的支持下克服这些挑战。鲑鱼养殖场爆发的病毒性疾病造成了重大的经济损失和福利问题。此外，由于气候变化，还存在新病毒性疾病进入水产养殖系统的持续威胁。目前没有控制鲑鱼病毒性疾病的治疗方案，疫苗接种仍然至关重要，市场上有几种用于商业用途的病毒疫苗。英国每年有超过5000万条鱼接种疫苗。虽然这有效地控制了细菌性疾病，但病毒性疾病仍然是一个未解决的问题。因此，开发新的和改进的疫苗来控制养殖鲑鱼中的病毒性疾病仍然至关重要。开发有效的疫苗需要广泛的鱼类使用，每次试验都要杀死数百只动物，以获得疾病挑战后的有效性数据。整个过程既昂贵又耗时。加快疫苗开发的方法，同时大大减少被杀动物的数量，将是动物福利和成本节约方面的重要一步。鱼类与哺乳动物共享免疫系统的许多组成部分，导致疫苗接种后的保护性反应。然而，我们对鱼类中不同免疫细胞类型的多样性在保护性免疫应答和免疫记忆中所起的作用了解甚少。新技术使我们能够量化单个细胞中的全局基因表达（所谓的“单细胞转录组学”），并有望改变我们对鱼类接种疫苗后免疫保护细胞多样性的理解。我们的目标是在理解针对主要问题病毒性疾病（称为胰腺疾病）的疫苗接种如何通过免疫细胞的动态变化导致免疫保护方面迈出一大步。我们将单细胞转录组学应用于从精心设计的疫苗接种实验中采集的样本，旨在将免疫细胞表达的早期变化与数月内产生的免疫保护联系起来。第一个主要目标是描述鲑鱼免疫系统主要组织中不同细胞类型的全部多样性，包括这些细胞如何对病毒疫苗接种作出反应。我们将比较两种注册的具有非常不同配方的胰腺疾病疫苗，以了解导致疾病保护差异的细胞机制。第二个主要目的是鉴定与疫苗保护相关的免疫细胞类型和这些细胞的特异性标记基因。最后一个目标是利用这些结果开发一个具有成本效益的平台，可以用来准确预测疫苗接种后早期的疾病保护。除了在鱼类保护性免疫反应的细胞基础上创造重大知识进步外，这些结果还将应用于疫苗研究和开发，开辟使用更快、更具成本效益的策略和更少的动物来评估疫苗效力的策略。这可能会导致疫苗设计和测试的改进，从而对鲑鱼水产养殖的可持续性产生积极影响，同时促进鱼类福利。

Salmon farming is a key UK food sector, producing more than 200,000 tonnes of fish in 2019, representing the top national food export. This sector provides an economic contribution of £1.8-billion per year and is responsible for around 8,000 jobs, concentrated in rural regions of Scotland. The salmon industry has ambitious growth targets, aiming to double its contribution to the economy and job market by 2030. This ambition is hindered by negative impacts caused by infectious disease to fish welfare and the environment, with a range of viral diseases being a major current problem. To help the sector grow sustainably, such challenges need to be overcome with the support of scientific innovation.Viral disease outbreaks on salmon farms cause major financial losses and welfare problems. There further exists a continuous threat of new viral diseases entering aquaculture systems due to climate change. There are no treatment options to control salmon viral diseases, and vaccination remains critical, with several viral vaccines on the market for commercial use. Over 50 million fish are vaccinated in the UK each year. While this effectively controls bacterial diseases, viral disease remains an unsolved problem. Consequently, the development of new and improved vaccines to control viral diseases in farmed salmon remains critical.Developing effective vaccines requires extensive fish use, with hundreds of animals killed per trial to gain data on efficacy after disease challenge. The whole process is expensive and time consuming. Methods that accelerate vaccine development, while substantially reducing the number of animals killed, will represent an important step forward in terms of animal welfare and cost savings. Fish share many components of the immune system with mammals leading to protective responses following vaccination. However, we have a poor understanding of the role played by the large diversity of different immune cell types in protective immune responses and immune memory in fishes. New technologies allow us to quantify global gene expression in individual cells (so-called 'single cell transcriptomics') and hold exceptional promise to transform our understanding of cell diversity responsible for immune protection following vaccination in fish. Our aim is to create a large up-step in understanding of how vaccination against a major problem viral disease (called pancreas disease) leads to immune protection through dynamic changes in immune cells. We will apply single cell transcriptomics to samples taken from a carefully designed vaccination experiment, designed to link early changes in immune cell expression to immune protection generated over months. The first major aim is to describe the full diversity of different cell types in the major tissues of the salmon immune system, including how these cells respond to viral vaccination. We will compare two registered pancreas disease vaccines with very different formulations to understand cellular mechanisms leading to differences in disease protection. The second major aim is to identify immune cell types, and specific marker genes for these cells, correlated with vaccine protection. A final objective is to use the results to develop a cost-effective platform that can be used to accurately predict disease protection early post-vaccination.In addition to creating major knowledge advancement on the cellular basis of protective immune responses in fish, the results will have applications in vaccine research and development, opening up strategies to assess vaccine efficacy using faster more cost-effective strategies and fewer animals. This may lead to improvements in vaccine design and testing that can positively impact the sustainability of salmon aquaculture while promoting fish welfare.