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MRC DiMeN Doctoral Training Partnership: From bench to bedside; using patient-based assays that model the gut microbiome-host interface to aid diagnosis and inform treatment of immune dysregulation

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  • Full or part time
    Dr R Payne
    Prof S Hambleton
    Dr C Stewart
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Immune dysregulation and impaired gut mucosal barrier function are intimately linked features of two paediatric inflammatory gut disorders; namely graft-versus-host disease (GVHD) and necrotizing enterocolitis (NEC). There is growing evidence of the cross-talk between gut microbes and immune populations. Lack of gut bacterial diversity and specific anaerobic bacterial strains have been implicated in disease outcome, however, the direction of causality remains undetermined. Indeed, a better understanding of the complex interplay between gut epithelium, gut microbes and immune cells will be critical for future therapeutic advance.

The overarching aim of this project is to test the hypothesis that immune cell function can be modulated by microbial “therapy”. As such, this project has direct translational consequences with the potential to aid diagnosis and treatment of inflammatory gut disorders.

1. To develop an immune atlas of the paediatric peripheral blood and gut compartments, in health and disease, as an aid to diagnosis and discovery.
2. To investigate the complex interplay between gut epithelium, microbes and immune cells, using an ex vivo model of primary gut epithelium

The student will develop a novel physiologically relevant model of the gut epithelial monolayer that will incorporate both strictly anaerobic “commensal” bacteria (apical surface) and immune cells (basolateral surface) on either side of the gut epithelium.
The “mini gut” model is a cutting-edge technique and an invaluable tool for investigating the documented interplay between gut bacteria and immune cells in a human-based system and holds exciting potential to develop patient-based assays.

Experimental Approach
The student will be trained in the cutting-edge technique mass cytometry (Helios) for high-dimensional single-cell immunophenotyping. CD45+ immune cells will be extracted from neonatal gut resections and analysed by mass cytometry in health (no-NEC) and disease (NEC). In addition, CD45+ immune cells from paediatric peripheral blood will be analysed in health (no-NEC, no-GVHD) and disease (NEC, GVHD). The student will be trained in high-dimensional data exploration and visualization techniques, such as viSNE and FLOWSOM, which they will use to identify cell populations and look for disease-specific changes in the blood and gut.
To test the hypothesis that anaerobic microbes can modulate gut immunopathology, the student will generate patient-based in vitro models of the human gut epithelium. Anaerobic gut bacteria, gut-resident immune cells and gut enteroids will be concurrently isolated from neonatal gut resections, for co-culture under a physiological relevant oxygen gradient.
This novel co-culture system will be utilized to systematically test the effect of microbial sensing on gut epithelium integrity (trans-epithelial electrical resistance measurements) and functioning (transcriptomics). Concurrently, immune cell function will be assessed (mass cytometry, RNA-seq). The student will use this novel model to test the hypothesis that immune cell function can be modulated by microbial “therapy”.

Additional links
Dr Christopher Stewart –
Dr Rebecca Payne
Prof Sophie Hambleton

Benefits of being in the DiMeN DTP:
This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.
We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.
Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here:
Further information on the programme can be found on our website:

Funding Notes

Studentships are fully funded by the Medical Research Council (MRC) for 3.5yrs
Stipend at national UKRI standard rate
Tuition fees
Research training and support grant (RTSG)
Travel allowance
Studentships commence: 1st October 2019.

To qualify, you must be a UK or EU citizen who has been resident in the UK/EU for 3 years prior to commencement. Applicants must have obtained, or be about to obtain, at least a 2.1 honours degree (or equivalent) in a relevant subject. All applications are scored blindly based on merit. Please read additional guidance here:
Good luck!


Vento-Tormo R, Efremova M, Botting RA, Turco MY, Vento-Tormo M, Meyer KB, Park JE, Stephenson E, Polański K, Goncalves A, Gardner L, Holmqvist S, Henriksson J, Zou A, Sharkey AM, Millar B, Innes B, Wood L, Wilbrey-Clark A, Payne RP, Ivarsson MA, Lisgo S, Filby A, Rowitch DH, Bulmer JN, Wright GJ, Stubbington MJT, Haniffa M, Moffett A, Teichmann SA. Single-cell reconstruction of the early maternal-fetal interface in humans.
Nature. 2018 Nov;563(7731):347-353. doi: 10.1038/s41586-018-0698-6. Epub 2018 Nov 14.

Payne RP, Muenchhoff M, Mann JK, Roberts HE, Matthews PC, Adland E, Huang KH, Brockman M, Brumme Z, Sinclair M, Miura T, Frater J, Essex M, Shapiro R. Impact of HLA-driven HIV adaptation and of anti-retroviral therapy on HIV virulance. Proceedings of the National Academy of Sciences of the United States of America 2014, 111(50), E5393-E5400.

Payne RP, Kløverpris H, Sacha JB, Brumme Z, Brumme C, Buus S, Sims S, Hickling S, Riddell L, Chen F, Luzzi G, Edwards A, Phillips R, Prado JG, Goulder PJ. Efficacious early antiviral activity of HIV Gag- and Pol-specific HLA-B*2705-restricted CD8+ T-cells. J Virol 2010, 84(20), 10543-57.

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