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  • Project No: #OxKEN-2023/16
  • Intake: OxKEN 2023

Our research group is interested in the cellular basis of early infection events that define virus tropism and how this knowledge translates into new anti-viral strategies. We want to address the fundamental question of 'how, when and where viruses replicate' and to understand how they evade immune recognition. Viruses are intracellular pathogens and understanding the host pathways that define susceptibility to infection and disease are essential for the design of new therapies. Viral replication is shaped by the cellular microenvironment and one key factor is local oxygen tension, where hypoxia regulates the transcription of genes involved in metabolism and inflammatory responses.

Hepatitis B virus (HBV) is a global health challenge and major cause of liver disease and cancer. Chronic hepatitis B is an inflammatory disease that reflects a dynamic interaction between the virus and host immune system. The liver is a naturally hypoxic organ and our recent studies identify a role for hypoxia inducible factors (HIFs) to activate HBV transcription. Hypoxia can also suppress anti-viral cellular immunity by recruiting regulatory T-cells (Tregs) and myeloid-derived suppressor cells (MDSCs) to low oxygen areas of the liver, thereby providing an environment for viral persistence. Understanding the pathways that define host susceptibility to viral mediated inflammation is the 'holy grail' of this field.

Hypoxic signalling

This DPhil will use Digital Spatial transcriptional Profiling (DSP) to identify immune cell populations and infected hepatocytes at the whole transcriptome level in liver biopsies. We will focus on immunosuppressive Tregs and assess whether hypoxic gene signatures impact on cell frequency, location and activation status. Nearest neighbour analysis will examine these cellular interactions at the micro-anatomic level. Staining liver sections for HBV RNAs will enable us to identify immune cells with intracellular viral nucleic acids. For example, liver resident macrophages or Kupffer cells may scavenge HBV and identifying their sub-cellular localisation will uncover new aspects of immune surveillance. Key genes and immune cell types that associate with HBV replication parameters in the tissue will be validated using in vitro viral replication model systems. Pharmacological inhibitors of HIF signalling will define the mechanism underlying the hypoxic control of immune cell activity and virus regulation. The DPhil student will apply these exciting technologies allow us to study virus-host interplay at the single cell level in unprecedented detail. Collectively, this project will test our hypothesis that localised hypoxia regulates the accumulation and function of key effectors such as tissue resident memory T cells and localised suppressor mechanisms, providing new therapeutic insights.


Spatial, hepatitis, Inflammation, hypoxia, virus

training opportunities

The student will join a dynamic and lively team of biologists funded by a prestigious Wellcome Discovery Award that will provide a unique training environment to gain expertise in super resolution imaging techniques to visualize viral RNAs in complex tissues, digital spatial profiling and bio-informatic analysis of inflammatory transcriptomic data sets.  Transferable skills include oral presentations at joint lab meetings, critical review of published scientific literature by contributing to journal clubs and scientific writing by reviewing and drafting manuscripts for publication. The student will work in Nuffield Department of Medicine Research Building and Department of Surgical Sciences (John Radcliffe Hospital, Oxford)  and will have the opportunity to interface with a network of collaborators in Oxford, UK and internationally to translate their data to the wider biomedical community.

key publications

  1. Wing PAC et al.  Hypoxia inducible factors regulate hepatitis B virus replication by activating the basal core promoter. J Hepatol. 2021 Jul;75(1):64-73. doi: 10.1016/j.jhep.2020.12.034.
  2. Wing PAC et al. Hypoxic and pharmacological activation of HIF inhibits SARS-CoV-2 infection of lung epithelial cells. Cell Rep. 2021 Apr 20;35(3):109020. doi:10.1016/j.celrep.2021.109020.
  3. Wing PAC et al. Hypoxia inducible factors regulate infectious SARS-CoV-2, epithelial damage and respiratory symptoms in a hamster COVID-19 model. PLoS Pathog. 2022 Sep 6;18(9):e1010807. doi: 10.1371/journal.ppat.1010807.
  4. Cross AR et al. Spatial transcriptomocs characterization of COVID-19 pneumonitis identifies immune circuits related to tissue injury. JCI Insights 2022, in press.
  5. Bottomley MJ et al. Dampened Inflammatory Signalling and Myeloid-Derived Suppressor-Like Cell Accumulation Reduces Circulating Monocytic HLA-DR Density and May Associate With Malignancy Risk in Long-Term Renal transplant patients. Front Immunol 2022 Jul 1;13:901273.doi: 10.3389/fimmu

contact information of all supervisors

Email: and and informal enquiries are welcome.