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(ICF)- IMMPROVE: Immune Memory and Mechanisms of Protection from Vaccines

Lead Research Organisation: University of Oxford
Department Name: Paediatrics

Abstract

The COVID-19 pandemic saw the rapid development and deployment of a range of vaccine platforms. While essential to protect against severe disease, these vaccine platforms need further optimisation to provide long-term and local protection against infection including future variants. This vaccine optimisation requires an improved understanding of how a protective immune response is induced, how it is maintained, and the role of immunity in the nose and the lungs.

Building on the experience our consortium amassed during the COVID-19 pandemic, we will answer some of the key outstanding questions in the field:

1.MEMORY We will delineate the mechanisms which influence the duration of protective immune responses. Improving understanding of immune memory is critical for the development and deployment of future vaccines with long-lasting protection against both pandemic and endemic pathogens.
2. LOCATION We will determine the role of the immune response in the airways, as the entry route for virus, in protection against infection. The aim is to understand if nasally administered vaccines can stop infection and onward transmission, as well as protect against severe disease.
3. PROTECTION We will define which aspects of the immune response protect against disease and how to maximise these responses. This will enable vaccine developers to focus on new vaccines that deliver improved protection.
4. DATA There exist large datasets from clinical trials and real-world studies that, if combined with the data from this programme, would generate a unique resource for understanding how vaccines work. To achieve this, we will develop an integrated data structure and open-source computational tools to integrate disparate data and maximise data usefulness.
5.IMPACT We will bolster pandemic preparedness by the training and empowerment of future leaders in vaccine development and engaging public understanding of the need for vaccines.
Targeting these questions will lead to increased capability for rational, immunologically-driven vaccine development and uptake.

Technical Summary

The contribution of the expert scientists in this consortium, their accumulated knowledge, unique facilities and proven methodologies places this consortium at the epicentre of enabling rapid control not only of SARS-CoV-2 but other potential pandemics. Through mechanistic immunology, we will deliver a new tool-kit for pandemic responsiveness, we will be ideally positioned for future vaccine design.

Harnessing the current and future expertise of this consortium, its PIs, future-leaders, data-sets, public and patient involvement and engagement experts, we will consolidate learnings from COVID-19 and enable outbreak and pandemic readiness to meet the challenges of changing infection patterns in the 21st century.

The core objectives of the consortium are:
1. To understand the immune mechanisms required for long-lived and broad protection against SARS-CoV-2, and how to effectively induce these responses through vaccination.
2. To understand the duality of systemic and local immunity against SARS-CoV-2, their corresponding roles in protection against disease and infection/transmission, and how to replicate these advantages through vaccination.
3. To define mechanistic correlates of protection, empowering next-generation pan-coronavirus vaccine development.
4. To build resilient long-term capacity in pandemic preparedness via bolstering the global network of scientists; training, developing and empowering early-career researchers in vaccinology and vaccine design; and augmenting the biosciences capability for vaccine development and rapid response to emergent pathogens.
5. Build upon the strong links of the consortium with the public, extend the network of public engagement and involvement to early-career researchers, and act as a bidirectional bridge between the public and vaccine developers / policy makers to aid support and uptake of vaccination.

People

ORCID iD

Teresa Lambe (Principal Investigator)
Lance Turtle (Co-Investigator) orcid http://orcid.org/0000-0002-0778-1693
Helen McShane (Co-Investigator)
Alex Richter (Co-Investigator)
Daniela Ferreira (Co-Investigator) orcid http://orcid.org/0000-0002-0594-0902
Paul Moss (Co-Investigator)
Pontiano Kaleebu (Co-Investigator)
Donald Palmer (Co-Investigator)
Mark Coles (Co-Investigator)
Sarah Teichmann (Co-Investigator)
Paul Klenerman (Co-Investigator)
Adrian Liston (Co-Investigator) orcid http://orcid.org/0000-0002-6272-4085
Mala Maini (Co-Investigator)
Susan Hopkins (Co-Investigator) orcid http://orcid.org/0000-0001-5179-5702
Saul Faust (Co-Investigator) orcid http://orcid.org/0000-0003-3410-7642
Tao Dong (Co-Investigator)
Brian Marsden (Co-Investigator)
Julian Knight (Co-Investigator) orcid http://orcid.org/0000-0002-0377-5536
Marko Nikolic (Co-Investigator) orcid http://orcid.org/0000-0001-6304-6848
Thushan De Silva (Co-Investigator) orcid http://orcid.org/0000-0002-6498-9212
John Tregoning (Co-Investigator)
Michelle Linterman (Co-Investigator) orcid http://orcid.org/0000-0001-6047-1996
Christopher Chiu (Co-Investigator) orcid http://orcid.org/0000-0003-0914-920X
David Clifton (Co-Investigator)
Cecilia Johansson (Co-Investigator)
Samantha Vanderslott (Researcher)
Adam Dale (Researcher Co-Investigator) orcid http://orcid.org/0000-0001-8163-7481
Joannah Fergusson (Researcher Co-Investigator)
Iman Satti (Researcher Co-Investigator)
Nicholas Provine (Researcher Co-Investigator) orcid http://orcid.org/0000-0002-9694-2216

Publications

10 25 50

 
Title Cell2TCR identifies activated antigen-responding T?cells based on a gene expression signature and clusters these into clonotype groups 
Description Cell2TCR is a tool for inference of T cell receptor (TCR) motifs. A TCR motif describes a group of TCRs with sufficient sequence similarity to likely recognise a common epitope. 
Type Of Material Improvements to research infrastructure 
Year Produced 2024 
Provided To Others? Yes  
Impact Our new computational pipeline Cell2TCR identifies activated antigen-responding T cells based on a gene expression signature and clusters these into clonotype groups and motifs. Overall, our detailed time series data can serve as a Rosetta stone for epithelial and immune cell responses and reveals early dynamic responses associated with protection against infection. 
URL https://github.com/Teichlab/Cell2TCR
 
Title Ex vivo Model of Functioning Human Lymph Node Reveals Pivotal Role for Innate Lymphoid Cells and Stromal Populations in Response to Vaccine Adjuvant 
Description We describe precision-cut human lymph node (LN) slices as architecturally-preserved, functioning lymphoid tissue model system, and explore early inflammatory responses to a potent vaccine liposomal adjuvant containing a TLR4-agonist and QS21 saponin. Combining scRNA-seq, multiplexed immunofluorescence and secretome analysis, we dissect direct and indirect signalling pathways in both leukocytes and stromal cells to reveal communication networks linking innate and adaptive immunity. Application of molecular inhibitors reveals that secretion of IL 1b, but not IL-18, is TLR4-dependent in human LN. Retaining donor-to-donor immune variation, this ex vivo LN model system enables the study of pathways previously difficult to observe in humans, paving the way towards precision medicine. 
Type Of Material Model of mechanisms or symptoms - in vitro 
Year Produced 2024 
Provided To Others? Yes  
Impact The ex vivo human LN slice approach described here offers a versatile platform for studying mode of action and early cell signalling responses, and could be applied to a variety of compounds, from novel small molecule drugs to a range of immunostimulants and existing therapeutics. Cumulatively, evaluating responses to immune or inflammatory perturbation on a per donor basis, and building our understanding of the principles and nuances of the underlying mechanisms, could pave the way for the rational design of vaccines and drugs towards achieving precision medicine. 
URL https://www.biorxiv.org/content/10.1101/2024.08.21.608943v1.full.pdf
 
Title Multi-site Ultrasound-guided Fine Needle Aspiration to Study Cells and Soluble Factors From Human Lymph Nodes 
Description This minimally invasive technique allows collection of both immune cells and cell-free material that are relevant to both neuroimmune diseases and basic lymphatic functions. Downstream use of cellular material can include multiplexed flow cytometry, single-cell transcriptome sequencing (RNA-seq), and B cell cultures. The cell-free supernatant can be used for proteomics or other similar 'omics approaches. This unit describes collection of samples by FNA as well as processing and storage of samples for downstream assays. 
Type Of Material Model of mechanisms or symptoms - human 
Year Produced 2024 
Provided To Others? Yes  
Impact We describe the application of FNA under ultrasound guidance to sample human LNs, with cervical LN sampling used as an exemplar. FNA is a commonplace physical investigation in various medical contexts, including pathology involving LNs, but driven by advances in downstream '-omic' technologies, the technique has in recent years been shown to be highly adaptable to healthy LNs in a clinical research context and to address the temporal and anatomical considerations discussed above. 
URL https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.70063
 
Title Ex vivo Model of Functioning Human Lymph Node Reveals Pivotal Role for Innate Lymphoid Cells and Stromal Populations in Response to Vaccine Adjuvant 
Description We describe precision-cut human lymph node (LN) slices as architecturally-preserved, functioning lymphoid tissue model system, and explore early inflammatory responses to a potent vaccine liposomal adjuvant containing a TLR4-agonist and QS21 saponin. Combining scRNA-seq, multiplexed immunofluorescence and secretome analysis, we dissect direct and indirect signalling pathways in both leukocytes and stromal cells to reveal communication networks linking innate and adaptive immunity. Application of molecular inhibitors reveals that secretion of IL 1b, but not IL-18, is TLR4-dependent in human LN. Retaining donor-to-donor immune variation, this ex vivo LN model system enables the study of pathways previously difficult to observe in humans, paving the way towards precision medicine. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact We describe precision-cut human lymph node (LN) slices as architecturally-preserved, functioning lymphoid tissue model system, and explore early inflammatory responses to a potent vaccine liposomal adjuvant containing a TLR4-agonist and QS21 saponin. Combining scRNA-seq, multiplexed immunofluorescence and secretome analysis, we dissect direct and indirect signalling pathways in both leukocytes and stromal cells to reveal communication networks linking innate and adaptive immunity. Application of molecular inhibitors reveals that secretion of IL 1b, but not IL-18, is TLR4-dependent in human LN. Retaining donor-to-donor immune variation, this ex vivo LN model system enables the study of pathways previously difficult to observe in humans, paving the way towards precision medicine. 
URL https://www.biorxiv.org/content/10.1101/2024.08.21.608943v1.full.pdf
 
Title Human SARS-CoV-2 challenge uncovers local and systemic response dynamics 
Description The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the dynamics of early cellular responses to this disease remains limited1. Here in our SARS-CoV-2 human challenge study, we used single-cell multi-omics profiling of nasopharyngeal swabs and blood to temporally resolve abortive, transient and sustained infections in seronegative individuals challenged with pre-Alpha SARS-CoV-2. Our analyses revealed rapid changes in cell-type proportions and dozens of highly dynamic cellular response states in epithelial and immune cells associated with specific time points and infection status. We observed that the interferon response in blood preceded the nasopharyngeal response. Moreover, nasopharyngeal immune infiltration occurred early in samples from individuals with only transient infection and later in samples from individuals with sustained infection. High expression of HLA-DQA2 before inoculation was associated with preventing sustained infection. Ciliated cells showed multiple immune responses and were most permissive for viral replication, whereas nasopharyngeal T cells and macrophages were infected non-productively. We resolved 54 T cell states, including acutely activated T cells that clonally expanded while carrying convergent SARS-CoV-2 motifs. Our new computational pipeline Cell2TCR identifies activated antigen-responding T cells based on a gene expression signature and clusters these into clonotype groups and motifs. Overall, our detailed time series data can serve as a Rosetta stone for epithelial and immune cell responses and reveals early dynamic responses associated with protection against infection. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact Our new computational pipeline Cell2TCR identifies activated antigen-responding T cells based on a gene expression signature and clusters these into clonotype groups and motifs. Overall, our detailed time series data can serve as a Rosetta stone for epithelial and immune cell responses and reveals early dynamic responses associated with protection against SARS-CoV-2 infection. 
URL https://www.nature.com/articles/s41586-024-07575-x#citeas
 
Description Collaboration with the MUSICC Consortium 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Our work in the MUSICC Consortium involves conducting controlled human infection studies, using intranasal challenge with the SARS-CoV-2 Omicron BA.5 variant and a new SARS-CoV-2 variant (strain TBD). Samples collected during these studies will be used in characterising the immune mechanisms associated with SARS-CoV-2 infection and identifying correlates of protection. Our work includes assay development and selecting candidate assays aimed at evaluating mucosal immunity (e.g assays for mucosal proteomics profiling). In addition, the spectral flow cytometry panels developed as part of the IMMPROVE WP5 project will be used in these studies.
Collaborator Contribution We work closely with partners from the MUSICC Consortium to advance the development, standardisation, harmonisation, and qualification of immune assays, with a special focus on characterising mucosal immune responses. We also benefit from reagent sharing.
Impact We are in the process of developing standard operating procedures and will also be drafting methodology papers outlining our work in assay development and standardisation.
Start Year 2024
 
Description G2P2/ProVac Consortium 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution As IMMPROVE, we regularly communicate with G2P2 and ProVac. We approach this by inviting the other consortium members to present at our monthly meetings and also extend an invite to both G2P2 and ProVac to our annual meeting. These meetings provided a platform to share progress on ongoing research activities and promoting knowledge sharing and interdisciplinary collaboration.
Collaborator Contribution Knowledge exchange and integration of diverse expertise.
Impact Generation of significant research findings, interdisciplinary collaboration and knowledge exchange
Start Year 2024
 
Description Mucosal Study 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution - Development of SOPs for nasal cell immunophenotyping - Development of methodology for the detection of antigen-specific T responses in the upper and lower airway mucosa - Development of methodology for the detection of antigen-specific B cell responses in the upper and lower airway mucosa
Collaborator Contribution Characterisation of SARS-CoV-2 humoral and cellular responses in the lower airways of infected and/or vaccinated individuals in Malawi
Impact Both Malawi/ UK study are running or ready to start, so no publications/ data uploaded to repositories yet.
Start Year 2024
 
Description PITCH Consortium 
Organisation Newcastle University
Country United Kingdom 
PI Contribution 1. Used longitudinal samples from extensively characterised PITCH cohort to establish how phenotype of T cell memory evolves with repeated exposure 2. Provided healthy control samples for comparison of mRNA vs ChAdOx in HSCT recipients and healthy controls
Collaborator Contribution Knowledge exchange, sample and reagent sharing
Impact https://onlinelibrary.wiley.com/doi/10.1111/bjh.19874 - also used in evidence submission to JCVI on dosing interval in HSCT revaccination regimes in UK Greenbook.
Start Year 2024
 
Description PITCH Consortium 
Organisation University of Birmingham
Country United Kingdom 
Sector Academic/University 
PI Contribution 1. Used longitudinal samples from extensively characterised PITCH cohort to establish how phenotype of T cell memory evolves with repeated exposure 2. Provided healthy control samples for comparison of mRNA vs ChAdOx in HSCT recipients and healthy controls
Collaborator Contribution Knowledge exchange, sample and reagent sharing
Impact https://onlinelibrary.wiley.com/doi/10.1111/bjh.19874 - also used in evidence submission to JCVI on dosing interval in HSCT revaccination regimes in UK Greenbook.
Start Year 2024
 
Description PITCH Consortium 
Organisation University of Liverpool
Country United Kingdom 
Sector Academic/University 
PI Contribution 1. Used longitudinal samples from extensively characterised PITCH cohort to establish how phenotype of T cell memory evolves with repeated exposure 2. Provided healthy control samples for comparison of mRNA vs ChAdOx in HSCT recipients and healthy controls
Collaborator Contribution Knowledge exchange, sample and reagent sharing
Impact https://onlinelibrary.wiley.com/doi/10.1111/bjh.19874 - also used in evidence submission to JCVI on dosing interval in HSCT revaccination regimes in UK Greenbook.
Start Year 2024
 
Description PITCH Consortium 
Organisation University of Sheffield
Country United Kingdom 
Sector Academic/University 
PI Contribution 1. Used longitudinal samples from extensively characterised PITCH cohort to establish how phenotype of T cell memory evolves with repeated exposure 2. Provided healthy control samples for comparison of mRNA vs ChAdOx in HSCT recipients and healthy controls
Collaborator Contribution Knowledge exchange, sample and reagent sharing
Impact https://onlinelibrary.wiley.com/doi/10.1111/bjh.19874 - also used in evidence submission to JCVI on dosing interval in HSCT revaccination regimes in UK Greenbook.
Start Year 2024
 
Description Scientific Advisory Board (SAB) 
Organisation Mount Sinai Hospital
Country United States 
Sector Hospitals 
PI Contribution Our team has contributed to the SAB collaboration by facilitating regular scientific meetings, coordinating stakeholder engagement, and ensuring effective communication between partners.
Collaborator Contribution The Scientific Advisory Board to the IMMPROVE Consortium has provided and continues to provide key scientific feedback on optimal approaches to meet our proposed outcomes and our ongoing activities in both the short and long-term.
Impact The SAB made significant contributions at annual scientific meeting recently held in January 2025 and we will be implementing the suggestions and recommendations made in the areas of Early Career Research (ECR) Training and Support, Future Research directions, our ongoing the age-based cohort studies and further funding.
Start Year 2024
 
Description Scientific Advisory Board (SAB) 
Organisation University Libre Bruxelles (Université Libre de Bruxelles ULB)
Department Institute for Medical Immunology
Country Belgium 
Sector Academic/University 
PI Contribution Our team has contributed to the SAB collaboration by facilitating regular scientific meetings, coordinating stakeholder engagement, and ensuring effective communication between partners.
Collaborator Contribution The Scientific Advisory Board to the IMMPROVE Consortium has provided and continues to provide key scientific feedback on optimal approaches to meet our proposed outcomes and our ongoing activities in both the short and long-term.
Impact The SAB made significant contributions at annual scientific meeting recently held in January 2025 and we will be implementing the suggestions and recommendations made in the areas of Early Career Research (ECR) Training and Support, Future Research directions, our ongoing the age-based cohort studies and further funding.
Start Year 2024
 
Description Scientific Advisory Board (SAB) 
Organisation University of Glasgow
Country United Kingdom 
Sector Academic/University 
PI Contribution Our team has contributed to the SAB collaboration by facilitating regular scientific meetings, coordinating stakeholder engagement, and ensuring effective communication between partners.
Collaborator Contribution The Scientific Advisory Board to the IMMPROVE Consortium has provided and continues to provide key scientific feedback on optimal approaches to meet our proposed outcomes and our ongoing activities in both the short and long-term.
Impact The SAB made significant contributions at annual scientific meeting recently held in January 2025 and we will be implementing the suggestions and recommendations made in the areas of Early Career Research (ECR) Training and Support, Future Research directions, our ongoing the age-based cohort studies and further funding.
Start Year 2024
 
Description Scientific Advisory Board (SAB) 
Organisation University of Oxford
Department Nuffield Department of Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution Our team has contributed to the SAB collaboration by facilitating regular scientific meetings, coordinating stakeholder engagement, and ensuring effective communication between partners.
Collaborator Contribution The Scientific Advisory Board to the IMMPROVE Consortium has provided and continues to provide key scientific feedback on optimal approaches to meet our proposed outcomes and our ongoing activities in both the short and long-term.
Impact The SAB made significant contributions at annual scientific meeting recently held in January 2025 and we will be implementing the suggestions and recommendations made in the areas of Early Career Research (ECR) Training and Support, Future Research directions, our ongoing the age-based cohort studies and further funding.
Start Year 2024
 
Description Networking event for recruiting peer researchers 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact About 50 ethnic minority community members attended a Health Research engagement event to learn about community researchers and we discussed how to participate as peer researchers for social science research.
Year(s) Of Engagement Activity 2024
 
Description Pop-up event at Festival of Tomorrow 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact We held a pop up event with NHS and community partners about 'The Future of Health' and engaged with about 60 people.
Year(s) Of Engagement Activity 2025
 
Description Stand at IF Oxford Science + Ideas Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact We held a stall at a science fair that about 200 people participated in engagement activities aimed at families about vaccines and the immune system. We conducted some light touch evaluations that indicated understandings improved after taking part.
Year(s) Of Engagement Activity 2024