Vyas Group: Genetic And Epigenetic Mechanisms Leading To Acute Myeloid Leukaemia. Developing New Targeted Therapeutic Approaches

Supervisor: Paresh Vyas

About the Research 

This exciting project brings together the Vyas and Nerlov laboratories with established international reputations in haemopoietic stem cell biology haematopoiesis, transcription factor and epigenetic regulation of gene expression using haemopoiesis and blood cancers as models and the biology and treatment of AML (see publications at the end).

Humans make ~10¹³ blood cells daily. Haemopoiesis is sustained by ~10⁵-10⁶ haemopoietic stem cells (HSCs) that divide infrequently (1-4 times/year). HSCs give rise to proliferative haemopoietic progenitor clones, which we have extensively characterised in human and mouse. Relevant here, we identified lymphoid primed multipotential progenitors (LMPP) that differentiate into lymphoid & myeloid progenitors, including granulocyte-macrophage progenitor (GMP). These progenitors differentiate to myeloid precursors that terminally differentiate. Haemopoietic stem/progenitor cells (HSPCs) accumulate somatic mutations and epigenetic changes throughout life. Some mutations/changes give selective advantage, leading to expanded clones (clonal haemopoiesis CH). The mechanism of clonal advantage in CH is not understood, but we recently showed that CH HSCs better resist inflammation that negatively impacts HSC function. CH clones complete differentiation but have myeloid lineage bias. Over time, CH clones can acquire further genetic/epigenetic change, gaining additional competitive advantage, leading to dysplasia and cytopenia and myelodysplastic syndrome (MDS). Some MDS clones evolve further, exhibit differentiation arrest, leading to acute myeloid leukaemia (AML). In AML, haemopoiesis is largely replaced by progenitor-like, or precursor-like cells with leukaemic stem cell (LSC) potential. Thus, there are inter-twined clonal genetic, and hematopoietic, hierarchies as oncogenic genetic and epigenetic changes perturb haemopoiesis leading to AML.

The aim of this project is to study and understand how pathogenic recurrent genetic mutations in a transcription factor called RUNX1 and an epigenetic regulator called BCOR commonly collaborate to cause MDS that progresses to AML. RUNX1 and BCOR mutations are co-selected. We have previously shown that RUNX1 mutations cause differentiation arrest at the progenitor stage. Furthermore, an additional BCOR mutation causes further arrest at the most proliferative LMPP stage. Now we wish to understand the mechanisms by which this occurs and specifically the precise deregulation of gene expression that leads to clonal dominance and differentiation arrest that characterises AML.

The student will join a team of post-doctoral scientists and a PhD student studying patient samples from the MDS and AML stages of disease and samples from a novel complex animal model of the RUNX1 and BCOR mutation.

Specifically, the student will:

1. Learn single cell (sc) RNA-Seq, ATAC-Seq, CUT-TAG and bulk cell DNA methylation methods, including FACS analysis, FACS-sorting cells, making sc libraries and computational analysis of sc data. Prior experience of R and Python and use of computational pipelines would be helpful.
2. CRISPR screens in primary human and mouse cells. Advanced primary cell culture, growing primary cells on stromal cell layers, designing and executing CRISPR screens, and analysing data from CRISPR screens.
3. Screens using chemical inhibitors on primary human and mouse cells.

Translational Potential. This project aims to identify novel targeted therapies for specific genetic subgroups of AML and other myeloid cancers.

Training Opportunities 

The student will be trained in: (i) fundamental aspects of gene regulation using normal haemopoiesis and myeloid blood cancers as models; (2) molecular and cellular biology, cell-based CRISPR and chemical screens; (3) computational analysis; (4) use of in vitro and in vivo models. The training will be focused on skill sets critical to discovering mechanisms of altered gene expression leading to cancer and to developing targeted small molecule therapies.

Key methods include:

1. Molecular biology: complex molecular cloning, protein expression, sc approaches: RNA-Seq, ATAC, CUT-TAG.
2. Use of computational pipelines using Python and R to analyse sc data.
3. Complex multi-colour flow cytometric analysis and FACS-sorting. All students will aim to independently use flow analysers and sorters.
4. Lentiviral and adeno-associated viral transduction of primary cells.
5. CRISPR screens of cell lines and primary cells.
6. In vitro and in vivo assays of primary cell function.

Students will be enrolled on the MRC Weatherall Institute of Molecular Medicine DPhil Course, which takes place in the autumn of their first year. Running over several days, this course helps students to develop basic research and presentation skills, as well as introducing them to a wide range of scientific techniques and principles, ensuring that students have the opportunity to build a broad-based understanding of differing research methodologies.

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.

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.

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 build a happy and rewarding environment where all staff and students are supported to achieve their full potential.

1. Claus Nerlov

Publications