WIMM PI
Curriculum Vitae
Personal Data
Name
Thomas Milne
Nationality
Canadian
Email
thomas.milne@imm.ox.ac.uk
Present Position
2010 – present
Group Leader, MRC Molecular Haematology Unit (WIMM)
Previous Positions
Nov.2004 – Nov 2010
Postdoctoral Fellow, Dr. C. David Allis, Lab of Chromatin
Biology The Rockefeller University, NY, NY
Sept. 2001 – Nov 2004
Ph.D., awarded May 2005, Supervisor: Dr. Hugh Brock
University of British Columbia, Vancouver, B.C., Co-supervisor:
Dr. Jay Hess, University of Pennsylvania, Philadelphia, PA
Mar 1 2000 – Aug 31 2001
Lab Technician, Dr. Jay Hess, University of Pennsylvania,
Dept. Pathology and Lab medicine.
June 1 1998 – Dec 31 1999 Lab Technician, Dr. Hugh Brock, Zoology, UBC; Dr. Vett Lloyd,
University of Dalhousie; Dr. T.A. Grigliatti, Zoology, UBC.
1995 – 1998
M.Sc., awarded May 1998, Supervisor: Dr. Hugh Brock
University of British Columbia, Vancouver, B.C.
1995
B.Sc. Genetics, 1995, University of British Columbia,
Vancouver, B.C.
Research Achievements
Main research achievements to date (1998-2014)
I started my scientific career studying the role of epigenetic proteins in cell fate decisions.
Epigenetic changes are generally defined as heritable changes in gene expression that do
not alter the underlying DNA sequence. One way epigenetic proteins are thought to control
gene regulation is through the covalent modification of histone proteins.
There are four canonical histone proteins (H2A, H2B, H3, and H4) and they form the
DNA/protein complex termed chromatin. Histone proteins can be covalently modified with
"marks" such as phosphorylation (P), acetylation (Ac), methylation (Me, which can be added
as a mono (1), di (2) or tri (3) methyl mark) and ubiquitination (Ub). Many proteins that
control gene expression and are implicated in human disease are involved in “writing” (ie.
adding modifications), “erasing” (ie. removing modifications) or “reading” (ie. binding to)
histone modifications.
As a PhD student, I began to study the function of the Mixed Lineage Leukemia (MLL)
protein, a developmentally important protein that is mutated in a subset of aggressive
leukaemias. At the time, the general consensus in the field was that MLL had no enzymatic
activity. We were able to show that the MLL SET domain could direct H3K4 methylation at
target genes in cells and that it also had direct activity in vitro (Milne, TA.,et al. (2002). Mol
Cell 10, 1107-1117). This paper initiated my interest in further analyzing the molecular details
of MLL function. Several other papers followed that highlighted additional mechanisms of
wild type MLL activity.
MLL is mutated in a subset of aggressive leukaemias where chromosome translocations
fuse MLL in frame to a wide variety of partners creating novel fusion proteins. MLL fusion
proteins lose the SET domain, thus we reasoned that H3K4 methylation had little to do with
their function in leukaemia. Using an inducible MLL fusion protein model, we exhaustively
surveyed multiple histone modifications and found that MLL fusion proteins specifically
recruit high levels of H3K79 methyltransferase activity to target genes in vivo (Milne, TA.,et
al. (2005). Can Res 65 11367-11374). Important work in Yi Zhang’s lab (Okada, Y.et al.
(2005). Cell 121, 167-178.) identified the H3K79 methyltransferase to be DOT1L. Thus
combined with Okada et al., our work was the first in the field to establish a link between
MLL leukaemias and mistargeting DOT1L activity. This has led to the seminal work of others
and the eventual development of DOT1L inhibitors that are currently in clinical trials.
During my postdoc I initiated several collaborations that led to multiple papers on epigenetic
reader and writer proteins. As well, I continued to work on MLL and MLL leukemias and
along with Andy Muntean in Jay Hess’ lab, I found that wild type and leukaemic MLL
proteins interact with a polymerase associated factor 1 (PAF1) transcription elongation
complex (Milne, TA.,et al. (2010). Mol Cell 38, 853-863).
Although I had worked on MLL for much of my career, I became specifically interested in
MLL-AF4 mutations once I became an independent group leader, mainly because of the
prognostic impact on childhood leukaemia and the fact that this mutation had been relatively
neglected by biochemical approaches. Although MLL-AF4 leukaemias have very few
cooperating mutations, they have been very difficult to model in mice. Work from the lab of
Rolf Marschalek suggests that MLL-AF4 cooperates with the reciprocal translocation, AF4MLL to produce acute leukaemias. Furthermore, MLL-AF4 leukaemias have very complex
gene expression patterns, suggesting that this may be a heterogenous group of leukaemias
that is different than other MLL mutations. In a recent paper (Wilkinson,et al. (2013). Cell
Rep 3 116-127), we used ChIP sequencing to identify the direct targets of MLL-AF4
regulation. We identified a key target gene, RUNX1, which is a transcription factor that is
often mutated in myeloid leukaemias. Our work further showed that RUNX1 expression
correlates with a poor prognosis in MLL leukaemias and that the RUNX1 protein can actually
cooperate with the product of the AF4-MLL translocation. Together, these results provided a
novel mechanism for MLL-AF4 leukaemogenesis and also provided a potential therapeutic
target in the RUNX1 protein. On a personal note, this paper is also significant as the first
major paper produced from my lab as an independent researcher.
Future Aims of Current Group over the next 5 years
The focus of the research activity in my laboratory is centered on understanding how
epigenetic proteins impact gene activation and repression in normal and leukaemic cells. To
achieve this, we have so far focused our analysis on the function of the Mixed Lineage
Leukaemia (MLL) protein, an important epigenetic protein that is required for the
maintenance of active gene expression during development and is also mutated in a subset
of aggressive leukaemias.
Working with MLL has provided a useful model for studying the link between epigenetic
changes and leukaemia. It has also allowed us to develop tools that include ChIPsequencing protocols and a nascent RNA-seq approach for quantifying changes in
transcription rates. We have also developed an effective bioinformatics pipeline in the lab.
With this as a foundation, we wish to expand our work towards a more general
understanding of epigenetic proteins in transcription and leukaemia.
Research in the lab can be broken down into two specific questions:
1) How does MLL control gene expression in leukaemia cells?
2) What key downstream gene targets are essential for MLL leukaemogenesis and do
any of these gene targets contribute to other leukaemias?
Answering these questions will help us cooperate with chemists and structural biologists to
one day develop specialized small molecule inhibitors designed to target aberrant epigenetic
processes.
How do These Aims Contribute to the Understanding and/or Management of Human
Disease
The philosophy of the WIMM, originally established by David Weatherall, was to use clinical
observation to initiate research programmes in applied and basic science with the ultimate
aim of addressing important questions in human health. Children and adults with mutations in
the Mixed Lineage Leukaemia (MLL) gene do not respond well to conventional therapies and
thus have very poor survival rates. This is likely due to the fact that MLL is a master regulator
that modifies the “epigenetic” information content of a cell. It is becoming clear not only that
aberrant epigenetic changes are common in many human diseases such as leukaemia, but
that these changes by their very nature are reversible.
Interestingly, some of the molecular data assembled to identify and analyze recent small
molecule inhibitors that could affect a wide range of different cancers comes from the
analysis of MLL leukaemias. This recent exciting work has provided proof of principle for our
approach, as two small molecule inhibitors that target a specific epigenetic “reader” can stop
MLL leukaemia growth in mice. Effective therapies in different individuals may require the
use of combinations of inhibitors, thus the aim of our work is to provide important information
for the future development of other small molecule inhibitors. MLL provides a useful model
for studying the link between epigenetic cell memory and human disease and we anticipate it
will also provide information on pathways and targets that are more generally applicable to a
wider range of different cancers.
Lay Summary of Research
There has been much progress in treating human cancers, especially leukaemias, but many
remain resistant to treatment. A potentially exciting approach is the development of small
molecule inhibitors that specifically target aberrant processes in cancer cells but leave
normal cells unharmed. In order to be successful, such an approach requires highly detailed
information about normal and aberrant cellular processes on the molecular level.
Children with mutations in the Mixed Lineage Leukaemia (MLL) gene do not respond well to
conventional therapies and thus have very poor survival rates. This is likely due to the fact
that MLL is a master regulator that modifies the “epigenetic” information content of a cell.
Epigenetic information is not stored in the DNA itself, but in specialized proteins called
histones. Histones can have chemical modifications or “marks” attached to them that can
code for gene activation or repression. It is becoming clear not only that aberrant epigenetic
changes are common in many human diseases such as leukaemia, but that these changes
by their very nature are reversible.
Epigenetic therapies used in the clinic have been effective in certain limited cases and have
also been surprisingly non-toxic. This is spurring the increased development of more
targeted epigenetic drugs. The overall goal of the lab is to try and identify ways in which MLL
leukaemias may rewrite the epigenetic code of the cell. This will lay the groundwork for the
next step of designing small molecule inhibitors designed to target these epigenetic
changes. The end goal will be to use these drugs to treat MLL leukaemias and potentially
other cancers.
All Publications Over the Past 5 Years
Wilkinson A.C.*, Ballabio E.*,Geng H., North P., Tapia M., Kerry J., Biswas D., Roeder RG,
Allis C.D., Melnick A., de Bruijn M.F.T.R. and Milne T.A. (2013) RUNX1 Is a Key Target
in t(4;11) Leukemias that Contributes to Gene Activation through an AF4-MLL Complex
Interaction. Cell Rep, 3, 116-127.
Ballabio E., Milne T.A. (2012) Molecular and epigenetic mechanisms of MLL1 in human
leukaemogenesis. Cancers, 4, 904-944.
Geng, H.; Brennan, S.; Milne, T.A.; Chen, W.-Y.; Li, Y.; Hurtz, C.; Kweon, S.-M.; Zickl, L.;
Shojaee, S.; Huang, C., et al., (2012) Integrative epigenomic analysis identifies
biomarkers and therapeutic targets in adult b-acute lymphoblastic leukemia. Cancer
Discovery, 2, 1004-1023.
Akalin A., Garrett-Bakelman F.E., Kormaksson M., Busuttil J., Zhang L., Khrebtukova I.,
Milne T.A., Huang Y., Biswas D., Hess J.L., Allis C.D., Roeder R.G., Valk P.J.M.,
Löwenberg B., Delwel R., Fernandez H.F., Paietta E., Tallman M.S., Schroth G.P.,
Mason C.E., Melnick A. and Figueroa M.E. (2012) Base-pair resolution DNA methylation
sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid
Leukemia PLoS Genet, 8, e1002781
Kowalczyk M. S., Hughes J.R., Garrick D., Lynch M.D., Sharpe J.A., Sloane-Stanley J.A.,
McGowan S.J., de Gobbi M., Hosseini M., Vernimmen D., Brown J.M., Gray N.E.,
Collavin L., Gibbons R.J., Flint J., Taylor S., Buckle V.J., Milne T.A., Wood W.G. &
Higgs D.R. (2012) Intragenic enhancers act as alternative promoters. Mol Cell, 45, 447458.
Biswas, D., Milne, T.A., Basrur, V., Kim, J., Elenitoba-Johnson, K.S., Allis, C.D. & Roeder,
R.G. (2011) Function of leukemogenic mixed lineage leukemia 1 (MLL) fusion proteins
through distinct partner protein complexes. Proc Natl Acad Sci U S A, 108, 15751-15756.
Ruthenburg, A.J., Li, H., Milne, T.A., Dewell, S., McGinty, R.K., Yuen, M., Ueberheide, B.,
Dou, Y., Muir, T.W., Patel, D.J. & Allis, C.D. (2011) Recognition of a Mononucleosomal
Histone Modification Pattern by BPTF via Multivalent Interactions. Cell, 145, 692-706.
Milne, T.A., Kim, J., Wang, G.G., Stadler, S.C., Basrur, V., Whitcomb, S.J., Wang, Z.,
Ruthenburg, A.J., Elenitoba-Johnson, K.S., Roeder, R.G. & Allis, C.D. (2010) Multiple
interactions recruit MLL1 and MLL1 fusion proteins to the HOXA9 locus in
leukemogenesis. Mol Cell, 38, 853-863.
Wang, Z., Song, J., Milne, T.A., Wang, G.G., Li, H., Allis, C.D. & Patel, D.J. (2010) Pro
isomerization in MLL1 PHD3-bromo cassette connects H3K4me readout to CyP33 and
HDAC-mediated repression. Cell, 141, 1183-1194.
Ferris, A.L., Wu, X., Hughes, C.M., Stewart, C., Smith, S.J., Milne, T.A., Wang, G.G., Shun,
M.C., Allis, C.D., Engelman, A. & Hughes, S.H. (2010) Lens epithelium-derived growth
factor fusion proteins redirect HIV-1 DNA integration. Proc Natl Acad Sci U S A, 107,
3135-3140.
Hunter, R.G., McCarthy, K.J., Milne, T.A., Pfaff, D.W. & McEwen, B.S. (2009) Regulation of
hippocampal H3 histone methylation by acute and chronic stress. Proc Natl Acad Sci U
S A, 106, 20912-20917.
Milne, T.A., Zhao, K. & Hess, J.L. (2009) Chromatin immunoprecipitation (ChIP) for analysis
of histone modifications and chromatin-associated proteins. Methods Mol Biol, 538, 409423.
Kim, J., Guermah, M., McGinty, R.K., Lee, J.S., Tang, Z., Milne, T.A., Shilatifard, A., Muir,
T.W. & Roeder, R.G. (2009) RAD6-Mediated transcription-coupled H2B ubiquitylation
directly stimulates H3K4 methylation in human cells. Cell, 137, 459-471.
Ten Key Publications Throughout your Career
Wilkinson A.C.*, Ballabio E.*,Geng H., North P., Tapia M., Kerry J., Biswas D., Roeder RG,
Allis C.D., Melnick A., de Bruijn M.F.T.R. and Milne T.A. (2013) RUNX1 Is a Key Target
in t(4;11) Leukemias that Contributes to Gene Activation through an AF4-MLL Complex
Interaction. Cell Rep, 3, 116-127.
Milne, T.A., Kim, J., Wang, G.G., Stadler, S.C., Basrur, V., Whitcomb, S.J., Wang, Z.,
Ruthenburg, A.J., Elenitoba-Johnson, K.S., Roeder, R.G. & Allis, C.D. (2010) Multiple
interactions recruit MLL1 and MLL1 fusion proteins to the HOXA9 locus in
leukemogenesis. Mol Cell, 38, 853-863.
Dou, Y., Milne, T.A., Ruthenburg, A.J., Lee, S., Lee, J.W., Verdine, G.L., Allis, C.D. &
Roeder, R.G. (2006) Regulation of MLL1 H3K4 methyltransferase activity by its core
components. Nat Struct Mol Biol, 13, 713-719.
Wysocka, J., Swigut, T., Xiao, H., Milne, T.A., Kwon, S.Y., Landry, J., Kauer, M., Tackett,
A.J., Chait, B.T., Badenhorst, P., Wu, C. & Allis, C.D. (2006) A PHD finger of NURF
couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature, 442, 8690.
Milne, T.A., Martin, M.E., Brock, H.W., Slany, R.K. & Hess, J.L. (2005) Leukemogenic MLL
fusion proteins bind across a broad region of the Hox a9 locus, promoting transcription
and multiple histone modifications. Cancer Res, 65, 11367-11374.
Dou, Y., Milne, T.A., Tackett, A.J., Smith, E.R., Fukuda, A., Wysocka, J., Allis, C.D., Chait,
B.T., Hess, J.L. & Roeder, R.G. (2005) Physical association and coordinate function of
the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase MOF. Cell, 121,
873-885.
Milne, T.A., Hughes, C.M., Lloyd, R., Yang, Z., Rozenblatt-Rosen, O., Dou, Y., Schnepp,
R.W., Krankel, C., Livolsi, V.A., Gibbs, D., Hua, X., Roeder, R.G., Meyerson, M. & Hess,
J.L. (2005) Menin and MLL cooperatively regulate expression of cyclin-dependent kinase
inhibitors. Proc Natl Acad Sci U S A, 102, 749-754.
Martin, M.E., Milne, T.A., Bloyer, S., Galoian, K., Shen, W., Gibbs, D., Brock, H.W., Slany,
R. & Hess, J.L. (2003) Dimerization of MLL fusion proteins immortalizes hematopoietic
cells. Cancer Cell, 4, 197-207.
Milne, T.A., Briggs, S.D., Brock, H.W., Martin, M.E., Gibbs, D., Allis, C.D. & Hess, J.L.
(2002) MLL targets SET domain methyltransferase activity to Hox gene promoters. Mol
Cell, 10, 1107-1117.
Milne, T.A., Sinclair, D.A. & Brock, H.W. (1999) The Additional sex combs gene of
Drosophila is required for activation and repression of homeotic loci, and interacts
specifically with Polycomb and super sex combs. Mol Gen Genet, 261, 753-761.
Markers of Esteem
1) Canadian Institutes of Health Research (CIHR) Fellowship July1/05 to July1/08
2) Member of the editorial board for the journal Leukemia
3) Member of the British Society for Cell Biology
Invited Presentations
1) June 3, 2014; Department of Pharmaceutical and Pharmacological Sciences, UZ St.
Rafael, Leuven, Belgium. Host: Zeger Debyser/Jan de Rijck
2) Mar.19, 2014; International Institute of Molecular and Cellular Biology, Warsaw,
Poland. From gene to phenotype – Interdisciplinary Research in Molecular Biology
and Biomedicine – symposium Mar.17-19, 2014. Host: Prof Bozena Kaminska.
3) Mar.18, 2014; University of Birmingham, School of Cancer Sciences, Birmingham,
UK. Host: Professor Peter Cockerill.
4) Mar.5, 2014; Ludwig Institute for Cancer Research, Oxford, UK. Host: Dr. Skirmantas
Kraucionis.
5) Nov.27, 2013; The Wessex Regional Genetics Laboratory, Salisbury, UK. Host: Nick
Cross.
6) Aug 6, 2013; The British Columbia Cancer Research Centre, Vancouver, B.C.,
Canada.
7) June 18, 2013; EMBO workshop "RUNX Transcription Factors in Disease
Development.", Wilsede, Germany.
8) Apr 5, 2013; Invited talk at the Department of Haematology Cambridge Institute for
Medical Research, Wellcome Trust-Medical Research Council Stem Cell Institute,
University of Cambridge. Host: Dr. Katrin Ottersbach.
9) Mar 21, 2013; Invited talk at the Institute for Biomedical Research Georg-SpeyerHaus, Hörsaal, Frankfurt, Germany. Host: Prof Rolf Marschalek.
10) Feb 28, 2013; Ludwig Maximilians-University Munich (LMU), Collaborative
Research Centre - SFB TR5 Chromatin. Munich, Germany. Host: Dr. Sandra Hake.
11) Feb 24, 2013; Invited talk for the “Acute Leukemias XIV” conference; organized by
the German AML Cooperative Group (AMLCG) and SFB 684 Molecular Mechanisms
of Normal and Malignant Hematopoesis together with the Ludwig MaximiliansUniversity Munich (LMU), HelmholtzZentrum München, German Research Center for
Environmental Health, German Society for Hematology and Oncology, Verein für
Leukämieforschung und –Therapie e.V. at the Klinikum Grosshadern, Munich,
Germany
12) Nov 27, 2012; Paterson Institute, Invited speaker, host: Dr. Georges Lacaud
13) Oct 26, 2012; Kings College London, Rayne Institute, King’s Denmark Hill Campus,
123 Coldharbour Lane, London SE5 9RT Haematological Medicine Educational
Seminar Programme Invited speaker, host: Dr. Eric So
14) Dec 13, 2011; TriRhena seminar series, Friedrich Miescher Institute for Biomedical
Research (FMI), Basel, Switzerland, host: Dr. Antoine Peters.
15) Sept 14, 2011; MRC Clinical Sciences Centre (CSC) Seminar Series, Imperial
College London, London, UK
16) Feb 14, 2011; Weatherall Institute of Molecular Medicine (WIMM), Headington,
Oxford, UK
17) Apr 11, 2008; Epigenetics: From Basic Science to the Clinic, co-sponsored by
Pharmion Corporation, Gladstone Institute of Virology and Immunology University of
California, San Francisco, Epigenetics Division Cell Cycling and Signalling Program
UCSF Cancer Center, Celgene. Gladstone Institute Auditorium, 1650 Owens Street,
San Francisco, CA USA.
18) Dec.6, 2004 1:45 pm; American Society of Hematology, 46th Annual Meeting, San
Diego CA, Dec.4-8, 2004. Thomas A. Milne, Mary Ellen Martin, Robert K. Slany, Jay
L. Hess. Leukemogenic MLL Fusion Proteins Promote MLL Association with HOX
Loci Resulting in Persistent Expression.
19) Dec, 2002; American Society of Hematology, 44th Annual Meeting, Philadelphia PA,
Dec.6-10, 2002. Thomas A Milne, Scott D Briggs, Hugh W Brock, Denise Gibbs,
C.David Allis and Jay L Hess. The Mixed Lineage Leukemia Protein (MLL) targets
SET domain methyltransferase activity to Hox gene promoters.
Past Grant Support
1) MRC Centenary Award, OGT and EZH2 in MLL-AF4 leukaemogenesis – Sept 1,
2012 – Apr. 30, 2013. £33,000
2) Children with Cancer UK, Epigenetic mechanisms of MLL-AF4 leukaemogenesis,
Feb. 1,2013 – Jan. 31, 2014. £48,104
Current Grant Support
3) MRC Unit Award, Doug Higgs (director), Group Leaders: Tom Milne, Roger Patient,
Marella de Bruijn, Catherine Porcher, Sten Eirik Jacobsen, Claus Nerlov, Terry
Rabbitts, Paresh Vyas, Veronica Buckle, Richard Gibbons, David Weatherall, 20122017. Milne lab: The Epigenetic Control of Gene Expression in Leukaemia and
Haematopoiesis. Milne lab funding: £1.57M