Defining mechanisms of CD8+ T-cell mediated immunity - using an integrated longitudinal model to achieve an elusive goal.

Lead Research Organisation: Earlham Institute
Department Name: Research Faculty

Abstract

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Technical Summary

Virally vectored vaccines have been shown to be highly immunogenic in eliciting CD8+ T-cell responses; however in humans and veterinary target species these responses confer only limited protection. Failure to understand the qualitative defects of vaccine-induced CD8+ T-cells that lead to functional deficiencies results in a substantial empiricism in the design of new candidate vaccine delivery systems, retarding the development of urgently required vaccines. Comparative analysis of how non-protective vaccine-induced and equivalent but protective T-cell responses differ offers the most direct route to delineate which parameters are critical in determining the protective efficacy of CD8+ T-cells.

Building on data from recent Theileria parva Ad/MVA vaccine trials, this proposal aims to exploit a novel 'longitudinal' T. parva model (in which animals serially receive an immunogenic but non-protective Ad/MVA heterologous prime-boost immunisation followed by a protective 'infection-and treatment method' immunisation) to conduct comprehensive functional and transcriptomic analysis of CD8+ and CD4+ T-cell responses as they transition from a non-protective to a protective phenotype. The longitudinal model offers a number of advantages over conventional 'cohort studies', including the application of single-cell RNA sequencing to track the transcriptional changes within individual clonotypes. By enabling intra-individual comparison of protective and non-protective T-cells, the study offers a direct route to defining correlates for protection using a model that is difficult to replicate in other relevant pathogen models. The data generated from this study will define fundamental immunological mechanisms that determine vaccine efficacy and will have relevance not only to T. parva but to other human and veterinary pathogens.

Planned Impact

Theileria parva remains one of the most economically significant diseases of cattle in a large area of sub-Saharan Africa and novel control approaches remain a priority for improving livestock productivity in this region. By identifying the immunological parameters that dictate CD8+ T-cell protective efficacy this project aims to generate the data that can accelerate development of next generation vaccines. As well as the direct impact of this research on T. parva, the continued need for vaccines capable of inducing protective CD8+ T-cell responses for many of the major human and veterinary pathogens means the output of the project will have impact in the broader academic community.

Academic research communities: see Academic Beneficiaries for the direct impact of the project in fundamental academic research.

Animal Heath NGOs, funders and industry: the combination of the currently available vaccine delivery platforms' failure to induce protective CD8+ T-cells and the paucity of data to support the rational development of novel alternatives has become a major hurdle in advancing vaccine development against T. parva. The potential to progress our understanding of relevant 'correlates of protection' will be of interest to NGOs such as GALVmed and BMGF that seek to translate new knowledge acquired from such studies into novel interventions for tackling livestock diseases that have profound consequences on the livelihoods of small-holder farmers in sub-Saharan Africa. If successful these groups could be engaged to support further work applying the system (e.g. to other current vaccine delivery platforms to provide a detailed profile of the potential 'defects'; potentially with the aim of establishing if combination of multiple platforms can have synergistic benefits by reciprocal compensation of the defects of the individual platforms).

Livestock owners and agricultural production in LMICs: the impact on livestock owners and agricultural production in LMICs will realistically be a longer term effect (by definition this project doesn't aim to generate a novel vaccine but to generate the data that can accelerate future vaccine development). The benefits will come from the direct consequence of provision of an effective vaccine; reduced animal losses and costs of disease control resulting in improved food and financial security, improved animal health and welfare and reduced environmental impact from the use of acaricides. There will also be indirect benefits as East Coast Fever (ECF) has indirectly constrained the genetic improvement of local agricultural production by limiting the feasibility of introducing the more productive European (Bos taurus) cattle due to their high levels of susceptibility to ECF.

UK governmental policy and BBSRC's strategic priorities: by focusing on a pathogen that is prevalent in sub-Saharan Africa the proposal falls within the remit of the International Development Act (2002) which defines the UK government's statutory requirement to provide assistance leading to the reduction of poverty in LMICs and contribute towards the achievement of the Millennium Development Goals. The project is also aligned with the BBSRC's strategic priority for Agriculture and food security, contributing to a 'programme on veterinary vaccinology to accelerate research into next generation vaccines to combat major diseases of livestock', and by providing opportunities for the PDRA to receive training in a portfolio of immunological and bioinformatic skills will help to 'address skills shortages in areas of specialist research expertise' which includes veterinary vaccinology and scientists with cross-over expertise in immunology and bioinformatics.

Publications

10 25 50
 
Description In this project, we are leading on delivery of single-cell sequencning appraoches for bovine T-cells.

As part of this we have developed methods for increasing the number of cells we can sequence at the same time using a barcoding strategy. This enables >1,500 cells to be sequenced in parallel, and results in signficant cost savings for this and similar projects. We have also automated this process and are using it to support other projects.

We have also undertaken related work to use long-read sequencing on single-cell transcriptomes to explore immune cell receptor sequences, although we have not directly applied this in cattle, the work in this project (focussed on TCRs) has informed this work and the development of new processes to study human biology and that of other "non-model" organisms. This has resulted in a number of commercial interactions (Astra Zeneca, Isogenix, Agilent) over the last year.
Exploitation Route The methods described can readily be applied to other systems and there is a widespread need for better tools for single-cell studies of immunological systems.
Sectors Healthcare

Manufacturing

including Industrial Biotechology

Pharmaceuticals and Medical Biotechnology

 
Title High throughput single-cell library preparation 
Description Using the IDOT liquid handling robot to produce 1536 indexed single-cell libraries 
Type Of Material Improvements to research infrastructure 
Year Produced 2022 
Provided To Others? No  
Impact Major reduction in plastic use (95%), reagent use (90%) and sequencing cost (40%) over previous approaches. 
 
Description Industry Research gift award supporting Proof of Concept single cell industry applications 
Organisation Agilent Technologies
Country United States 
Sector Private 
PI Contribution Review IP and agreements, liaise and coordinate project and finance set up
Collaborator Contribution Provision of products and in-kind intellectual contributions as mentor
Impact N/A
Start Year 2023
 
Description Presentation - Festival of Genomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact ~100 attendees at the Festival of Genomics were present for my talk on Single-cell long read sequencing
Year(s) Of Engagement Activity 2023
 
Description Single-cell show-and-tell: Activity based tours of the EI single-cell labs 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact 40 staff from EI were given an interactive tour of the single-cell labs. We introduced them to the different platforms and concepts behind single-cell analysis. We hosted staff from operations, communications, business development and faculty, all staff at EI were invited. The event stimulated questions and discussion about both the biology and technology associated with single cell work.
Year(s) Of Engagement Activity 2023