The Epigenetic Control of Gene Expression in Leukaemia and Haematopoiesis
Lead Research Organisation:
University of Oxford
Department Name: UNLISTED
Abstract
There are many specialized cells in our body designed to carry out different specific tasks, and yet they all contain the same genetic information. During development, cells receive information that they translate into specific developmental outputs, usually without altering their DNA sequence. Changes in cell phenotype that do not alter the DNA sequence are referred to as “epigenetic”. Human diseases such as cancer often result from changes in gene expression patterns that are not always associated with DNA mutations, thus epigenetic changes are also a key mechanism in human disease. In living cells, genes do not exist as “naked” DNA, but as a highly conserved protein/DNA complex termed chromatin. The basic subunit of chromatin is the nucleosome, which consists of DNA wrapped around an octamer core of globular histone proteins, two each of H2A, H2B, H3, and H4.The N terminal "tails" of these histone proteins are chemically modified with "marks" such as methylation or acetylation. The specific carriers of epigenetic information have not been completely worked out, but emerging work over the past decade has suggested that epigenetic information is established in part by the modification of histone tails. We are specifically interested in how changes in histone methylation lead to transcriptional misregulation in human disease. As a system for asking specific questions about this very complex problem, I work on the Mixed Lineage Leukemia 1 (MLL1) protein, a histone methyltransferase that controls gene activation during development. Mutations in MLL1 also cause aggressive leukaemias in both children and adults. Specific information about MLL1 activity will not only provide potential therapeutic information for this subset of human leukemias, but will also have broader implications for stem cell development and the epigenetic regulation of gene expression in other human diseases.
Technical Summary
The Mixed Lineage Leukaemia 1 protein (MLL1) protein is important for the epigenetic regulation of gene expression during stem and progenitor cell development but is also mutated in a subset of aggressive human leukaemias. The most common leukaemic disruptions of the MLL1 gene are chromosome translocations that fuse the N terminus of MLL1 in frame with over 40 different partner genes creating novel fusion proteins. Recent work has suggested that wild type MLL1 and MLL1 fusion proteins cooperate in leukaemogenesis by together causing aberrant epigenetic profiles at target genes in vivo. Epigenetic changes are often defined as heritable changes in gene expression or chromosome stability that don’t alter the underlying DNA sequence. We are interested in identifying the key molecular events in MLL1 mediated leukaemogenesis in order to fully understand the epigenetic basis for this disease. This major goal has been divided into three key questions: 1) What key downstream gene targets are essential for MLL1 mediated leukaemogenesis?; 2) how do MLL1 and MLL1 fusion proteins control epigenetic gene regulation on a molecular level?; and 3) how are MLL1 and MLL1 fusion proteins recruited to important gene targets in the cell? To answer these questions, we are using xenograft transplant assays to identify Leukaemic Stem Cells (LSCs) in MLL1 patient samples, ChIP-seq to identify and characterise direct gene targets in specific haematopoietic cell populations, small molecular inhibitors and siRNA combined with ChIP and ChIP-seq to determine how MLL1 fusion proteins regulate gene targets in the cell and MLL1 domain analysis coupled with genome wide techniques to determine how MLL1 is recruited to gene targets in the cell. Answering these questions may not only be useful for future therapeutic strategies, but will also inform our basic understanding of epigenetic gene regulation during normal stem and progenitor cell development.
Publications
Wu Q
(2017)
In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering.
in Nature communications
Thomas AM
(2023)
Mutate and Conjugate: A Method to Enable Rapid In-Cell Target Validation.
in ACS chemical biology
Schneider P
(2023)
Modelling acquired resistance to DOT1L inhibition exhibits the adaptive potential of KMT2A-rearranged acute lymphoblastic leukemia.
in Experimental hematology & oncology
Rice S
(2021)
A human fetal liver-derived infant MLL-AF4 acute lymphoblastic leukemia model reveals a distinct fetal gene expression program.
in Nature communications
Pasricha SR
(2017)
Hepcidin is regulated by promoter-associated histone acetylation and HDAC3.
in Nature communications
Park K
(2023)
Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation
in Nature Cardiovascular Research
Related Projects
Project Reference | Relationship | Related To | Start | End | Award Value |
---|---|---|---|---|---|
MC_UU_00016/1 | 01/04/2017 | 31/03/2022 | £3,035,000 | ||
MC_UU_00016/2 | Transfer | MC_UU_00016/1 | 01/04/2017 | 31/03/2022 | £3,411,000 |
MC_UU_00016/3 | Transfer | MC_UU_00016/2 | 01/04/2017 | 31/03/2022 | £1,366,000 |
MC_UU_00016/4 | Transfer | MC_UU_00016/3 | 01/04/2017 | 31/03/2020 | £3,017,000 |
MC_UU_00016/5 | Transfer | MC_UU_00016/4 | 01/04/2017 | 31/03/2020 | £497,000 |
MC_UU_00016/6 | Transfer | MC_UU_00016/5 | 01/04/2017 | 31/03/2022 | £2,530,000 |
MC_UU_00016/7 | Transfer | MC_UU_00016/6 | 01/04/2017 | 31/03/2022 | £2,018,000 |
MC_UU_00016/8 | Transfer | MC_UU_00016/7 | 01/04/2017 | 31/03/2018 | £1,131,000 |
MC_UU_00016/9 | Transfer | MC_UU_00016/8 | 01/04/2017 | 31/03/2022 | £2,500,000 |
MC_UU_00016/10 | Transfer | MC_UU_00016/9 | 01/04/2017 | 31/03/2018 | £1,171,000 |
MC_UU_00016/11 | Transfer | MC_UU_00016/10 | 01/04/2017 | 31/03/2022 | £1,387,000 |
MC_UU_00016/12 | Transfer | MC_UU_00016/11 | 01/04/2017 | 31/03/2022 | £446,000 |
Title | A novel human fetal liver-derived model reveals that MLL-AF4 drives a distinct fetal gene expression program in infant ALL |
Description | Using CRISPR/Cas9 editing of human cells we developed a model of ninfant leukaemia and provided a molecular characterization of the model with the data deposited in GEO. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | This is a paper deposited in bioRxiv and currently in review at Nature Communications |
URL | https://www.biorxiv.org/content/10.1101/2020.11.15.379990v2 |
Title | ChIPseq in MLL-AF6 leukemia cells |
Description | ChIPseq for various chromatin proteins and epigenetic marks in MLL-AF6 leukemia cells, an incurable acute myeloid leukemia |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | A paper is published at Nature communications and is available open access. |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi |
Title | Dataset for the paper H3K79me2/3 controls enhancer promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells |
Description | ChIP-seq and ATAC-seq superseries genomic analysis of leukaemia cells |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | Publication of this paper: doi: 10.1038/s41375-020-0808-y |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135026 |
Title | Dataset for the paper MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia |
Description | Extensive genome wide ChIP-seq, RNA-seq and siRNA datasets in MLL-AF4 leukaemia cells |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | Publication of this paper: doi: 10.1016/j.celrep.2016.12.054 |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83671 |
Title | Epigenetic ChIP sequencing in normal and patient leukemia cells |
Description | It is a collection of different types of epigenomic data (such as ChIP-seq, RNA-seq, ATAC-seq) that have been made publicly available for other researchers to access. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | Generation of these datasets helped publish a paper (see DOI below) that can be used to help predict useful drug combinations for a subset of aggressive leukaemias. In addition, these datasets are available for other scientists to aid in their research. |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83671 |
Title | Full dataset for the paper DOT1L inhibition reveals a distinct class of enhancers dependent upon H3K79 methylation |
Description | Genome wide ChIP-seq, RNA-seq, ATAC-seq and Capture C superseries in leukaemia cells with and without DOT1L inhibitor treatment |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Publication of this paper: doi: 10.1038/s41467-019-10844-3 |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117865 |
Title | Genomic analysis for the paper BET inhibition disrupts transcription but retains enhancer-promoter contact |
Description | This is deposited datasets for Capture C, ChIP-seq, RNA-seq and ATAC-seq in leukaemia cells with and without drug treatment |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | Publication of this paper: doi: 10.1038/s41467-020-20400-z |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139437 |
Description | Developing a model of Infant MLL-AF4 leukemia |
Organisation | University of Oxford |
Department | Radcliffe Department of Medicine |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We are collaborating with the labs of Dr. Irene Roberts and Dr. Anindita Roy. We are providing help and expertise on designing contructs and providing genomic analyses of the first known model of incurable infant leukaemia. |
Collaborator Contribution | Our collaborators are providing expertise on human B cell development and on targeting the correct cell type to produce a model for this aggressive infant leukaemia. |
Impact | A paper deposited to bioRxiv (doi: https://doi.org/10.1101/2020.11.15.379990) is currently in review at Nature Communications. |
Start Year | 2017 |
Description | Lab282 drug discovery project |
Organisation | Evotec (UK) Ltd |
Country | United Kingdom |
Sector | Private |
PI Contribution | We tested a novel epigenetic inhibitor for its ability to disrupt leukaemic growth and analyzed its function on a molecular level using genomics approaches. |
Collaborator Contribution | They provided funding for the research as well as chemistry to develop new compounds and provided PK/PD analysis, and in vivo efficacy work. |
Impact | A publication will likely result from this work but discussions are in place to find further investment funding to pursue a drug development program. |
Start Year | 2019 |
Description | Lab282 drug discovery project |
Organisation | Oxford Sciences Innovation Plc |
Country | United Kingdom |
Sector | Private |
PI Contribution | We tested a novel epigenetic inhibitor for its ability to disrupt leukaemic growth and analyzed its function on a molecular level using genomics approaches. |
Collaborator Contribution | They provided funding for the research as well as chemistry to develop new compounds and provided PK/PD analysis, and in vivo efficacy work. |
Impact | A publication will likely result from this work but discussions are in place to find further investment funding to pursue a drug development program. |
Start Year | 2019 |
Description | Lab282 drug discovery project |
Organisation | University of Oxford |
Department | Oxford University Innovation |
Country | United Kingdom |
Sector | Private |
PI Contribution | We tested a novel epigenetic inhibitor for its ability to disrupt leukaemic growth and analyzed its function on a molecular level using genomics approaches. |
Collaborator Contribution | They provided funding for the research as well as chemistry to develop new compounds and provided PK/PD analysis, and in vivo efficacy work. |
Impact | A publication will likely result from this work but discussions are in place to find further investment funding to pursue a drug development program. |
Start Year | 2019 |
Description | Screening for drug targets in leukemia cells |
Organisation | University of Oxford |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | I co-supervised a student with another laboratory on finding drugs targets that would induce resistance in a leukemia cell line when exposed to the drug venetoclax. |
Collaborator Contribution | Prof Tudor Fulga was the other co-supervisor |
Impact | This work has resulted in a paper submitted to bioRxiv (doi: https://doi.org/10.1101/2020.06.30.179796) and currently in review at Genome Research |
Start Year | 2018 |
Title | METHOD FOR MODIFYING GENES |
Description | The present invention relates to method of modulating the level of expression of an endogenous gene in a cell, the method comprising inserting a heterologous microRNA (miRNA) response element (MRE) into the 3'-untranslated region (3'-UTR) of the gene. The binding of endogenous miRNAs to the MRE results in or leads to a repression of the level of expression of the gene. The invention also relates to cells and transgenic animals whose endogenous genes comprise heterologous MRE in their 3'-UTRs. |
IP Reference | WO2018011590 |
Protection | Patent application published |
Year Protection Granted | 2018 |
Licensed | No |
Impact | Publication of a paper in Nature Communications. Other patents applied for: US Patent Application no. 16/636,764 Project 13338, Project Title:- MicroRNA checkpoint inhibitor |
Company Name | DARK BLUE THERAPEUTICS LTD |
Description | Dark Blue Therapeutics, an oncology focused spin-out from the LAB282 therapeutic accelerator program, is a pre-clinical biotech company tackling cancer with new therapies that target cancer cells' vulnerabilities and dependencies. |
Year Established | 2020 |
Impact | Dark Blue Therapeutics has secured additional external investment and is in the process of creating a novel drug pipeline |
Description | Annual Molecular Haemopoiesis conference |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I have continued to help plan and organize the annual Molecular Haemopoiesis meeting. The meeting provides a platform to showcase the latest developments in UK and European haematopoiesis research, and culminates in a Keynote Lecture by an internationally renowned scientist. |
Year(s) Of Engagement Activity | 2015,2016,2017,2018,2019,2020 |
URL | https://www.stemcells.cam.ac.uk/whats-on/molecular-haemopoiesis-23 |
Description | Invited presentation at Einstein University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I was invited to give a presentation at the Einstein Biochenistry Seminar Series and I met with students and professors afterwards to discuss science. |
Year(s) Of Engagement Activity | 2021 |
Description | Raised money for the Congenital Anemia Network (CAN) charity by running the Oxford Half Marathon |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | I ran the Oxford Half marathon and wore a T-shirt displaying CAN logo and raised awareness of this charity. The goal was to raise money for the charity and to also raise awareness of the existence of the charity itself which is directly engaged with patient needs. |
Year(s) Of Engagement Activity | 2018 |
URL | https://uk.virginsport.com/event/oxford-2018/results |