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Project ID: 637840
Funded under: H2020-EU.1.1.

Periodic Reporting for period 1 - QUANTPATTERN (Quantitative analysis of Nodal/Lefty-mediated pattern formation)

Reporting period: 2015-07-01 to 2016-12-31

Summary of the context and overall objectives of the project

How a homogeneous population of cells self-organizes to form a patterned embryo is a long-standing mystery in the field of developmental biology. In 1952, Alan Turing postulated the reaction-diffusion model to explain how embryos might self-organize to develop tissues and organs. The reaction-diffusion model comprises a system of two diffusible substances that must satisfy two requirements in order to form a pattern: (i) one substance activates its own production and is inhibited by the other, and (ii) the diffusivity of the inhibitor has to be higher than the diffusivity of the activator. Genetic and embryological experiments suggest that several patterning events in developing embryos are controlled by reaction-diffusion systems, but a mechanistic, quantitative understanding of how these systems dynamically control robust pattern formation in developing tissues is currently lacking.

It has been proposed that the two developmental signals Nodal and Lefty form a reaction-diffusion system during zebrafish mesendoderm patterning. Within the QUANTPATTERN project, we are addressing three key questions about how the Nodal/Lefty system leads to patterning. First, how do activator/inhibitor pairs such as Nodal and Lefty achieve their different diffusivities despite their high sequence similarity and similar molecular weights? Second, how does the range of reaction-diffusion systems such as Nodal and Lefty adjust to natural fluctuations in embryo size? Finally, how do reaction-systems such as Nodal and Lefty self-organize to induce spatially restricted tissues in the absence of pre-patterns?

The QUANTPATTERN project uses a combination of quantitative experimental and theoretical approaches to address these questions and has three major aims:

Aim 1: Identify the factors regulating the dispersal of Nodal and Lefty during zebrafish development
Aim 2: Determine how the Nodal/Lefty system mediates scale-invariant patterning of zebrafish embryos
Aim 3: Quantitative analysis of self-organized patterning in mouse embryonic stem cells

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We have made progress on all three research aims of the QUANTPATTERN project. To identify factors regulating Nodal and Lefty dispersal during zebrafish development, we have generated mutations in candidate diffusion regulators and optimized unbiased screening approaches, subcellular localization methods, and biophysical measurement techniques. To understand how the Nodal/Lefty system mediates scale-invariant patterning of zebrafish embryos, we have performed large-scale computational screens to identify realistic signaling networks. Using quantitative experimentation and systems biology approaches, we have systematically tested the predictions of the resulting models. Our work demonstrates that a size-dependent increase in Lefty levels is crucial to adjust Nodal-dependent germ layer proportions in smaller embryos. Finally, to understand self-organized patterning in mouse embryonic stem cells, we have quantitatively characterized the kinetics of developmental markers during embryoid body formation using live imaging by light-sheet fluorescence microscopy. Based on a mathematical screen for gene regulatory networks that can drive self-organization in mouse embryonic stem cells, we are developing realistic models to describe the interactions and diffusion of Nodal and Lefty during self-organized patterning.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

We will identify mechanisms underlying spatial regulation of germ layer patterning to improve our molecular understanding of signal movement and stability, long-standing questions in the fields signal transduction and development. Our experiments on self-organized patterning are likely to provide a long-sought experimental foundation for our understanding of symmetry-breaking patterning systems, could uncover intriguing parallels to other self-organizing processes during development, disease and regeneration, and might inform new strategies for human tissue engineering from embryonic stem cells.
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