Molecular Haematopoiesis and Epigenetics

runxGroup Leader: Professor Constanze Bonifer, Chair of Experimental Haematology

Overview

Our main research interest is to study the mechanism of cell fate decisions at the level of gene regulation. All blood cells arise from pluripotent stem cells of the bone marrow. We want to understand in mechanistic detail how different genetic programs are activated and silenced at specific stages of blood cell development and which factors are involved in this process. In addition, we study how this finely balanced process is subverted in leukaemic cells.

Our research group

In our work, we address the general question of how the regulators of transcription, the sequence-specific DNA binding proteins or transcription factors, interact with the chromatin template and activate transcription.

We know from genetic studies that chromatin modification complexes play essential roles in all phases of the development of multicellular organisms and transcription factors bring these epigenetic regulatory proteins to specific genes. Together, they are responsible for the expression of cell type-specific gene expession. Our research has shown that even the process of expressing one gene at the right time and in the right cell is a breathtakingly complex process that involves the coordinate action of hundreds of different molecules. We have also made progress in understanding how these intricately balanced processes are disturbed in leukaemia.

We have now taken these studies one step further. One of the great challenges for future biological and medical research will be to understand how all genes and all molecules in a cell work together to generate different cells that each express only one set of genes. This means that we will have to study all genes simultaneously. To this end, we employ sophisticated genome-wide methods such as ChIP-sequencing and DNaseI-sequencing to generate such data.

We also collaborate with computational biologists to reconstruct models of the molecular interactions driving blood cell development. However, we also study the global consequences of expression of aberrant transcription factors in form of nuclear oncogenes on how the epigenetic landscape is altered in leukaemic cells. The outcome of such studies will shed light on the complex deregulation processes that turn normal into leukaemic cells and will uncover novel therapeutic targets to combat a disease with a high death toll, in particular amongst the elderly.

The results of our experiments are therefore not only important for our understanding of how blood cells form, but are extremely important for how we may diagnose and treat patients in the future.

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Current projects

1. Mechanistic insights into aberrant transcriptional programming in acute myeloid Leukaemia. Bloodwise programme grant (with Peter Cockerill)

Postdocs: Anetta Ptasinska, Salam Assi, Paulynn Chin, Dan Coleman. PhD students: Assunta Adamo and Sandeep Potluri (Clinical Fellow).

Collaborators: Olaf Heidenreich, University of Newcastle, JJ Schuringa, University of Groningen, Dan Tenen, Harvard Stem Cell Institute and National University of Singapore, Manoj Raghavan, Haematology, Birmingham.

In this program, we examine the molecular mechanisms underlying how normal and aberrant leukaemic transcription factors interact with the epigenetic regulatory machinery, reprogram the epigenetic landscape of normal human precursor cells and initiate the vast deregulation phenomena that we observe in malignant cells. We are also developing methods and computational tools that will allow us to model how the human epigenome swings back to normal, once we eliminate specific leukaemia-initiating oncogenes and/or block aberrant signalling through therapy.

2. Finding therapeutic targets in FLT3-ITD AML using a systems biology approach. MRC project grant (with P.Cockerill and Olaf Heidenreich / Helen Blair, Newcastle)

Postdocs: Dan Coleman, Peter Keane

Collaborators: John Bushweller, University of Virginia and Manoj Raghavan, Haematology, Birmingham.

Acute myeloid leukemia (AML) is an aggressive haematological malignancy which is caused by mutations interfering with hematopoietic differentiation (class II) followed by mutations conveying a proliferative advantage (class I). Activating mutations of FMS-like Tyrosine Kinase 3 (FLT3-receptor) are the most common class I mutations and occur in 30% of de novo AML. The prognosis of FLT3-ITD AML is extremely poor and new drugs and combination therapies are therefore urgently needed. Importantly, we need to obtain systems-level information on the targets affected by drugs and mechanistic information on how drugs work. It is now clear that the FLT3-ITD mutation does not just promote growth, but also has a profound influence on the transcriptional and epigenetic landscape. Our recent publications uncovered a common set of FLT3-ITD specific deregulated genes, identified the core deregulated transcriptional network of this type of AML and determined FLT3-ITD-specific deregulated pathways. In this project we build on this work to define the role of such genes and pathways with respect to the maintenance of FLT3-ITD AML development and maintenance as well as the development of drug resistance.

3. Understanding the interplay of enhancers, chromatin priming elements and signals regulating dynamic gene expression in development. BBSRC project grant (with JB Cazier and James Bentley Brown, Centre for Computational Biology).

Postdocs:  Benjamin Edgington White, Wakil Sarfaraz. PhD student: Alexander Maytun.

In this project we are using the in vitro differentiation of embryonic stem cells into blood cells to ask the question of how genes are activated in development and which role outside signals play in this process. We are using these data to generate mathemathical models that would allow us to predict the activity of different types of cis-regulatory elements at specific stages of development.  

4. System-wide analysis of transcriptional and chromatin reprogramming by EVI1 and RUNX1-EVI1 oncoproteins. Kay Kendall Leukaemia Fund.

Postdoc: Sophie Kellaway

The transcription factor RUNX1 is crucial for the establishment of haemopoiesis and mutation of this gene plays an important role in myeloid leukemia. However, little is known about the mechanistic details of how mutant versions of RUNX1 subvert normal haemopoietic development and counteract normal RUNX1 activity. Using the differentiation of mouse embryonic stem (ES) cells as model we address this question.

5. Modelling acute myeloid leukaemia in human ES cell derived haematopoietic precursor cells. U21 Melbourne studentship

PhD student: Monica Nafria I Fedi

Co-applicants: Andrew Elefantly, University of Melbourne

Genetic changes in cancer cells disturb the finely tuned balance of the interaction of the transcription regulatory machinery with the genome. However, tumour development does not occur in one step. After the first mutation, cells accumulate additional mutations and undergo extensive selection which completely alters their transcriptional network. For haematopoietic malignancies such as acute myeloid leukaemia (AML), we know therefore very little about how the first genetic change that occurs in stem/early precursor cells alters the epigenetic landscape. To address this question, the Bonifer lab and the Elefanty lab in Melbourne who is a world leader in blood cell differentiation from human embryonic stem (hESCs) cells have collaborated and established genetically engineered hESC lines carrying inducible versions of leukaemic oncogenes and learned how to differentiate these cells into blood precursors. We are now using this system to systematically test how the successive expression of leukaemic oncoproteins impact of human haematopoiesis. 

Recent publications

  • Gilmour J, O’Connor L, Middleton CP, Keane P, Gillemans N, Cazier JB, Philipsen J and Bonifer C (2019) Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors. Epigenetics & Chromatin. 2019 Jun 4;12(1):33.
  • Edginton-White B, Cauchy P, Assi SA, Hartmann S, Riggs AG, Mathas S, Cockerill PN, Bonifer C (2019). Global long terminal repeat activation participates in establishing the unique gene expression programme of classical Hodgkin lymphoma. Leukemia. 2018 Dec 13. doi: 10.1038/s41375-018-0311-x. [Epub ahead of print] 
  • de Boer B, Prick J, Pruis MG, Keane P, Imperato MR, Jaques J, Brouwers-Vos AZ, Hogeling SM, Woolthuis CM, Nijk MT, Diepstra A, Wandinger S, Versele M, Attar RM, Cockerill PN, Huls G, Vellenga E, Mulder AB, Bonifer C*, Schuringa JJ (*Senior author). Prospective Isolation and Characterization of Genetically and Functionally Distinct AML Subclones. Cancer Cell 34(4):674-689.
  • Assi SA, Imperato MR, Coleman DJL, Pickin A, Potluri S, Ptasinska A, Chin PS, Blair H, Cauchy P, James SR, Zacarias-Cabeza J, Gilding LN, Beggs A, Clokie S, Loke JC, Jenkin P, Uddin A, Delwel R, Richards SJ, Raghavan M, Griffiths MJ, Heidenreich O, Cockerill PN, Bonifer C. Subtype-specific regulatory network rewiring in acute myeloid leukemia. Nature Genetics. 51(1):151-162. 
  • Gilmour J, Assi SA, Obier N, and Bonifer C. The Co-operation of RUNX1 with LDB1, CDK9 and BRD4 Drives Transcription Factor Complex Relocation During Haematopoietic Specification. Scientific Reports 8(1):10410. 
  • Martinez-Soria N, McKenzie L, Draper J, Ptasinska A, Issa H, Potluri S, Blair HJ, Pickin A, Isa A, Chin PS, Tirtakusuma R, Coleman D, Nakjang S, Assi S, Forster V, Reza M, Law E, Berry P, Mueller D, Elder A, Bomken SN, Pal D, Allan JM, Veal GJ, Cockerill PN, Wichmann C, Vormoor J, Lacaud G, Bonifer C*, Heidenreich O*. (*Joint corr. Authors). An Aberrant Transcription Factor Corrupts the Cell Cycle to Drive Leukemic Transformation. Cancer Cell 34(4):626-642.e8. 
  • Loke J, Chin PS, Keane P, Pickin A, Assi SA, Ptasinska A, Imperato MR, Cockerill PN, Bonifer C. C/EBPα overrides epigenetic reprogramming by oncogenic transcription factors in acute myeloid leukemia. Blood Adv. 2018 Feb 13;2(3):271-284.
  •  Shan Lin, Anetta Ptasinska, Xiaoting Chen, Mahesh Shretha, Salam A. Assi, Paulynn S. Chin, Maria R. Imperato, Bruce Aronow, Jingsong Zhang, Matthew T. Weirauch, Constanze Bonifer, and James C. Mulloy. AML1-ETO-induced FOXO1 activates a self-renewal program in pre-leukemia stem cells. Blood. 2017 Sep 7;130(10):1213-1222. 
  • Loke J, Assi SA, Imperato MR, Ptasinska A, Cauchy P, Grabovska Y, Soria NM, Raghavan M, Delwel HR, Cockerill PN, Heidenreich O, Bonifer C. (2017). RUNX1-ETO and RUNX1-EVI1 differentially re-program the chromatin landscape in t(8;21) and t(3;21) AML. Cell Reports. 19(8):1654-1668. With press release. 
  • Shan Lin, Roger T. Luo, Anetta Ptasinska, Mark Wunderlich, Toshihiko Imamura, Joseph J. Kaberlein, Ahmad Rayes, Mark J Althoff, John Anastasi, Maureen M. O’Brien, Constanze Bonifer, James C. Mulloy and Michael J. Thirman (2016) Instructive role of MLL fusion proteins revealed by a faithful model of t(4;11) proB acute lymphoblastic leukemia. Cancer Cell;30(5):737-749. With accompanying editorial. 
  • Obier N, Cauchy P, Assi SA, Gilmour J, Lie-A-Ling M, Lichtinger M, Hoogenkamp M, Noailles L, Cockerill PN, Lacaud G, Kouskoff V and Bonifer, C. (2016). Cooperative binding of AP-1 and TEAD4 regulates the balance between vascular smooth muscle and hemogenic cell fate. Development;143(23):4324-4340 (highlighted article).
  • Illendula A, Gilmour J, Grembecka J, Sesha Srimath Tirumala V, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pullikan JA, Zong H, Parlak M, Kuscu C, Pickin A, Zhou Y, Gao Y, Mishra L, Adli M, Castilla LH, Rajewski RA, Janes KA, Guzman ML, Bonifer C and Bushweller JH (2016). Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers. eBiomedicine. ePub April 2016.
  • Goode DK, Obier N, Vijayabaskar MS, Lie-A-Ling M, Lilly AJ, Hannah R, Lichtinger M, Batta K, Florkowska M, Patel R, Challinor M, Wallace K, Gilmour J, Assi SA, Cauchy P, Hoogenkamp M, Westhead DR, Lacaud G, Kouskoff V, Göttgens B, Bonifer C. (2016). Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation.  Dev Cell. 36(5):572-87. 

Staff

Research Group Staff  Members

Postdocs: Sophie Kellaway, Anetta Ptasinska, Dan Coleman, Peter Keane, Salam A. Assi, Paulynn Chin, Ben Edington-White, Wakil Sarfaraz

PhD Students: Monica Nafria I Fedi, Alexander Maytun, Assunta Adamo

Clinical training fellow: Sandeep Potluri

Technical staff: Nunzia Nirchio