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AML is the most common aggressive human leukaemia with a poor outcome. It is a complex leukaemia with an average of 5 exonic mutations/patient arranged in multiple clones; a likely underestimate of the complexity of the disease. One biologically simpler model of human AML is that seen in newborns and young children with Down Syndrome called myeloid leukaemia of DS (ML-DS) that is preceded by a preleukaemic phase called Transient Abnormal Myelopoiesis (TAM).

The disease requires germline trisomy 21 (T21), acquisition of a mutation in the transcription factor GATA1[1] and additional mutations([2] and Vyas and Roberts unpublished data). In our large study of the genetics of TAM and ML-DS, T21, a singe allele GATA1 mutation and a single allele mutation in a gene encoding one of the cohesin family of proteins was sufficient for ML-DS (Vyas and Roberts unpublished data). Using murine models, we have also shown GATA1 mutation and a heterozygous mutation in a cohesin family protein cause defined perturbations in myeloid progenitors (Vyas and Roberts unpublished data). We are now investigating the molecular mechanisms for these findings.

This project will build on these studies and now construct a model of human ML-DS. Using cord blood, and possibly fetal liver, cells from individuals with DS we will use Cas9-CRISPR to engineer pathogenic mutations in GATA1 alone, and GATA1 and gene encoding a cohesin family protein member. Isogeneic cells from the three backgrounds will be compared to disomic control cells. Cas9-CRISPR technology in primary human cells is established in the Vyas laboratory. The aim of the project is to define at a detailed molecular level, genome-wide mechanisms leading to differentiation arrest at defined stages of haemopoiesis that arise from cooperation of T21, a mutant transcription factor and a gene family (the cohesin gene family) that regulates transcription through topological mechanisms. To generate hypotheses for mechanisms the applicant will perform a detailed study of gene expression (RNA-Seq), chromosomal accessibility (ATAC-Seq), chromosome topology (Capture-C and/or High-C), in purified haemopoietic progenitors. Functional experiments will then be required to test mechanisms. The applicant will work with members of the Vyas laboratory expert in these areas and collaborate with other laboratories in the MRC Molecular Haematology Unit, more broadly in Oxford and our collaborators outside Oxford.

This highly ambitious project will aim to establish general principles on transcriptional deregulation important in cancer by studying a very well defined blood cancer.

Training 

The project: This project will provide a comprehensive training in generation of human models of disease. It will focus on detailed functional haemopoietic stem/progenitor cell biology, transcriptional and epigenetic control of differentiation and self-renewal using powerful in vivo approaches, computational biology and bioinformatics, flow cytometry, gene editing, molecular and biochemical approaches.

The environment: The Vyas laboratory is based in the MRC Molecular Haematology Unit (MHU), Weatherall Institute of Molecular Medicine (WIMM) (www.imm.ox.ac.uk). There is a world-class single cell facility, a large computational biology core with a dedicated training core (CGAT), largest FACS facility in Europe, expertise in in vitro and in vivo functional analysis of blood cells at a single cell level.

Formal Training:

(a) 2-day WIMM Induction course.

(b) Weekly 2 hour, a year-long small group technique teaching sessions.

Informal Training

(a) Weekly meeting with Professor Vyas.


(b) Day-to-day supervision by senior post-doctoral fellows.


Presentation

(a) Formal data presentation to the weekly laboratory meeting.


(b) Presentation of published papers at the weekly journal club.

(c) The applicant will present at locally and at national/international meetings.

Academic activities

MHU and WIMM have separate weekly international/national speaker seminar series

As well as the specific training detailed above, students will have access to a wide-range of seminars and training opportunities through the many research institutes and centres based in Oxford. Students are also able to attend the Methods and Techniques course run by the MRC Weatherall Institute of Molecular Medicine. This course runs through the year, ensuring that students have the opportunity to build a broad-based understanding of differing research techniques.

Generic skills training is offered through the Medical Sciences Division's Skills Training Programme. This programme offers a comprehensive range of courses covering many important areas of researcher development: knowledge and intellectual abilities, personal effectiveness, research governance and organisation, and engagement, influence and impact. Students are actively encouraged to take advantage of the training opportunities available to them.

The department has a successful mentoring scheme, open to graduate students, which provides an additional possible channel for personal and professional development outside the regular supervisory framework. We hold an Athena SWAN Silver Award in recognition of our efforts to support the careers of female students and staff.

References

 

1.         Roberts, I., et al., GATA1-mutant clones are frequent and often unsuspected in babies with Down syndrome: identification of a population at risk of leukemia. Blood, 2013. 122(24): p. 3908-17.

2.         Yoshida, K., et al., The landscape of somatic mutations in Down syndrome-related myeloid disorders. Nat Genet, 2013. 45(11): p. 1293-9.

Research Themes, Tools and Technologies

Supervisors

Additional Supervisors

Prof Irene Roberts, Department of Paediatrics

Key Dates for October 2018 Entry

Application deadline:  12 noon GMT on Monday 8 January 2018

Interviews for shortlisted candidates: Week commencing Monday 22 January 

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How to apply

To apply for a place on the DPhil in Medical Sciences you will need to submit an application using the online application form.

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