Transcriptional control of haematopoietic specification and differentiation
Lead Research Organisation:
University of Oxford
Department Name: UNLISTED
Abstract
Our interests focus on the mechanisms that underlie blood formation and differentiation into mature blood cells (such as those fighting infection, involved in coagulation or in oxygen transport). Many inherited and acquired diseases are associated with anaemia and leukaemia in which production of certain types of blood cells is disrupted. Understanding these disorders depends on knowing how blood normally forms in the bone marrow and throughout development. Recently, there has been considerable accumulation of knowledge about the factors that direct formation of the blood. One such factor (called SCL, Stem Cell Leukaemia) plays several critical roles in this process. We plan to understand how this factor controls the formation of blood at a molecular level. Our main experimental model makes use of mouse embryonic stem (mES) cells that can reproduce the early steps of embryonic development in vitro (in a culture dish). We aim at understanding how a blood-specific protein complex forms, how it regulates the coordinated expression of the critical players involved in this pathway and how, when it is deregulated, it may lead to leukaemia and anaemia.
Technical Summary
Understanding how stem cells are specified during embryonic development and how lineages differentiate to produce mature and specialised cells are central questions in biology and are of crucial interest to elucidate pathways involved in diseases. The main aim of this programme is to characterise some of the molecular mechanisms engaged by key regulators of blood development (such as SCL/Tal1), with a particular focus on the early stages of mesoderm patterning and haematopoietic specification. Functional identification of protein complexes and their nuclear targets combined with molecular characterisation of their mechanisms of action and structural biology approaches will give insights into genetic interactions and transcriptional networks critical in decision pathways. Using in vitro differentiation of mouse ES cells, mouse haematopoiesis and Xenopus embryos as experimental models, we will start building networks of genetic interactions at the heart of haematopoietic development. These approaches are instrumental for our understanding of how a haematopoietic stem cell-specific protein complex might form and how, when this process is deregulated, this leads to leukaemia. Moreover, this might help characterise the pathways leading to definitive haematopoiesis and HSCs from hES and iPS cells that remain poorly characterised. This is important if one wants to be able to produce HSCs in vitro for regenerative medicine purposes.
Organisations
- University of Oxford (Lead Research Organisation)
- UNIVERSITY OF OXFORD (Collaboration)
- Heidelberg University (Collaboration)
- University of California, San Diego (UCSD) (Collaboration)
- University of Helsinki (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- Medical Research Council (MRC) (Collaboration)
Publications
Chagraoui H
(2018)
SCL/TAL1 cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells.
in Nature communications
Harland L
(2021)
The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors
in Nature Cell Biology
Ho VW
(2022)
Specification of the haematopoietic stem cell lineage: From blood-fated mesodermal angioblasts to haemogenic endothelium.
in Seminars in cell & developmental biology
Juban G
(2021)
Oncogenic Gata1 causes stage-specific megakaryocyte differentiation delay.
in Haematologica
Karamitros D
(2018)
Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells.
in Nature immunology
Karia D
(2020)
The histone H3K4 demethylase JARID1A directly interacts with haematopoietic transcription factor GATA1 in erythroid cells through its second PHD domain.
in Royal Society open science
Li L
(2019)
Etv6 activates vegfa expression through positive and negative transcriptional regulatory networks in Xenopus embryos.
in Nature communications
Porcher C
(2017)
SCL/TAL1: a multifaceted regulator from blood development to disease.
in Blood
Related Projects
Project Reference | Relationship | Related To | Start | End | Award Value |
---|---|---|---|---|---|
MC_UU_00016/1 | 31/03/2017 | 30/03/2022 | £3,035,000 | ||
MC_UU_00016/2 | Transfer | MC_UU_00016/1 | 31/03/2017 | 30/03/2022 | £3,411,000 |
MC_UU_00016/3 | Transfer | MC_UU_00016/2 | 31/03/2017 | 30/03/2022 | £1,366,000 |
MC_UU_00016/4 | Transfer | MC_UU_00016/3 | 31/03/2017 | 30/03/2020 | £3,017,000 |
MC_UU_00016/5 | Transfer | MC_UU_00016/4 | 31/03/2017 | 30/03/2020 | £497,000 |
MC_UU_00016/6 | Transfer | MC_UU_00016/5 | 31/03/2017 | 30/03/2022 | £2,530,000 |
MC_UU_00016/7 | Transfer | MC_UU_00016/6 | 31/03/2017 | 30/03/2022 | £2,018,000 |
MC_UU_00016/8 | Transfer | MC_UU_00016/7 | 31/03/2017 | 30/03/2018 | £1,131,000 |
MC_UU_00016/9 | Transfer | MC_UU_00016/8 | 31/03/2017 | 30/03/2022 | £2,500,000 |
MC_UU_00016/10 | Transfer | MC_UU_00016/9 | 31/03/2017 | 30/03/2018 | £1,171,000 |
MC_UU_00016/11 | Transfer | MC_UU_00016/10 | 31/03/2017 | 30/03/2022 | £1,387,000 |
MC_UU_00016/12 | Transfer | MC_UU_00016/11 | 31/03/2017 | 30/03/2022 | £446,000 |
Description | John Fell Fund |
Amount | £45,000 (GBP) |
Funding ID | 0011784 |
Organisation | University of Oxford |
Sector | Academic/University |
Country | United Kingdom |
Start | 05/2022 |
End | 02/2023 |
Title | Development of protocols supporting mouse and human ES cell differentiation towards the hematopoietic stem cell lineage |
Description | We are currently developing protocols supporting the stepwise differentiation of mouse and human ES cells towards the hematopoietic stem cell lineage. We now have protocols that sustain the initial steps of mouse and human ES cell differentiation. These will be extended in the coming months to support the later stages of this differentiation. |
Type Of Material | Technology assay or reagent |
Year Produced | 2019 |
Provided To Others? | No |
Impact | No impact yet |
Title | Reporter SCL-Cre mouse |
Description | Creation of a reporter mouse that will allow identification of all lineages derived from angioblasts expressing a key haemato-endothelial regulator. |
Type Of Material | Biological samples |
Year Produced | 2020 |
Provided To Others? | No |
Impact | No impact yet. |
Title | Scl:mCherry ES cell line |
Description | Insertion of the mCherry reporter gene into the Scl locus in mouse ES cells |
Type Of Material | Cell line |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | We can now follow the cellular fate of Scl-null cells. This has allowed to report a cell fate change from blood to cardiac/paraxial lineages in absence of this transcriptional regulator. This is a critical finding for our mechanistic understanding of lineage specification. |
URL | https://www.nature.com/articles/s41467-018-07787-6 |
Title | Single molecule RNA FISH |
Description | Development of a multiplexed single molecule RNA technology - This allows to visualise expression of up to 32 individual genes in single cells at a single molecule resolution. We use it on embryonic sections to quantitate expression of key genes whilst retaining spatial information. |
Type Of Material | Technology assay or reagent |
Year Produced | 2020 |
Provided To Others? | No |
Impact | We have identified the microenvironmental niche of the angioblasts, precursors of blood cells. This will allow identification of the signaling molecules that instruct these early cells for a better understanding of haematopoietic specification processes. Ultimately, this will help refine protocols aiming at supporting in vitro differentiation of the haematopoietic stem cell lineage from pluripotent stem cells. |
Title | Chromatin landscape of blood-fated cells |
Description | ATAC-sequencing profile of willd-type angioblasts and angioblasts deleted in the master regulator SCL. |
Type Of Material | Data analysis technique |
Year Produced | 2020 |
Provided To Others? | No |
Impact | This analysis has revealed genetic loci activated at the earliest stages of blood development. This gives information about some of the pathways required to impose a blood fate to angioblasts. |
Title | Pipeline for lineage tracing analysis |
Description | Developed new computational pipelines for analysis of lineage tracing data and tree reconstruction |
Type Of Material | Computer model/algorithm |
Year Produced | 2022 |
Provided To Others? | No |
Impact | Expected to improve current methods and generate more accurate lineage trees |
Title | Proteomics in Flk1+ cells |
Description | Proteomics database of SCL partners in blood-fated mesodermal cells. |
Type Of Material | Database/Collection of data |
Provided To Others? | No |
Impact | This is contributing to our understanding of the molecular mechanisms underlying lineage specification. More specifically, how a tissue-specific regulator activates a lineage-specific gene expression programme and represses alternative fates in the same cell. This is an important concept likely to apply to other cellular systems. |
Title | Single cell transcriptomics and barcode datasets |
Description | Experimental datasets from several developmental timepoints used for lineage tree reconstructions |
Type Of Material | Data analysis technique |
Year Produced | 2021 |
Provided To Others? | No |
Impact | No impact yet. |
Title | Single cell transcriptomics of endothelial cells |
Description | Single cell transcriptomics of extra- and intra-embryonic endothelial cells. This will allow the identification of new markers distinguishing extra- and intra-embryonic endothelial cells. |
Type Of Material | Data analysis technique |
Year Produced | 2022 |
Provided To Others? | No |
Impact | No impact yet, but expected to help develop in vitro culture conditions for the generation of intra-embryonic endothelial cells at the origin of haematopoietic stem cells. |
Title | Transcriptomes of posterior caudal region of mouse embryos |
Description | Single cell RNA-sequencing datasets of posterior caudal region of day 8 mouse embryos. |
Type Of Material | Data analysis technique |
Year Produced | 2022 |
Provided To Others? | No |
Impact | These datasets will be used to identify regulators and signalling pathways controlling early stages of blood specification in endothelial cells. |
Title | Whole genome sequencing databases (Flk1+ cells) |
Description | RNA-seq, ChIP-seq, ATAC-seq databases from blood-fated mesodermal cells |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | This has provided new insight into the molecular mechanisms underlying lineage specification and highlighted the functional importance of repression mechanisms. More specifically, how a tissue-specific regulator activates a lineage-specific gene expression programme and represses alternative fates in the same cell. This is an important concept likely to apply to other cellular systems. |
URL | https://www.nature.com/articles/s41467-018-07787-6 |
Description | Applying lineage tracing system to haematopoietic stem cell clonal expansion analyses |
Organisation | University of Oxford |
Department | Weatherall Institute of Molecular Medicine (WIMM) |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Experimental and intellectual contributions. Provided mouse lines and expertise in computational analyses. |
Collaborator Contribution | Provided experimental data. |
Impact | Collaboration in the early days. No output yet. |
Start Year | 2021 |
Description | Computational analyses |
Organisation | University of Oxford |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Experimental and intellectual contribution |
Collaborator Contribution | Intellectual contribution |
Impact | No output yet. Work in progress. |
Start Year | 2020 |
Description | Cryo-EM |
Organisation | University of Oxford |
Department | Oxford Hub |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Intellectual and experimental: choice of protein complex to analyse structurally; performing experiments. |
Collaborator Contribution | Experimental: advice and help to produce and analyse the structure of multi-protein complexes by cryo-EM |
Impact | In progress |
Start Year | 2019 |
Description | Functional analyses of signalling pathways in zebrafish embryos |
Organisation | University of California, San Diego (UCSD) |
Country | United States |
Sector | Academic/University |
PI Contribution | Intellectual and experimental - Sharing data and expertise. |
Collaborator Contribution | Expertise and intellectual input. Access to experimental models we do not study. |
Impact | No outcomes yet. |
Start Year | 2023 |
Description | HSC production from mouse and human ES cells |
Organisation | Medical Research Council (MRC) |
Department | MRC Molecular Haematology Unit |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Expertise in mouse and human ES cell cultures and differentiation |
Collaborator Contribution | Expertise in haematopoiesis during embryonic development to help design protocols aiming at reproducing blood development in vitro. |
Impact | We are currently characterising ES cell-derived haematopoiesis in order to be in a better position to produce blood stem cells in vitro. If successful, we will be closer to making blood stem cells from patient's own cells. This is a long-term project. |
Start Year | 2014 |
Description | Mathematical and Statistical analyses of edited barcodes for lineage tree reconstructions |
Organisation | Heidelberg University |
Country | Germany |
Sector | Academic/University |
PI Contribution | Provided single cell RNA-sequencing datasets |
Collaborator Contribution | Established mathematical pipelines to analyse datasets |
Impact | Muti-disciplinary collaboration. Involves mouse genetics, molecular biology, statistical and mathematical analyses. Allows stringent analyses of lineage tracing data. |
Start Year | 2021 |
Description | Mouse and human ES cell differentiation cultures with NIH |
Organisation | National Institutes of Health (NIH) |
Country | United States |
Sector | Public |
PI Contribution | Expertise in mouse ES cells and developmental haematopoiesis |
Collaborator Contribution | Expertise in human ES cell differentiation cultures that complement our mouse ES cell expertise. |
Impact | Mouse ES cell differentiation protocol that recapitulates some of the milestones occurring during embryonic development of blood stem cells. |
Start Year | 2014 |
Description | Normal human hematopoiesis |
Organisation | University of Oxford |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Intellectual |
Collaborator Contribution | Intellectual and experimental |
Impact | Better understanding of the hematopoietic hierarchy in humans. |
Start Year | 2015 |
Description | Role of Gata1s in fetal megakaryopoiesis |
Organisation | University of Oxford |
Department | Radcliffe Department of Medicine |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Co-supervision of a post-doctoral scientist. Bringing expertise in Cellular and Molecular Biology. |
Collaborator Contribution | Expertise in megakaryopoiesis and function of GATA1 in hematopoiesis |
Impact | No outputs yet. |
Start Year | 2016 |
Description | Spatial genomic analysis |
Organisation | University of Helsinki |
Country | Finland |
Sector | Academic/University |
PI Contribution | Experimental |
Collaborator Contribution | Intellectual and analytical |
Impact | Analysis of complex imaging data generated by quantitative, in situ single molecule RNA FISH. |
Start Year | 2019 |
Description | Meet the expert session on career development (ISEH 2018) |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | I had a discussion with 3 groups of 10 students and post-docs about careers in academia versus industry and issues related to women in science. These workshops are intended to provide role models to young scientists and to engage them into a reflection about their career. |
Year(s) Of Engagement Activity | 2018 |
Description | School visit (MCS) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | The talk inspired discussions and reflection on biomedical/science-related careers. Following the talk, I had request from pupils wanting to do work experience in my lab. We hosted 4 of those in the summer. |
Year(s) Of Engagement Activity | 2015,2016,2017,2018,2019 |
Description | Science Bazaar |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | Stand in Oxford Brookes University with activities about DNA folding targeting children aged 5-14. This sparked questions and discussions with the children and their parents. |
Year(s) Of Engagement Activity | 2020 |
Description | Science Festival |
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 | Public Engagement stand on cancer immunotherapy in a shopping centre. 700 people attended and engaged into discussion and children participated in hands-on activities. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk to school |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | About 80 school children attended a Zoom webinar where I presented the research I do on blood development together with some of the technologies we employ. This was followed by many discussions at school during the biology classes. |
Year(s) Of Engagement Activity | 2020 |
Description | Video DG |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Short video of PhD student explaining what his thesis project is about. Organised by University of Oxford Graduate Study to inspire prospective students. |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.youtube.com/watch?v=5jSJ4sYYySM |
Description | Women in Leadership programme |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Other audiences |
Results and Impact | 12 women post-doctoral scientists attended a leadership programme designed to equip them with tools required to develop their leadership skills. |
Year(s) Of Engagement Activity | 2021 |
Description | Work experience in the lab |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | 2 pupils from disadvantaged background spent 2 weeks in our laboratory to gain experience in biomedical research. They participated in various scientific experiments, discussions, lectures and workshops. |
Year(s) Of Engagement Activity | 2019 |