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MRC DiMeN Doctoral Training Partnership: Genomic translocations, super-enhancer hijacking and oncogene activation: from mechanism to therapy


Project Description

Background
Haematopoiesis is a developmental process which culminates in the formation of all the blood cells required in our immune system. Errors in this process leads to the accumulation of cells held at a specific stage of differentiation, resulting in the development of haematological malignancies.

Genomic translocations are a hallmark of cancer. Their identification has led to improvements in diagnosis and outcome in haematological malignancies. We are particularly interested in leukaemias and lymphomas resulting from translocations in the immunoglobulin (Ig; antibody) locus in B lymphocytes. Normal rearrangement of Ig gene loci and their super-enhancers is needed to generate the antibody repertoire, but these super-enhancers can be aberrantly rearranged and “hijacked” by oncogenes. However, our understanding of this genomic information is very limited and therapeutic strategies exploiting this data are yet to be developed.

Over 70 genes are translocated to the Ig loci and overexpressed as a result of the rearrangement, but this is not a random process. Recurrent translocations imply a common mechanism that supports developmental stage-specific, long-range interactions between particular promoters and enhancers. A strong candidate mechanism would be shared transcriptional regulatory proteins (TRPs) that might bind regulatory regions at each locus, favouring the translocation.

Objectives
This project will develop and apply computational methods together with complementary laboratory experiments to identify key TRPs in normal and malignant human B-cell development.

This PhD aims to:
Use artificial intelligence (AI) to mine epigenomic datasets to identify TRPs that bind Ig and partner gene enhancers and promoters.
Use public and in-house chromosome conformation data to connect enhancers with gene promoters by developing maps of promoter-enhancer interactions.
Identify TRPs actually bound to enhancer and promoter regions by CAS9 driven immunoprecipitation and mass spectrometry.


Experimental Plan
Using the IHEC epigenomes (http://ihec-epigenomes.org), we aim to identify the TRPs that bind Ig and partner gene regulatory regions in B‐cells at different stages of differentiation. We will identify TRP binding motifs in those regions. We will compare this epigenomic landscape with that obtained from the cell line data derived from patients with Ig translocated malignancies. To connect enhancers with gene promoters, we will use 3D-genome maps of human B‐cells. To complement this in silico analysis we will undertake a CAS9 driven immunoprecipitation and mass spectrometry approach. We will pull down TRP complexes and sequence regions at both Ig and partner gene regulatory regions. We will use machine learning to identify the drivers of these malignant interactions. Together these approaches will uncover key TRP signatures underpinning Ig translocations, enabling rational design of new therapeutic approaches.

By combining experimental work and bioinformatics training, the student will develop both expertise and knowledge relating to how translocations lead to oncogenic expression and transferable skills in the integrative analysis of complex types of quantitative data. This training will be underpinned by a supervisory team with the following expertise:

Experimental analysis of B-cell leukaemia:
Lisa Russell - https://www.ncl.ac.uk/nicr/staff/profile/lisarussell.html

Computational genomics:
Daniel Rico - https://www.ncl.ac.uk/icm/people/profile/danielrico.html

Immune system development:
Sophie Hambleton - https://www.ncl.ac.uk/icm/people/profile/sophiehambleton.html

Chromatin regulation of immunoglobulin loci:
Anne Corcoran - https://www.babraham.ac.uk/our-research/lymphocyte/anne-corcoran


Benefits of being in the DiMeN DTP:
This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.
We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.
Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here: http://www.dimen.org.uk/overview/student-profiles/flexible-supplement-awards
Further information on the programme can be found on our website:
http://www.dimen.org.uk/

Funding Notes

Studentships are fully funded by the Medical Research Council (MRC) for 3.5yrs
Includes:
Stipend at national UKRI standard rate
Tuition fees
Research training and support grant (RTSG)
Travel allowance
Studentships commence: 1st October 2019.

To qualify, you must be a UK or EU citizen who has been resident in the UK/EU for 3 years prior to commencement. Applicants must have obtained, or be about to obtain, at least a 2.1 honours degree (or equivalent) in a relevant subject. All applications are scored blindly based on merit. Please read additional guidance here: View Website
Good luck.

References

Lisa J Russell, Amir Enshaei, Lisa Jones, Amy Erhorn, Dino Masic, Helen Bentley, Karl S Laczko, Adele K Fielding, Anthony H Goldstone, Nicholas Goulden, Christopher D Mitchell, Rachel Wade, Ajay Vora, Anthony V Moorman, Christine J Harrison. [email protected] translocations are prevalent in teenagers and young adults with ALL and are associated with a poor outcome. J Clin Oncol. 2014 May 10;32(14):1453-62.

Pancaldi V, Carrillo-de-Santa-Pau E, Javierre BM, Juan D, Fraser P, Valencia A, Rico D. Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity. Genome Biology 2016, 17, 152.

Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A, The BLUEPRINT Consortium. Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Research 2017, 45(16), 9244-9259.

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