By examining the networks of genes that were active in these distinct populations of cells, the researchers identified two key signalling pathways - BMP and WNT – that were most strongly involved in the decision about ‘fingerness’ or ‘gapness’. “This analysis of gene expression was complemented by examination of the proposed pathways at the protein activity level, which also supported the conclusions,” says Dr Sharpe. Once enough molecular data had been gathered, the Barcelona lab began construction of a computer model to explore a system of development proposed by British computing pioneer Alan Turing, where chemicals react with each other and diffuse over space to create particular types of stripy or spotty patterns.
The most exciting thing was that we got the same result in the computer simulation and in the real experiments. “The computer model was essential, because Turing systems are very non-intuitive,” says Dr Sharpe. “But our initial step of screening for the molecular components was also key: if the model had been abstract – not based on data about real molecules involved – it would be unable to make predictions that we could experimentally test in the lab.” The researchers turned the BMP and WNT signalling up and down – both in the computer model and in in-vitro experiments – and watched what happened. When they switched off the BMP pathway all the cells became gaps. If they repressed the WNT pathway instead, all of the cells became fingers. And repressing both the BMP and WNT pathways at the same time but to different degrees rearranged the pattern into fewer, fatter fingers.
“The most exciting thing was that we got the same result in the computer simulation and in the real experiments. This interplay between the modelling and experimentation is at the heart of the systems biology approach, and it is the strongest proof we have that these molecules are part of a Turing system,” says Dr Sharpe. “For decades this idea was actively resisted, but our results provide good evidence for it, and we think this Turing mechanism possibly goes back all the way into fish, even though the number of digit structures they have is not the same.” Figuring out fingers is just one aspect of understanding limb development, and Dr Sharpe’s lab is also using systems biology to examine how a limb as a whole organises itself to form a humerus, ulna and radius, wrist bones and - finally - fingers. Understanding such aspects of limb development should also help to inform the wider field of regenerative biology and tissue engineering. “To be able to heal and maybe one day to even build multi-cellular tissues, we ought really to understand how multicellular tissues build themselves in the first place, and we still have a lot to learn about that,” says Dr Sharpe. “Our view is that a systems biology approach will ultimately be the only way to explain, understand and then engineer living multicellular tissues, either tissues in dish that can then be put back into patients, or by stimulating patients’ own tissues to heal and regenerate.”
Patterns in biology – the Turing connection
In August 1952, British computing pioneer Alan Turing published a seminal paper entitled The Chemical Basis of Morphogenesis. It outlined how just two distinct molecules (‘morphogens’) could underpin the spontaneous development of spotted and stripy patterns by diffusing and interacting in specific ways to form repetitive motifs. Turing died two years after the paper was published in Philosophical Transactions B, but the reaction-diffusion model it described has since been proposed to underpin numerous repetitive patterns in nature, including the stripes on a zebra, and now the more subtle patterns of digit formation.
Words: Claire O’Connell May 2015
further Information Centre for Genomic Regulation crg.es
ISBE - www.isbe.eu
8