Transcriptional regulation of endoderm formation

Each organ in the body is made up of different types of specialized cells that perform particular functions, such as liver cells that clean the blood and pancreas cells that secrete insulin. However, during the earliest stages of embryonic life these cells have not yet become specialized and must go through a several steps of being first partially and then fully specialized before forming into different organs.

This series of specialization steps is directed by the genome, or genetic code, of the cells. The genome is built from genes and control modules. The genes are activated in a specific order during embryonic life and cause cells to become specialized. The control modules ensure genes are activated in the correct order. By understanding how genes and control regions work together we will be better able to understand the process of cell specialization, and in due course will aid in designing the best ways to generate cells in the lab for therapeutic purposes.

Research over the past few decades has discovered many of the genes that become activated as cells are specialized, but scientists know much less about the control modules and how these work to ensure genes are activated in the correct order during specialization steps. This project will identify and characterize how a set of specific control modules function, so as to better understand how to control gene activation during the formation of organs. The project will concentrate on one particular cell type, called endodermal cells, which are partially specialized cells that will in turn become the more specialized cells of the lung, liver, pancreas and intestine.

To characterize the control regions that activate genes in endoderm cells we need to gather data in cells that are easy to experiment on but that give us relevant information about the normal process of cell specialization. Therefore, we plan to use zebrafish embryos because we know that the genes activated in zebrafish endodermal cells are the same as the genes activated in humans, but zebrafish offer a simple, experimentally amenable system in which to study the process. We have previously used zebrafish to generate data on potential control regions, and in this study we propose to test whether these regions do indeed act to control gene activation and how they do it.

This analysis will give us very detailed information on the control regions, providing an insight into how to activation of endodermal genes and consequently the formation of specialized cells is controlled by the genome. We hope it will also give us information on the general mechanisms of gene activation control during embryo formation. This insight can be applied to the generation of endodermal cells in the lab with the aim of treating diseases of endodermal organs, such as liver failure or diabetes, in the future.

Developmental gene regulatory networks (GRNs) drive the sequential gene expression changes that specify and then differentiate cells of an embryo. GRN models allow the interrogation of regulatory inputs (signaling and transcription factors; TFs) into gene cis-regulatory modules that control downstream events such as cell type specification, thereby providing mechanistic insight into cell fate decisions. Endoderm forms specialized cells lining the gastrointestinal and respiratory tracts, and associated organs, such as liver and pancreas. Treatment for diseases of these organs, such as diabetes, will benefit from the production of endodermal cell types in vitro. Generation of endodermal progenitors is the first step in this procedure, and protocols have been developed that make use of signaling pathways employed by the embryo. An alternative method that can generate cell types in vitro is expression of TFs, often in combination, or in sequence, which act to manipulate GRNs and consequently cell fate. However, despite advances in the field, efficient production of pure populations of endodermal progenitors remains challenging. To accelerate efforts to efficiently produce endodermal progenitors, a detailed understanding of the GRN that governs normal endoderm formation in the embryo is important, in order to manipulate it in a controlled fashion during in vitro generation. Previous endodermal GRNs have been limited by incomplete experimental evidence for direct transcriptional regulation. Here we propose to build an experimentally validated GRN for endoderm development in a vertebrate model, which will provide mechanistic insight into the combinatorial action of TFs that initiate and maintain correct gene expression in endoderm progenitor cells. The detailed understanding we will generate has important implications for lifelong health since the future development of efficient protocols for in vitro tissue production will lead to disease therapies and improved wellbeing.

The implementation of this project and the research generated from it will have a wide impact on the UK's knowledge economy in both the short and long term. The beneficiaries of this research will be:

1. Staff employed on this project
A highly-skilled workforce is essential for the long-term success of the UK economy. The researchers employed on this project will gain critical thinking, data analysis, team-working, and communications skills, among others, all of which are sort after by employers. Such transferable skills will therefore enhance the employability of both researchers, in either academia or other sectors, and contribute to the knowledge economy.

2. Academic researchers
This study combines different areas of research, including developmental biology and genome regulation. The results of this study will be disseminated widely to the different academic communities at meetings and seminars and will be published in open access scientific journals. This will allow other researchers to access the data and incorporate our findings into their own studies to advance knowledge.

3. Private companies
The research skills that the staff working on this project will gain are much sort after by private sector companies, such as those in pharmaceutical research, regenerative medicine, biotechnology, intellectual property and software development. For instance, the postdoc will gain knowledge and expertise in both the biological and computational methods required to interrogate genomes, which is transferable to many other systems, technologies and therapies being developed in private companies (e.g. stem/iPS cells; personalized medicine). Staff will also gain skills in project management, presentations, writing and other communication skills through working on the project, which are of high value to employers.

4. A level students
A level students from South East London will benefit from the workshops that will be delivered in this proposal, in collaboration with Science Gallery London, which are designed to facilitate learning in the A level biology curriculum areas, specifically genetics and working scientifically. In addition to informing and engaging students with current scientific advancements, these events have the potential to inspire students to enter a wide range of STEM careers that enhance the UK's economy and global competitiveness in the longer term.