VACCINE: Defining signature responses at the innate-adaptive interface to inform the design of vaccines inducing cellular immunity

Preventing and controlling infectious disease by vaccination is critical to the productivity and welfare of farmed animals worldwide, and necessary to maintain global food security. However, for many prevalent diseases, and in particular those for which immunity requires cell-mediated responses, effective deployable vaccines are not available and are proving extremely challenging to develop. Furthermore, the current approach for screening candidate vaccines involves inoculation of animals followed by disease challenge to test immunity. This is lengthy and costly, and frequently offers little insight into why a particular vaccine has failed.

We aim to generate novel tools to address these problems by identifying features of the early immune response associated with initiating protective immune responses. Central to this process are specialised cells called dendritic cells (DCs). DCs reside in peripheral tissues (including skin) and, on encounter with a pathogen or vaccine, migrate via the lymphatic ducts to the lymph node. They carry with them both antigen and signals regarding the nature of the pathogen/vaccine, which together they use to initiate appropriate immune responses. The ability of the DCs to stimulate fully functional immune responses appears to be critically dependant on nature of the signals it received at the point of pathogen/vaccine encounter in the tissues. However the location of these processes makes them extremely difficult to access and study. We have established expertise in a model system (lymphatic cannulation) that allows us to collect large numbers of DCs from calves as they drain from the skin, following interactions with pathogens/vaccines. This provides a unique opportunity, not possible in other species, to investigate this pivotal early phase of the immune response in a natural setting.

In this project we will collect DCs for laboratory analysis before, and immediately after, the administration of live pathogens selected on the basis that they stimulate predictable and well described immune responses. We will then use a range of techniques to investigate the response of the DCs to these pathogens, including recently developed sequencing tools that provide detailed resolution of the processes occurring, in which we have additional expertise. We will focus on defining responses to different categories of pathogen (a bacterium, parasite and virus) selected on the basis that they are expected to generate different responses in the DCs.

We aim to define the processes that occur within DCs that enable them to induce immunity (as opposed to those processes which occur when immunity is not induced). This will provide us with 'signatures' that can be used as a basis for assessing vaccine-induced responses in future studies aiming to generate novel/improved vaccines. From these 'signatures' we may also be able to identify particular processes that we know are associated with immunity that could be targets for improved vaccines in the future. We will also assess whether these 'signatures' can be detected if DCs are exposed to pathogens or vaccines in the lab.

This work aims to develop two novel tools
1. Open-access reference data that could be exploited in future studies to design improved vaccine formulations that specifically induce defined protective signatures
2. Proof-of-concept for a laboratory based screening system whereby candidate vaccines can be tested and rationally selected

These tools will offer a totally novel approach to development of more efficacious vaccines applicable across a wide-range of animal diseases, and so could have far-reaching impact. They will aid the development of cheaper, more efficient research and development methods, with less reliance on animal models. Furthermore, such tools are highly relevant to human medicine where improved methods to test new vaccines are required but where traditional infection studies to test vaccines are not possible.

An urgent need exists to understand why current vaccine formulations incorporating defined antigens fail to induce protective cell-mediated immune responses, and how to rationally design more effective, deployable vaccines. To address this it is necessary to identify both the features of the early immune response associated with generating protective responses, and targets for its manipulation. Dendritic cells (DCs) play a key role in initiating T cell responses and determining their functional differentiation. In this proposal, we plan to utilise well established models that generate protective cell-mediated immune responses, to determine the transcriptomic profiles of DCs harvested as they drain from sites of vaccination. Our approach exploits two technologies in a combined novel approach to identify protective signatures: 1) a bovine lymphatic cannulation system which provides direct access to DCs draining from inoculation sites and 2) next generation transcriptome sequencing and network analysis using Biolayout Express3D. We will surgically cannulate the afferent lymphatic vessels draining the skin and inoculate vaccine preparations above these sites enabling collection of cells dynamically as they respond to vaccination. Using a combination of cellular analytical tools (flow cytometry, ELISA, ELISPOT) and RNASeq we will define signatures associated with protective immunity. These in vivo signatures will be compared to cells exposed to vaccines in vitro to assess the utility of DCs as an in vitro screening tool. This project will generate an open-access dataset for the vaccinology community, comprising gene networks associated with priming cell-mediated immune responses (protective signatures) which will serve as a key tool for future studies. Defining immune signatures will facilitate rapid screening of vaccine candidates and delivery systems to enable selection for those which induce protective signatures that can then be taken forward for further study.

Preventing and controlling infectious disease by vaccination is critical to the productivity and welfare of farmed animals worldwide, and necessary to maintain global food security. However, for many prevalent diseases, particularly those for which immunity requires cell-mediated responses, effective deployable vaccines are not available, e.g. bovine tuberculosis (bTB) and East Coast Fever (ECF). Such diseases have enormous economic and societal costs. In the UK from 2013-14, bTB control measures cost £99 million, and yet bTB is increasing in incidence by 18% each year, hindering the economic competitiveness of affected farms. Furthermore, in many developing countries, where there are no active control measures, the causative agent of bTB (Mycobacterium bovis) represents a significant threat to human health, causing up to 10% of human TB cases. In east Africa ECF causes high levels of cattle mortality, killing >1 million animals each year, and economic losses, which often impact heavily on small-scale farmers, are also incurred through cattle morbidity and production losses, and costs associated with controlling the tick vector.
Although we recognise that this project represents an early stage in the pathway towards new and improved vaccines, the research will provide tools offering a totally novel approach to vaccine development applicable across a wide-range of diseases, and so could have far-reaching impact. The current 'vaccinate and challenge' model for screening candidate vaccines is lengthy and costly and frequently offers little insight into why a vaccine has failed, making it difficult to employ a rational approach to improving their efficacy. This project will provide tools to help overcome this, with the aim of moving towards cheaper, more efficient research and development methods, with less reliance on animal models for screening and selection of candidate vaccines. This will bring benefit to both the pharmaceutical industry and academic institutions seeking to develop more efficacious vaccines. Furthermore, cheaper products with improved efficacy would help to maintain user confidence in products, which would therefore promote increased vaccine use by famers and so improve disease control. A lower-cost vaccine development model would also encourage vaccine research and development targeting diseases affecting emerging economies (such as ECF) where this would otherwise not be cost effective. The approach developed would also potentially impact human medicine, and in fact the diseases we have selected as model pathogens in this project have close parallels with diseases affecting humans (e.g. bTB and human TB; ECF and malaria), so providing direct translational relevance.