Organizers: orchestrators of developmental decisions

Development is an extraordinarily complex process, in which many cells, with identical genomes, have to specialize as well as to generate coherent arrangements so as to generate functional tissues, organs, systems and a viable whole organism. One way in which their behaviour is coordinated is by the action of signalling centres called "organizers". These are groups of cells that emit signals which both INDUCE (ie. change the fate) and PATTERN (generate a spatially coherent arrangement of elements) neighbouring cells. Until now, organizers have been discovered by transplanting groups of cells into new regions, looking for changes in the surrounding tissue. This led to the discovery of just 4 well defined organizers. But there must be more, so the challenge is whether we could use a more effective way to point to regions of the embryo where organizers might reside. In a previous BBSRC-funded project (2008-2013) we compared the genes expressed in 3 known organizers of the chick embryo and from this identified a set of about 50 genes that are expressed similarly in all 3. Using this, we then identified a new organizer, regulating aspects of heart development.

Encouraged by this success, we will now:

(a) refine the tool by including the fourth organizer,
(b) explore three new candidate regions to see if they are organizers, and what events they could pattern (in the brain, face and tail region)
(c) study the functions of some of the genes that are common to these organizers. Transcription factors seem to be depleted in organizers so we will explore whether they act as repressors of that signalling state
(d) genes that are enriched in organizers include five new signalling molecules, which have not been studied in the context of embryonic induction and patterning. We will assess their functions during neural induction, the event that first defines the central nervous system and starts to pattern it into brain and spinal cord regions.

Together this project will not only provide a lot of new information about these developmental events, but it should also set a precedent for using a transcriptomics and systems biology approach to look for new biological events and principles which could be more generally applicable: the idea is that comparing several sets of cells that are quite different but share some common property can reveal sets of genes that define that property, and this set can then be used as a tool.

Organizers are signalling regions capable of both induction and patterning of neighbouring tissues. But very few of these have as yet been discovered, probably mainly due to the fact that this requires transplantation of the appropriate region at the appropriate time into a suitably competent site. A previous BBSRC-funded project in our lab tested the idea that comparing the transcriptomes of known organizers could be used to define a small set of synexpressed genes which could in turn be used as a tool to point to otherwise unsuspected candidate organizers. Using this we identified the Anterior Intestinal Portal (AIP) as an organizer of the early heart in the chick embryo. The present project extends this by:

a. refining the gene set by including the transcriptome of a fourth organizer (the Mid-Hindbrain boundary, MHB) (compared to its most similar, non-organizer tissues: rostral hindbrain and caudal midbrain);
b. testing whether three new candidates revealed by the screen are indeed organizers, and if so, what is their patterning function. The candidates are: the Caudal Intestinal Portal (CIP), part of the pharyngeal arch ectoderm and the pineal gland. We will test them by embryological experiments.
c. explore whether a set of transcription factors that are depleted in organizers function as repressors of the organizer state, using gain- and loss-of-function approaches in vivo;
d. investigate the roles of five signalling molecules not previously studied in the context of early development in terms of their roles in neural induction and patterning, assaying the responses of cells to these factors by NanoString analysis.

Together these experiments will refine a new approach to point to new biological events in the embryo and provide considerably more knowledge about organizers and their functions.

Although this project addresses a quite specific question in developmental biology/embryology ("what defines the special regions of the embryo that emit signals that instruct cells to form coherent structures?"), the rationale behind it, and the experimental design it offers, are quite unique and have potential for much broader impact. In particular, it is usual in biology to take a system apart to study its components to understand how it works. This project turns this paradigm on its head - it suggests that comparing (in detail) quite different things that share a particular feature can be used to uncover the key determinants of that feature, and the collection of these determinants then used to hunt for more cases that share the feature. This "tool" would refine itself the more it is used. Here, we propose to use genes to discover new biology, rather than the reverse. Another aspect of this project is that it will identify a small set of genes that may act together to define whether a cell population has the property to signal or not. This has future potential in stem cell science, particularly for generating "organoids" in culture. Although it is currently possible to generate many different cell types in culture from stem cells, it is much more difficult to produce functional organs. In part is because cultured cells do not receive directional signals as they do in the embryo. Our research has potential to produce signalling populations that can be combined with such cultures.

Taken together, the main beneficiaries of this research are: stem cell scientists, with eventual applications in regenerative and diagnostic medicine and veterinary medicine and potentially in the pharmaceutical industry as a means to test drugs. More generally the project will have impact by introducing a new way of thinking that could be applied not only to developmental or biological problems but potentially beyond. We will explore these ways of thinking in teaching and public engagement. We will also engage in international activities to engage with other communities and disseminate our expertise.