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

   Department of Haematology

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  Dr Özgen Deniz  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project

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.

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. 

Candidate Background:

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.

Funding availability:

The CRUK studentship includes a non-taxable stipend (£21,000/year), running expenses and university fees at UK level. Non-UK applicants will need to secure additional funding for overseas student fees. The expected start date is January 2023 or April 2023.

How to apply:

If you are interested, please follow the official advert below:

All applicants should be directed to the BCI website as all applications must be submitted online via MySIS and the link is in the advert under ‘How to apply’. To apply you will need to complete online application form. Application deadline is 1st December.

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

For further information about our lab please visit Informal inquiries are welcome. The interviews will take place on 19th December.

Funding Notes

The CRUK studentship includes a non-taxable stipend (£21,000/year), running expenses and university fees at UK level. Please note that we will only be able to offer studentships to candidates that have UK home tuition fee status or provide evidence that they can fund the international portion of the tuition fee from external sources
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