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Characterising mechanisms of mononuclear phagocyte recruitment to the lung and their localisation specific function in respiratory viral infection.

   School of Biological Sciences

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  Prof J Schwarze, Dr Calum Bain  No more applications being accepted  Funded PhD Project (UK Students Only)

About the Project

Project offered for Ker Memorial PhD Studentship in Infectious Diseases

Despite upcoming modern vaccine technologies, respiratory viral infections will remain a key healthcare burden for many years, requiring the development of prophylactic interventions for high-risk individuals and therapies. The early protective immune response to respiratory viruses remains poorly understood.

We have begun to characterise the monocytic response to RSV using mouse models and have shown that monocyte derived mononuclear phagocytes (MNP) in the lung are crucial for the early antiviral response. These cells have the potential to play a key role throughout viral infection due to their highly plastic nature. Preliminary high-dimensional flow cytometry, alongside single cell transcriptomics indicate a high level of heterogeneity in lung MNPs with differentially expressed genes that may play critical roles in early antiviral responses. Furthermore, novel tissue localisation changes in MNPs during RSV infection may have functional implications. Similarly, in murine models of influenza A (IAV) infection lung MNPs are thought to be important for the antiviral response. MNPs are the primary responders to murine IAV infection with both recruitment and inflammatory polarisation dependent upon interferon (IFN) gamma, rather than type I IFN axis dependency in RSV.

In this PhD project, we seek to understand the factors responsible for virus-induced monocyte recruitment to the lung vasculature and then into lung tissues, their transition to MNPs, their exact localisation in lung tissues and how these contribute to antiviral function, and their role in the induction and resolution if virus induces pulmonary inflammation.

To this end, this project address the following aims:

1. Determine the molecular basis of MNP recruitment to the lung during RSV.


  • Use existing in-house and publicly available transcriptional data to identify key chemo-attractants in both RSV and IAV.
  • Trans-well migration assays using isolated monocytes to confirm responsiveness to identified chemo-attractants.
  • Chemoattractant neutralising antibodies, and where suitable signalling deficient mice, to confirm the importance of each path in monocyte recruitment and the subsequent effects upon viral diseases.

2. Characterise the spatial positioning/migration of MNP in response to viral infection.


  • Spatial transcriptomics or multiplex imaging will be developed to assess MNP localisation across the lung in viral infection.
  • Lung explants or in vivo imaging in parallel with MNP fluorescent reporters and vascular labelling to observe the changes in localisation at temporal resolution in response to viral challenge.

3. Align phenotypic and spatial changes in MNPs in viral infection.


  • Integration of existing single cell datasets and spatial characterisation generated through this project to identify viral infection induced inflammatory and antiviral pathways.
  • Where available use myeloid specific knockouts, including those currently being generated, to dissect the specific contributions of MNPs to viral disease.
  • Cell transfer experiments/bone marrow transplants where necessary to dissect lineage specificity of identified pathways.

The findings of this PhD project will define important common mechanistic factors of monocyte and MNP function in respiratory viral infections. This insight can then be translated to the human situation, e.g. by experimental respiratory virus challenge models, which have been established by several groups in the UK.

Training environment

The Schwarze lab has extensive expertise in analysing antiviral and inflammatory immune responses in the lung in multiple murine models of respiratory viral infections. This is complemented by the expertise of the Bain lab, which has a major focus on monocyte and macrophage biology in mucosal tissues, including a huge range of in vivo tools to track (lineage-trace), deplete or genetically target gene deletion to specific MNP subsets. Combining the expertise in close new partnership for this PhD project will provide us with a state of the art environment to dissect mechanisms and consequences of respiratory virus induced recruitment and localisation of lung mononuclear phagocytes.

Training and skills development

Training in pre-clinical models of viral infection, advanced flow cytometry, microbiology and imaging technologies (e.g., spectral confocal microscopy, CODEX) will be provided by the supervising research groups. Where necessary provision will be made for attendance of training course in transcriptomic analysis and the handling of other large datasets, particularly using R studio. Opportunities for public outreach are provided through the host institute. Attendance to at least one international conference is expected as part of this program and attendance to local and smaller conferences throughout is encouraged. Annual presentation at departmental PhD presentations, along with more frequent topic and laboratory specific meetings provides opportunities and support for development of presentation skills. Annual project progress reports and regular supervisor meetings ensure progress in acquiring a broad skill base and hands on mentoring as required. The PhD student would take part in our ‘Journal Club’ to gain experience in the critical (and positive) evaluation of the literature. Opportunities to write small grant applications for funding for additional travel and/or training will be encouraged via grant schemes available through learned societies (e.g., British Society for Immunology, Society for Mucosal Immunology, EAACI).     

This project would provide a very strong foundation in many of the techniques at the forefront of modern cellular immunology and leave the candidate well equipped for future primary or industrial life science research.

Funding Notes

All students will receive a stipend at UKRI levels (£18622 per annum from 1 October 2023 per annum), plus a total of £30K in travel and research funds across all four years of the Programme. All University fees will be covered.


Goritzka M et al., JEM. 2017 DOI: 10.1084/jem.20140825
Burgess MO et al., Authorea. 2023 DOI: 10.22541/au.168378133.32387824/v1
T’Jonck and Bain. IJBCB. 2023 DOI: 10.1016/j.biocel.2023.106421
Schmit T et al., Cell Rep. 2022 DOI: 10.1016/j.celrep.2022.110456
Rodero MP et al., eLIFE. 2015 DOI: 10.7554/eLife.07847

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