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Precision Medicine DTP - Identifying therapeutic targets for human chronic wounds using single cell transcriptomics and digital spatial profiling


College of Medicine and Veterinary Medicine

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Dr J Cash , Dr Stephen Jenkins , Dr P Ramachandran No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

Additional supervisor: Dr Kristina Kirschner (UoG)

Background

Chronic skin wounds are a major and increasing clinical burden as a result of an aging population and increased prevalence of risk factors including diabetes and obesity. These wounds are physically and psychologically debilitating, have a high risk of infection and reoccurrence, are the commonest cause of limb amputation and have a 5 year mortality rate of 45% (equivalent to colon cancer) [1, 2]. Despite this significant burden of disease there is a profound paucity of science-led therapeutics. This is in part due to the lack of a precision medicine-based approach, with a dearth of comparative data exploring the links between human disease and pre-clinical models.

Macrophages (MFs) are phenotypically plastic cells implicated both in supporting the ‘normal’ repair process and in playing detrimental roles in aberrant healing scenarios. Previous studies indicate that MFs are dysfunctional, exhibiting unrestrained activation in the context of impaired skin healing in both mouse and human. MFs therefore represent an attractive therapeutic target for chronic wounds. However, MFs are highly heterogeneous and dynamic cells, making it challenging to identify specific pathogenic and pro-repair subpopulations. To circumvent this, we are currently using an unbiased single-cell RNA-sequencing approach in two major projects: 1) defining the pro-repair MF population in murine acute skin wounds and 2) identifying pathogenic MF populations in our novel pre-clinical model of human chronic wounds. [2,3,4]. We have also performed Nanostring Digital Spatial Profiling (DSP) to define the immunological milieu of human chronic wounds and support the identification of “core” pathways in skin ulcer formation and persistence.

MFs in rodent skin wounds mirror a number of features of those identified in human chronic wounds. However, the precise corollary subpopulations between mouse pre-clinical models and human chronic skin wounds have not yet been defined. By generating data from human acute and chronic skin wounds, comprising single-cell RNA-sequencing and DSP, we will resolve the pro-repair and ulcerogenic MF subpopulations. We will proceed to map the transcriptomes of these cells to those currently being identified in our mouse acute and chronic wound models using cutting edge computational approaches. This project will enable the identification of ‘core’ pathways regulating skin ulcer formation and persistence versus effective wound healing across species and thus allow the definition of tractable therapeutic targets for chronic skin wounds.

Aims

- Dissect human and mouse skin ulcer MF heterogeneity and activation states using scRNA-seq and Nanostring Digital Spatial Profiling approaches.
- Integrate human acute and chronic wound scRNA-seq data with previously collected mouse wound data. This will facilitate the identification of corollary populations and ‘core’ chronic wound pathways.
- Perform therapeutic targeting of selected skin ulcer pathways in murine models of chronic wounds.

Training Outcomes

- Training in cutting-edge computational and statistical tools to allow the analysis and interpretation of single cell transcriptomic data generated using the 10X Genomics platform, data integration across species and identifying conserved pathways. This will include unsupervised clustering, Harmony and sc-map for data integration, transcriptomic network analysis, pseudotemporal dynamics and RNA velocity analyses.
- Performing and analysing murine models of acute and chronic skin wounds.
- Phenotyping and spatially resolving MF subpopulations from human acute wounds and chronic skin ulcers by multiparameter flow cytometry, DSP, histology and imaging.
- Designing, analysing and interpreting anti-ulcer interventional studies in mouse models.

This MRC programme is joint between the Universities of Edinburgh and Glasgow. You will be registered at the host institution of the primary supervisor detailed in your project selection.

All applications should be made via the University of Edinburgh, irrespective of project location. For those applying to a University of Glasgow project, your application along with any supporting documents will be shared with University of Glasgow.

http://www.ed.ac.uk/studying/postgraduate/degrees/index.php?r=site/view&id=919

Please note, you must apply to one of the projects and you must contact the primary supervisor prior to making your application. Additional information on the application process is available from the link above.

For more information about Precision Medicine visit:
http://www.ed.ac.uk/usher/precision-medicine

Funding Notes

Start: September 2021

Qualifications criteria: Applicants applying for an MRC DTP in Precision Medicine studentship must have obtained, or will soon obtain, a first or upper-second class UK honours degree or equivalent non-UK qualification, in an appropriate science/technology area. The MRC DTP in Precision Medicine grant provides tuition fees and stipend of at least £15,285 (UKRI rate 2020/21).

Full eligibility details are available: http://www.mrc.ac.uk/skills-careers/studentships/studentship-guidance/student-eligibility-requirements/

Enquiries regarding programme: [Email Address Removed]

References

1. Sen, C.K., Gordillo, G.M., Roy, S., Kirsner, R., Lambert, L., Hunt, T.K., Gottrup, F., Gurtner, G.C., and Longaker, M.T. (2009). Human skin wounds: a major and snowballing threat to public health and the economy. Wound Repair Regen 17, 763-771.

2. Cash, J.L., Martin, P. (2016). Myeloid cells in cutaneous wound repair. Microbiol Spectrum. doi: 10.1128/microbiolspec.MCHD-0017-2015.

3. Sindrilaru, A., Peters, T., Wieschalka, S., Baican, C., Baican, A., Peter, H., Hainzl, A., Schatz, S., Qi, Y., Schlecht, A., et al. (2011). An unrestrained proinflammatory M1 macrophage population induced by iron impairs wound healing in humans and mice. J Clin Invest 121, 985-997.

4. Ramachandran, P., Dobie, R., Wilson-Kanamori, J.R., Dora, E.F., Henderson, B.E.P., Luu, N.T., Portman, J.R., Matchett, K.P., Brice, M., Marwick, J.A., Taylor, R.S., Efremova, M., Vento-Tormo, R., Carragher, N.O., Kendall, T.J., Fallowfield, J.A., Harrison, E.M., Mole, D.J., Wigmore, S.J., Newsome, P.N., Weston, C.J., Iredale, J.P., Tacke, F., Pollard, J.W., Ponting, C.P., Marioni, J.C., Teichmann, S.A., Henderson, N.C. (2019). Resolving the fibrotic niche of human liver cirrhosis at single-cell level. Nature 575(7783):512-518.


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