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Understanding how epigenetics impacts gene regulation to develop new therapeutic strategies.

Milne

About the Research

Epigenetics is often described as mechanisms that maintain gene expression profiles through multiple cell divisions long after the initiating signal has been lost. In order to support normal development, epigenetic mechanisms must be stable when needed but dynamic enough to also be reversible when necessary. Aberrant epigenetic changes are now understood to be a driving force in many human cancers. However, the very reversibility of these epigenetic changes makes them potentially suitable for therapeutic targeting. The main interest of the Milne lab is in determining how different epigenetic modifications influence the 3D organization of DNA in the cell resulting in altered transcriptional states. To accomplish this, the lab has mainly focused on analysis of a rare leukaemia (blood cancer) caused by rearrangements of the Mixed Lineage Leukaemia (MLL) gene. MLL mutations are a major cause of incurable leukaemias in children and function in part by altering the epigenetic landscape of the cell. The key approaches used in studying this problem include genome wide computational approaches as well as basic molecular biology and biochemical techniques. In collaboration with the Hughes group, we aim to build on our expertise in leukaemia biology and epigenetics to use machine learning to further explore these basic questions. In a second project, in collaboration with Dominic Waithe will be to expand on our imaging capabilities to ask epigenetic questions at a single cell resolution.

One project available in the Milne group will be developed in collaboration with the Hughes group. This joint project focuses on combining the Milne group’s ability to use cutting edge genomics and epigenetic assays with the extensive bioinformatics expertise of the Hughes group to generate high quality genome wide maps of normal and leukaemia cells. These datasets will be further interrogated using machine learning approaches to determine how alterations of the epigenetic landscape drive leukaemogenesis. As part of this project the student will learn how to perform genomics assays, bioinformatics, machine learning techniques and genome engineering approaches.

A second project will be developed in collaboration with Dominic Waithe (https://www.rdm.ox.ac.uk/people/dominic-waithe). This joint project involves the use of dynamic imaging techniques and high resolution single cell imaging to analyse the function of specific nuclear proteins in the context of altering the epigenetic landscape of the cell. Although genome wide approaches are quite powerful, by necessity they analyze datasets generated from large populations of cells. Dynamic imaging techniques such as Single Molecule Tracking (SMT) techniques and fluorescence correlation spectroscopy (FCS) allow quantification and characterization of protein movement within single cells. Collecting data at the resolution of single molecules in single cells provides the possibility of capturing the stochastic nature of gene regulation. Even subtle modifications and effectors of proteins are measurable through the direct or indirect effect these changes have on how a protein of interest moves in a single cell for example.  More specifically, this project will involve the use of drugs or specific mutations to alter the epigenetic landscape of cells in order to analyse the searching and binding activity of key nuclear proteins required for gene regulation. Through careful study of the kinetics, through either measurement of individual protein movements (e.g. SMT) or through population movement kinetics (e.g. FCS) it will be possible to measure these alterations. This project will provide several different training opportunities including the use of high resolution microscopes and the analysis of dynamic imaging data.

 

Training Opportunities

The Milne group is expert in applying genome wide approaches to questions in leukaemia biology, specifically in the area of epigenetics and gene regulation. All members of the Milne group are trained in both “wet lab” molecular biology and biochemical techniques as well as in bioinformatics. Depending on interest and need, opportunities for more extensive bioinformatics training will be provided. In collaboration with the Hughes lab, the first project would also involve the use of machine learning techniques. The Milne group also works in close collaboration with several other groups in the WIMM and training in cutting edge CRISPR/Cas9 mediated genome editing techniques and high resolution imaging (see below) will also be provided if required by the chosen project. Students will be provided with an initial project but are also highly encouraged to develop their own independent and unique perspective on their work.

The WIMM is at the forefront of dynamical and high-resolution imaging techniques, playing host to the Wolfson Imaging Centre. Within this facility, students of the WIMM can expect to be trained to operate and utilize many forms of fluorescence microscopy specific to their imaging needs. The acquisition of images, especially in dynamical imaging, is only the beginning step however, as a large component of the experimental pipeline involves processing and analysis of the data. For this project students will be supported through this process by Dominic Waithe. Dominic is an expert in imaging and analysis techniques of dynamic processes and is also a group leader specializing in image analysis technique development. Dominic will support in the design and analysis of experiments and will assist the student in their development toward a theoretical and practical understanding of the techniques they employ.

 

Students will be enrolled on the MRC WIMM 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.

All MRC WIMM graduate students are encouraged to participate in the successful mentoring scheme of the Radcliffe Department of Medicine, which is the host department of the MRC WIMM. This mentoring scheme provides an additional possible channel for personal and professional development outside the regular supervisory framework. The RDM also holds 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.

 

Publications

DOT1L inhibition reveals a distinct class of enhancers dependent on H3K79 methylation.  Laura Godfrey, Nicholas T Crump, Ross Thorne, I-Jun Lau, Emmanouela Repapi, Dimitra Dimou, Jelena Telenius, A. Marieke Oudelaar, Damien Downes, Paresh Vyas, Jim R. Hughes, Thomas A. Milne.  doi: https://doi.org/10.1101/383489

The basic helix-loop-helix transcription factor SHARP1 is an oncogenic driver in MLL-AF6 acute myelogenous leukemia.  Numata A, Kwok HS, Kawasaki A, Li J, Zhou QL, Kerry J, Benoukraf T, Bararia D, Li F, Ballabio E, Tapia M, Deshpande AJ, Welner RS, Delwel R, Yang H, Milne TA, Taneja R, Tenen DG.  Nat Commun. 2018 Apr 24;9(1):1622.
    
MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia. Kerry J, Godfrey L, Repapi E, Tapia M, Blackledge NP, Ma H, Ballabio E, O'Byrne S, Ponthan F, Heidenreich O, Roy A, Roberts I, Konopleva M, Klose RJ, Geng H, Milne TA. Cell Rep. 2017 Jan 10;18(2):482-495.

MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation. Godfrey L, Kerry J, Thorne R, Repapi E, Davies JO, Tapia M, Ballabio E, Hughes JR, Geng H, Konopleva M, Milne TA.  Exp Hematol. 2017 Mar;47:64-75.
    
Mouse models of MLL leukemia: recapitulating the human disease.  Milne TA.  Blood. 2017 Apr 20;129(16):2217-2223.
    
MLL-Rearranged Acute Lymphoblastic Leukemias Activate BCL-2 through H3K79 Methylation and Are Sensitive to the BCL-2-Specific Antagonist ABT-199. Benito JM, Godfrey L, Kojima K, Hogdal L, Wunderlich M, Geng H, Marzo I, Harutyunyan KG, Golfman L, North P, Kerry J, Ballabio E, Chonghaile TN, Gonzalo O, Qiu Y, Jeremias I, Debose L, O'Brien E, Ma H, Zhou P, Jacamo R, Park E, Coombes KR, Zhang N, Thomas DA, O'Brien S, Kantarjian HM, Leverson JD, Kornblau SM, Andreeff M, Müschen M, Zweidler-McKay PA, Mulloy JC, Letai A, Milne TA, Konopleva M. Cell Rep. 2015 Dec 29;13(12):2715-27.

Supervisors