The Roles of Transposable Elements as Oncogenic Regulators in Acute Myeloid Leukaemia

Application deadline: 1 December 2022

Start date: January or April 2023

This non-clinical project will commence early 2023 and has funding for 4 years. The student will be based primarily at Barts Cancer Institute, Barts and the London Faculty of Medicine and Dentistry (FMD), Charterhouse Square in the City of London.

Primary Supervisor: Dr Özgen Deniz

Centre for Haemato-Oncology

We are looking for a talented and enthusiastic student fascinated by transposon and cancer biology. A fully funded four-year PhD studentship is available at the Barts Cancer Institute, Queen Mary University of London (QMUL) under the supervision of Dr Özgen Deniz to work on “The Roles of Transposable Elements as Oncogenic Regulators in Acute Myeloid Leukaemia”. The project aims to understand how transposable elements are dysregulated in cancer and how this contributes to generation and development of cancer. The project involves state-of-the-art molecular techniques for epigenomics, transcriptomics and CRISPR-based genome editing. The expected start date is January or April 2023. 

A major area of CRUK-funded research in our lab is to investigate the oncogenic roles of transposable elements in both adult and paediatric acute myeloid leukaemia. Transposons are mobile DNA segments that have expanded within the human genome throughout evolution and today compromise half of the human genome. They have evolved cis-regulatory sequences to exploit the host cellular machinery to promote their own transcription and replication. Whilst the vast majority of transposons in the human genome have been rendered immobile due to mutation, many have retained their regulatory function and can provide regulatory innovation for the host. Indeed, a number of discoveries have shown that transposons can be co-opted as tissue-specific gene regulatory elements, such as promoters and enhancers, and mediate important biological processes. Cancer cells provide epigenetically relaxed and permissive environments for their activation and therefore, transposable elements have the potential to be significant mediators of cancer progression. In support of this, we have previously demonstrated the driving role of transposons in cellular proliferation in myeloid leukaemia cell line models (Deniz et al, Nature Communications, 2020; PMID: 32665538).

The aim of the CRUK-funded PhD project is to investigate the oncogenic roles of transposons in adult acute myeloid leukaemia. Using cell line models and primary patient samples, the PhD student will investigate how epigenetic mechanisms regulate transposon activities and how disruption of epigenetic control in leukaemia favours the oncogenic activation of transposons. Combining CRISPR-based genome and epigenome editing with genomics analyses, we seek to understand how transposable elements are dysregulated in cancer and what consequences this has for the cancer cellular phenotype. By focusing on a previously understudied but important part of the genome, we hope to provide novel insights into cancer biology and uncover new determinants of oncogenic regulators that will contribute to development of new strategies in cancer therapies.

The project employs state-of-the-art molecular and cellular biology techniques, including flow cytometry, genomics techniques (e.g. ATAC-seq, ChIP-seq, CUT&RUN/CUT&Tag, RNA-seq, PCHi-C), CRISPR-mediated genetic and epigenetic editing in cell lines and primary cancer cells, bioinformatic analyses of genomics data.

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 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 studentship only covers tuition fees at the Home rate. Overseas applicants are welcome to apply, but will be required to fund the difference in tuition fees.

The studentship includes the following funding for 4 years:

  • A tax-free annual stipend of £23,000
  • Tuition fees at the Home rate*
  • Project consumables

*If you are considered an overseas student for fee purposes, you are welcome to apply for this studentship, however you will be required to cover the difference in tuition fees.

To apply you will need to complete an online application form.

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 bci-cancercourses@qmul.ac.uk

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