Applications are through the NDM Studentships portal. Prospective applicants are encouraged to email anita.milicic@ndm.ox.ac.uk with their CV and short statement of interest.

DPhil Theme Details

Theme Overview

Understanding the fundamental principles of the mamalian immune system is critical in the development of new prophylactic and therapeutic treatments, including vaccines. In vaccinology research in particular, much of the focus is on the adaptive immune response to the vaccine antigen, which usually peaks 1-3 weeks following immunisation. This has resulted in a poor understanding of the earliest cellular and molecular pathways activated in the hours and days post-vaccination, which ultimately determine the strength and longevity of the adaptive response. 

Epigenetic imprinting in myeloid innate immune cells which can lead to subsequent heightened responsiveness to infection has been amply demonstrated with the BCG vaccine inducing heterologous pathogen cross-protection. Other recent studies have reported vaccination-induced chromatin changes in human blood monocytes after immunisation with the H5N1 pandemic influenza vaccine in AS03 adjuvant and with Vaxzevria (ChAdOx1-Spike) Covid-19 vaccine. With access to different vaccine platforms and adjuvants, and ability to modulate the rate of vaccine delivery in mouse models, this project will investigate innate immune imprinting in the context of immunisation. It will assess epigenetic changes induced by different vaccine platforms (adjuvant, viral vectors, mRNA) and rate of delivery (bolus vs. sustained release) in classical monocytes (Mo) and myeloid DCs (mDCs) from peripheral blood, dLN and bone marrow, by screening for an enhanced cytokine response in vitro post-vaccination. Isolated cells will be stimulated with TLR agonists, e.g. TLR1/2 (Pam₃CSK₄) and TLR4 (LPS), and NLRP3 inflammasome activators (LPS + Nigericin), and supernatants analysed for multiplex cytokine and chemokine production (e.g. TNF, IL-6, IL-1β, IL-18, MCP-1, CXCL-1) to identify vaccine modalities that amplify the innate response upon re-stimulation. Any prominent innate signatures will be explored further by detailed epigenomic and transcriptomic analysis: the relevant cells/sites identified in the initial restimulation screen will be interrogated by parallel single cell Omni ATAC-seq (focusing on previously identified chromatin sites: H2BK5ac, H3K9ac, H3K27ac, and H4K5ac), and scRNA-seq to link regions of open chromatin to gene-expression maps of individual immune cells. With a view of accelerating the clinical translation of some of our immunisation strategies, these findings could be further validated by scATAC-seq and/or scRNA-seq in innate cells from human PBMC samples pre- and post- vaccination.

In parallel with the mouse models, we are investigating the inflammatory and immune activation in response to vaccines in human lymph nodes ex vivo. Here we study the changes in the transcriptional profile, tissue cell composition, architecture and microenvironment, mapped by single-cell sequencing, hyperplexed imaging and multiparameter flow cytometry. 

Integrating the data generated through these workstreams will enable comparative analyses of human and murine responses to vaccines and adjuvants, inform ongoing and future vaccine design programmes, and help bridge the existing translational gap between pre-clinical evaluation of vaccines and their clinical application.