Deciphering the epigenetic mechanisms of retrotransposon-mediated cancer immunity: identifying targets to combat tumour immune evasion

Application deadline: 15 April 2024

Start date: September 2024

We are looking for a talented and enthusiastic student fascinated by transposon, immunology and cancer biology to join our group at the Barts Cancer Institute, Queen Mary University of London (QMUL). This is a fully funded four-year PhD studentship under the supervision of Dr Özgen Deniz, as part of the UKRI-funded ERC Starting Grant. The candidate will work closely with scientists, clinicians and computational biologists. This project is at the interface of immunology, cancer biology, epigenetics and bioinformatics and aims to determine epigenetic mechanisms underlying retrotransposon-mediated immune signalling in cancer. A combination of innovative techniques for wet and dry lab analysis will be used with the ultimate goal of identifying novel therapeutic strategies for cancer patients. The student will be a part of an expanding and dynamic research team, be supported for career and personal development and trained in transferable skills, including bioinformatic analysis.

Primary Supervisor: Dr Özgen Deniz

Centre for Haemato-Oncology

Dysregulation of epigenome is a hallmark of cancer, where aberrant patterns of gene expression lead to uncontrolled cellular growth and drive the trajectory of cancer development. Given that epigenetic changes are reversible and distinguish cancers from their respective cell of origin, targeting epigenetic modifiers has emerged as a compelling therapeutic approach in cancer. Accumulating evidence suggests that epigenetic factors not only activate intrinsic oncogenic pathways but also involve extrinsic factors that modulate the immune system, contributing to immune evasion in cancer. Moreover, epigenetic therapies have demonstrated to reactivate retrotransposons, ancient remnants of viral DNA, stimulating an anti-tumor immune response and triggering immunogenic cell death. Despite these promising observations, the underlying molecular mechanisms governing this process remain poorly understood.

We aim to decipher the epigenetic regulation of retrotransposon-driven cancer immunity and identify novel vulnerabilities to abolish tumor immune evasion and enhance therapeutic outcomes. Combining epigenetic drug and CRISPR-Cas9 screens, we seek to identify key players in the immunomodulatory functions of retrotransposons, revealing potential targets for therapeutic intervention. The potential targetable candidates will be further tested in pre-clinical models, propelling the translational potential of our discoveries.

As part of this project, the PhD student will receive comprehensive training in state-of-the-art molecular and cellular biology techniques, including flow cytometry, various genomics techniques (ATAC-seq, CUT&RUN, RNA-seq, EM-seq, single cell multi-omics), epigenetic drug screening, and CRISPR-mediated genome editing across diverse cellular contexts, including cell lines, primary cancer cells, and patient-derived xenografts. Additionally, you will gain expertise in bioinformatic analyses of multi-omics data, equipping the student with a robust skill set for impactful contributions to cancer research.

The closing date for applications is 15 April 2024 with interviews expected to take place shortly after. For further information about our lab please visit For an informal discussion, please contact the lead project supervisor: Dr Özgen Deniz; subject ‘PhD applicant’.

Academic Entry Requirements

Essential requirements for this post include an undergraduate degree in a biological subject and research laboratory experience in general molecular and cellular biology techniques. Holding a Master’s degree in a related subject will be an advantage. The successful candidate will have excellent academic skills (at least a 2.1 honours degree or equivalent undergraduate degree) combined with strong communication and interpersonal skills.

English Language Requirements

Applicants for whom English is not a first language will also require a minimum IELTS score of 6.5 (with 6.0 in the written component) or equivalent, unless your undergraduate degree was studied in, and awarded by, an English speaking country. For more information on acceptable English language qualifications please see here.

Fee Status

The funding for this UKRI/ERC studentship only covers tuition fees at the Home UK rate.

The studentship includes the following funding for 4 years:

  • A tax-free annual stipend of £22,000
  • Tuition fees at the Home rate*
  • Project consumables

* Only students who are eligible to UK Home rate tuition fee status are eligible to apply.

To apply you will need to complete an online application form. Please select the non-clinical option.

The following supporting documents will be required as part of your application:

  • Your CV
  • Statement of purpose
  • Details of 2 referees
  • Copy of your transcript(s), including a breakdown of marks
  • Copy of your passport
  • If applicable, proof of English proficiency

If you have a question about the project, or would like to arrange an informal discussion, please contact the supervisor directly (subject ‘PhD applicant’). For general enquiries about the PhD studentship or application process please contact the Teaching Office.

Successfully shortlisted candidates will be invited to an interview at Barts Cancer Institute.