PhD Studentship: Computational Analysis of the Tumour Microenvironment of Gastrointestinal Stromal Tumours (GIST)

Main Supervisor: Dr Dean Bryant

Other members of the supervisory team: Dr Zoë Walters and Professor Tim Underwood

Duration of the award:  Four years

Start date:  23^rd September 2024 

Project description: 

Gastrointestinal stromal tumours (GISTs) are sarcomas that present with varying aggressiveness. Most GIST have activating mutations in KIT/PDGFRA, and respond well to Tyrosine Kinase Inhibitors but a significant portion of patients are wildtype, with limited therapeutic options and poorer outcomes. Additionally, the emergence of resistance to TKIs and high rates of recurrence underscore the urgent need for deeper insights into GIST biology. Single cell RNA sequencing studies have identified immune cells present within the GIST tumour microenvironment (TME) that vary between KIT/PDGFRA mutant and wild type GIST. However, single cell RNA-sequencing does not capture spatial information, restricting our understanding of TME-tumour cell interactions. Spatial transcriptomics (SpatialTx) is a cutting-edge approach that enables quantification of the tumour and normal (TME) cell transcriptomes whilst preserving the spatial arrangement of tumour and TME cells. This studentship focuses on analysis of these complex, multi-omic single cell and spatial transcriptomics datasets and is therefore ideal for those with an interest in computational biology, bioinformatics, computer sciences and/or genomics technologies.

The aim of the project is to elucidate the intricate relationships between GIST biology, microenvironmental factors and treatment responses, and holds immense promise for advancing our understanding of the GIST TME. The studentship is well supported by experts in computer sciences, systems biology, cell biology and oncology and holds immense promise for cancer immunology research. Informal enquiries are welcomed and should be directed to Dr Dean Bryant (D.J.Bryant@soton.ac.uk).

Our four-year Integrated PhD in Biomedical Science degree offers an opportunity to develop the advanced research and associated quantitative and bioinformatics skills required to become an independent researcher and leads to the award of Doctor of Philosophy (PhD). An interim Master of Research (MRes) is awarded to those that successfully complete the first year. Further detail on the iPhD programme can be found on our website:  https://www.southampton.ac.uk/medicine/postgraduate/research_degrees/degrees/iphd-biomed.page 

The successful candidate is likely to have the following qualifications:

A minimum 2:1 or equivalent international degree in a computational biology, genomics, biomedical sciences or computer sciences related subject

Funding information:

Due to funding restrictions this position is only open to UK applicants. This is a four funded project supported by the charities Sarcoma UK and GIST Cancer UK that includes UK tuition fees and a student stipend of £19,237.00 in line with UKRI rates

Administrative contact and how to apply:

Please complete the University's online application form, which you can find at

https://student-selfservice.soton.ac.uk/BNNRPROD/bzsksrch.P_Login?pos=9978&majr=9978&term=202425 

You should enter Dr Dean Bryant as your proposed supervisor. To support your application provide an academic CV (including contact details of two referees), official academic transcripts and a personal statement (outlining your suitability for the studentship, what you hope to achieve from the PhD and your research experience to date). 

Informal enquiries relating to the project or candidate suitability should be directed to Dr Dean Bryant (D.J.Bryant@soton.ac.uk) and Dr Zoe Walters (Z.S.Walters@soton.ac.uk)

Closing date:  31/05/2024

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