Cancer Experimental and Computational PhD

Project: Characterising the cancer-selective HLA immune-peptidome for Ewing Sarcoma

• Application deadline: 22nd September 2025
• Project start: 1st February 2026

The project will involve interaction with coinvestigators, including the proteomics team led by Prof Jyoti Choudhary of the Institute of Cancer Research, London, a member of the Bioinformatics Platform at the UCL Cancer Institute and members with immune-oncology expertise within the teams led by Professors Jon Fisher at the Institute of Child Health and Wenhui Song and the Royal Free Hospital.

Supervisors

Funding and duration

Funding will be for three years (full-time).  

• A non-taxable annual stipend of £22,780 per annum (current UKRI London rate)
• Tuition fees for Home status

There are no additional top-up funds for overseas tuition fees available. 

About the project 

This is a PhD student project funded by The Bone Cancer Research Trust. The Bone Cancer Research Trust is committed to educating the next generation of bone cancer researchers and acts to enable pioneering research that saves lives and improves outcomes for people with primary bone cancer. 

Project aim

This project aims to characterise the immune-peptidome of Ewing Sarcoma, comprehensively and at a genome-wide scale. The objective is to identify tumour-specific immune epitopes that could pave the way for innovative, next-generation treatments for these aggressive bone cancers. 

Background

Ewing sarcoma (EWS) comprises a group of aggressive tumours predominantly diagnosed in children and young adults.  The current treatment for EWS consists of an intensive regimen involving combined use of surgery, radiation and intensive multiagent chemotherapy. Although these treatments can achieve a cure in early-detected disease, they often have limited success in advanced cases and are further associated with significant side effects that impact long-term quality of life. Together, this underscores the urgent need for additional, alternative, more effective, and less toxic therapies. 

Rationale

Adoptive immune-based strategies that selectively target cancer cells represent an exciting, highly promising, and rapidly advancing approach for the treatment of cancers. A crucial element of these strategies is the identification and validation of tumour-specific and tumour-selective immune epitopes. These epitopes can serve as the foundation for developing immune-cell therapeutics capable of efficiently killing tumour cells while minimising toxicity to normal tissues. Identifying such epitopes for EWS is the core objective of this project.

Methodology

The project will leverage data from bespoke mass spectrometry-based HLA Class I peptidome mapping to identify tumour-selective immune epitopes based on the mining of in-house generated and publicly available transcriptomic datasets. Promising candidates will undergo proof-of-concept testing to evaluate their immunogenicity and their ability to elicit anti-EWS immune responses. 

Collaborative framework

This project provides an opportunity to work within a multidisciplinary consortium of co-investigators, including: 

• The proteomics team led by Prof. Jyoti Choudhary at the Institute of Cancer Research, London.
• Members of the Bill Lyons Bioinformatics Platform at the UCL Cancer Institute.
• Experts in immuno-oncology within teams led by Profs. Jon Fisher, at the Institute of Child Health, and Shao-An Xue and Wenhui Song and at the London Royal Free Hospital. 

Formal supervisory meetings will be once a week with the primary supervisor. The student will further be supported through interaction with the various co-investigators and the Thesis Committee, tailored to contribute project-relevant expertise and support and chaired by the secondary supervisor. The student will participate in the UCL Cancer Institute Research in Progress Seminars (CIRPS), departmental seminars, weekly laboratory meetings and, at regular intervals, discuss strategy and present progress to coinvestigator teams and the secondary supervisor. In addition, the student will attend structured UCL teaching and training meetings. All students take part in a compulsory first-year Cancer programme and are part of the UCL Doctoral School’s Development Training Programme.

About the department  

The PhD student will be based at the UCL Cancer Institute working within the team of Professor Sibylle Mittnacht, which is part of, and embedded within the CRUK City of London Centre of Excellence including The Francis Crick Institute, Barts, Queen Mary University of London and King’s College London, with periods of work and training at other locations when required. 

The UCL Cancer Institute is the hub for cancer research at one of the world’s leading universities. The Institute draws together over 400 talented scientists and over 150 PhD students, working together to translate research discoveries into developing kinder, more effective therapies for cancer patients.  

Entry requirements

• Experience in molecular biology techniques and computational biology related to transcriptomics data generation and analysis is essential. Experience in tissue culture, cell-based assays, and T cell immunology is desirable.
• A UK master’s degree, or a minimum of a first or an upper second-class UK Bachelor’s degree, in a relevant discipline, or an overseas qualification of an equivalent standard. Candidates will need to demonstrate a strong research component. We welcome applicants from disadvantaged backgrounds or via an unconventional career path.
• The project is multi-disciplinary in nature; therefore, the student should be motivated to carry out both dry lab and wet lab experiments. The student should have a background and/or skills in both biology and bioinformatics. 

Application process

Interviews will be at the end of September. Successful candidates will be invited to visit the laboratory and meet members of the teams. 

To apply for this studentship, you must:  

1. Submit the following two documents. 

• Your full CV including: 

  The names and contact details of two referees (at least one of whom must be an academic reference from your previous educational institution). 

  And a short summary (<500 words) detailing the following: 

  - Why do you want to do a PhD, and why this one
  - What are your career aspirations and previous experience
  - Please give details on your research experience in cell culture and wet lab techniques, molecular biology, data analysis and computational biology as part of your statement.

• A single PDF file containing scans of your award certificate and transcripts showing your unit/module marks for all of your degrees, undergraduate and postgraduate. If any of your original documents are not in English, you must submit an official English translation with them. 

These two documents must be emailed to ci.pgreducation@ucl.ac.uk by 22 September 2025. The subject line of your email should contain the studentship title and your surname. 

2. You must also contact your referees and ask them to submit their references by email to ci.pgreducation@ucl.ac.uk from a verifiable academic or professional email address. The studentship title and your surname must be in the email subject line.  

References must be received from your referees by 22 Sep 2025. Please ensure that your referees have submitted references for you, as we will not chase missing references. Incomplete applications will not be forwarded to the Shortlisting Panel.  

Queries about the application procedure or recruitment process should be directed to ci.pgreducation@ucl.ac.uk.