Establishment of the haemopoietic transcriptional programme: From systems approaches to molecular mechanisms

Lead Research Organisation: University of Cambridge
Department Name: Haematology

Abstract

Our genes control how our body develops from one fertilized egg cell and all cells in our body contain the same set of genes. This cell rapidly divides and develops into a large variety of distinct cell types that make up the various organs in our body. All these cells express different genetic programs, meaning that not all of our genes are always active in every cell type. This cell-type-specific gene activation pattern is governed by another layer of control (on top of the layer of the genes) that tells cells which genes to switch on and off, thereby deciding which cell type develops. This additional control layer is called the 'epigenetic' layer and consists of two components: (1) a genome-wide network through which genes regulate each other to generate the appropriate gene expression patterns; (2) the DNA packing apparatus. Each cell contains one meter of DNA, and to be able to fit it into the nucleus, it is densely compacted by so called chromatin proteins such that inactive genes are highly compact and their DNA hidden, whereas active genes are in areas of reduced compaction. To activate an inactive, compact gene, protein complexes, so called 'transcription factors' push chromatin aside or modify it, so that genes become accessible to the factors that activate them. Studies in the past years focused on one gene at a time and led to the discovery of the transcription factors and chromatin components that control their activity. We learned to extract the tune that individual genes play but failed to hear the symphony. Our understanding of how all the genes in mammals are orchestrated to switch on and off in the right order is still superficial. Moreover, much of what we know is based on studies from cell lines, which represent fixed cell types or are cancer cells, and from simpler organisms, such as yeast. The situation in mammals is much more complex because building an organism from a fertilized egg involves turning one cell type into another (so called 'differentiation') in a precise hierarchical order which requires tight coordination of the activity of all the genes. In other words, building an organism is like building a house: we have to put the individual components together in a precise order and not start with the roof before the cellar. This proposal will use blood cell development in the mouse as a model to investigate the dynamics of cell differentiation in mammals. We will study all genes of a given cell type and use a sophisticated in vitro system based on embryonic stem cells where we can generate and purify different blood cell types. We then will identify which transcription factors and chromatin components regulate which genes at the different developmental stages and study at which level and when they are expressed. Until recently such global or 'systems biology' studies were beyond reach since the technology was lacking. However, with the latest technology we can determine the entire DNA sequence of one cell type in a very short time. This technology has been modified to study epigenetic changes at all genes and can now be used to identify what distinguishes genes of one cell type from those of another. However, one feature of such experiments is that they produce enormous amounts of data and require specialist knowledge to make sense of them. This is achieved by bioinformaticians developing new computer programs and mathematical modelers running simulations to predict the integrated, 'collective' behavior of genes. To this end we have formed an interdisciplinary consortium consisting of experimental researchers and computational biologists who will collaborate to understand how thousands of genes work together to generate specific cell types. The ultimate aim of these studies is to be able to understand how individual development is encoded in the DNA-sequence and to predict how changes in the DNA sequence impact on developmental processes.

Technical Summary

A pivotal challenge for post-genomic research is to understand in a system-wide fashion how networks of transcription factors (TFs) and chromatin components regulate cell fate decisions in an integrated manner. While recent genome-wide studies have offered a first glimpse onto the complexity of transcription factor-DNA interactions in specific cell types, we know very little about the dynamical relationships between different network states during development. We also do not know how the ordered, bidirectional interplay between TFs and specific chromatin states leads to the stable expression of lineage specific genetic programs. This proposal will use the differentiation of haemopoietic cells from mouse embryonic stem cells as a model to investigate the molecular mechanisms and dynamics of cell differentiation in a system-wide fashion. To this end we have formed a consortium consisting of experimental researchers and computational biologists who will identify the genome-wide dynamics of TF assembly during development. We will perform experiments examining global DNA methylation and chromatin alterations, obtain mechanistic insights by manipulating the trans-regulatory environment and verify conclusions by examining specific genes in more detail. In doing so, we will address the following general questions: 1) What is the molecular basis of the hierarchical action of key regulators of haematopoietic development, 2) How are known key regulators integrated into wider transcriptional networks with a particular emphasis on the dynamical nature of network state transitions 3.) How do these transcription factors interact with the chromatin template and how do they regulate chromatin accessibility and chromatin modification? 4) Can we decipher the genomic regulatory blueprint for development of a mammalian organ system?

Planned Impact

Our work will have a tremendous impact not only on our immediate research field but also far beyond. The studies proposed here will lead to a better understanding of the biology of haemopoietic stem cells, and therefore have the potential to benefit all future therapeutic approaches utilizing these cells. Moreover, we will pioneer technological and conceptual advances that will be vital for exploiting post-genomic datasets in translational settings in biotechnology and medicine.. Through its substantial involvement with the human genome project as well as other post-genomic activities, UK-plc has heavily invested into the early phase of genomic and post-genomic biology. To ensure eventual translation of these early efforts into improved 'health and wealth' benefits, it is now vital to build on the early investment through strategic funding of research consortia that not only produce world-class science but also function as hubs for knowledge generation, integration and distribution. To achieve maximum impact we plan the following activities: (i) We will make our system-wide datasets and network models publicly available. It will be impossible for us to examine all sub-aspects of these huge data sets, they will therefore serve as paradigms for future studies of normal as well as aberrant differentiation. This will benefit anybody who studies normal or aberrant cell fate decisions in academia, industry or the clinic. (ii) We will generate network models and develop computational tools that will be highly relevant to scientists studying other developmental/differentiation pathways both in academia and industry. (iii) We will organize a workshop where the scientific community and members from industry will be invited to discuss our and their results and new developments in the field. (iv) One significant potential outcome of our work is the identification of transcription factor combinations that may be used to drive the production of HSCs from ES cells or in vitro expansion of cord blood derived HSCs. HSCs are not only of tremendous interest for regenerative medicine applications but would also provide a very attractive source of in vitro cell types for drug development and toxicity screening assays and may thus be of significant commercial benefit. We will make our expertise available to members from industry and academia who wish to explore this possibility. (v) Knowledge of gene networks in stem cells may instigate the development of new strategies to induce stem cells to cross lineage barriers or even trigger the reversal of lineage restrictions in terminally differentiated cells thus renewing stem cell populations with regenerative capacity. The generation of iPS cells, after all, was only possible after the elucidation of the gene regulatory network maintaining pluripotency. (vi) Specifically, we will gather information that will be vital to understand how embryonic endothelial cells can become haemopoietic cells and which transcription factors are required for this process. In addition, our studies of global chromatin accessibility will identify regions within the genome of endothelial cells that are amenable to reprogramming. This will benefit regenerative medicine. (vii) Through our international collaborations there will be a significant knowledge transfer into the UK (viii) Last, but not least, our work will enhance the skills base in the UK. Future advances in biology and medicine will depend on building a skills base consisting of researchers which will be capable of thinking both in molecular terms as well as in system-wide terms, and researchers working in this consortium will be exposed to the forefront of research in this field. In addition, both Leeds and Cambridge run MSc courses on Bioinformatics and Computational Biology respectively and this grant will enable to offer rotation projects to these students.

Publications

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Description All blood cells originate from stem cells that reside in the bone marrow. Healthy stem cells and their progeny churn out trillions of blood cells every day. However, in certain diseases such as cancers of the blood, stem cells can become dysfunctional and need to be replaced by healthy cells. It is therefore of vital importance to understand, how the blood system develops in the first place. Cells with the ability to give rise to blood develop very early in the embryo and are then maintained for life. Blood cell development is regulated by our genes and by the way their activity is controlled at different stages of embryo development. Importantly, this process involves not just one gene, but thousands of them.

Funded by a Longer and Larger grant from the BBSRC, a consortium of researchers from the University of Cambridge (Bertie Göttgens), University of Leeds (David Westhead), University of Manchester (Valerie Kouskoff and Georges Lacaud) and University of Birmingham (Constanze Bonifer) have now examined six different stages of blood cell development in fine detail, by collecting information on the activity of thousands of different genes, and they have identified the factors that control their activity. This study, published in Developmental Cell, shows the computational analysis of such "big data" and show experiments that reveal so far unknown regulators of blood cell development.
Exploitation Route Our findings will facilitate the development of protocols for the generation of blood cells for clinical use. They will also help other researchers work towards discovering additional regulators of cell development.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

URL http://www.haemopoiesis.leeds.ac.uk
 
Description Our findings have lead to a better understanding of the biology of haemopoietic stem cells, and therefore have the potential to benefit all future therapeutic approaches using these cells. Moreover, we have produced technological and conceptual advances which can be used to exploit post-genomic datasets in translational settings in biotechnology and medicine.
First Year Of Impact 2015
Sector Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal

 
Description Development of an executable model encapsulating blood cell development from pluripotent embryonic stem cells
Amount £70,000 (GBP)
Funding ID 2012-023 
Organisation Microsoft Research 
Sector Private
Country Global
Start 01/2013 
End 12/2015
 
Title Core regulatory network model for haematopoietic specification 
Description A dynamic core regulatory network model for haematopoietic specification which can be used for the design of reprogramming experiments. 
Type Of Material Computer model/algorithm 
Year Produced 2016 
Provided To Others? Yes  
Impact The model, as published in Goode et al. Dev Cell 2016, contributes to our understanding of how blood cells become malignant and will aid us in creating haematopoietic stem cells for regenerative medicine. It will also help other researchers work towards discovering additional regulators of cell development. 
 
Description Establishment of the haemopoietic transcriptional programme BBSRC LoLa consortium 
Organisation University of Birmingham
Country United Kingdom 
Sector Academic/University 
PI Contribution Transcription factor ChIP data generation and data analysis
Collaborator Contribution The group from the University of Manchester carried out cell differentiation and purification, RNA-seq data generation, reprogramming and in vivo and inhibitor studies. The group from the University of Birmingham was responsible for chromatin data generation. The group from the University of Leeds integrated and analysed data produced across the groups and presented it online.
Impact A dynamic core regulatory network model for haematopoietic specification which can be used for the design of reprogramming experiments, helping other researchers discover additional regulators. It contributes to our understanding of how blood cells become malignant and the possibility of creating haematopoietic stem cells for regenerative medicine. The collaboration brought together basic scientists and computational biologists.
Start Year 2011
 
Description Establishment of the haemopoietic transcriptional programme BBSRC LoLa consortium 
Organisation University of Leeds
Department School of Earth and Environment
Country United Kingdom 
Sector Academic/University 
PI Contribution Transcription factor ChIP data generation and data analysis
Collaborator Contribution The group from the University of Manchester carried out cell differentiation and purification, RNA-seq data generation, reprogramming and in vivo and inhibitor studies. The group from the University of Birmingham was responsible for chromatin data generation. The group from the University of Leeds integrated and analysed data produced across the groups and presented it online.
Impact A dynamic core regulatory network model for haematopoietic specification which can be used for the design of reprogramming experiments, helping other researchers discover additional regulators. It contributes to our understanding of how blood cells become malignant and the possibility of creating haematopoietic stem cells for regenerative medicine. The collaboration brought together basic scientists and computational biologists.
Start Year 2011
 
Description Establishment of the haemopoietic transcriptional programme BBSRC LoLa consortium 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution Transcription factor ChIP data generation and data analysis
Collaborator Contribution The group from the University of Manchester carried out cell differentiation and purification, RNA-seq data generation, reprogramming and in vivo and inhibitor studies. The group from the University of Birmingham was responsible for chromatin data generation. The group from the University of Leeds integrated and analysed data produced across the groups and presented it online.
Impact A dynamic core regulatory network model for haematopoietic specification which can be used for the design of reprogramming experiments, helping other researchers discover additional regulators. It contributes to our understanding of how blood cells become malignant and the possibility of creating haematopoietic stem cells for regenerative medicine. The collaboration brought together basic scientists and computational biologists.
Start Year 2011
 
Description Cambridge Literary Festival Spring 1-6 April 2014, "Thinking Aloud 1: Stem Cells" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Talk to the general public (over 100 ticket paying attendees) on the usage of genome science in stem cell research. 15 minutes talk, followed by 15 minutes of lively discussion, as part of the Cambridge Literary Festival.

no actual impacts realised to date
Year(s) Of Engagement Activity 2014