An exhaustive topological characterization of the gene regulatory networks capable of stationary pattern transformation via extracellular signaling

Abstract

Development is the process by which the complex anatomy of multicellular organisms is built in each generation and it constitutes one of the very few natural processes capable of generating so much complexity in such a relatively short period of time. From a broad and phenomenological point of view, development can be described as the sequence of transformations from one developmental pattern (i.e., a specific distribution of cell types along the developing embryo) to another, that begins with the fertilized egg and finishes with the complete functional adult individual. Although there are many intertwined mechanisms responsible for pattern transformation during development, in our work we focus only in what developmental biologists call inductive mechanisms, that is, we will only take into consideration those transformations that occur as a response to biochemical signals sent from one cell to another. In this sense, the main question we want to address is: ”which gene regulatory networks governing cell signaling (i.e, which network topologies of activating and inhibiting interactions between gene products) can actually lead to proper pattern transformations?”. Our theoretical analysis and numerical simulations, performed in the framework of reaction-diffusion equations, show that, regardless of the immense number of patterning gene networks that one can think of (specially when the number of gene products at hand is large), they can all be sorted out into just three fundamental classes of gene networks capable of pattern transformation, and their combinations. Gene networks within each of these three classes share the same topological properties, exhibit similar reaction-diffusion dynamics and lead to analogous final patterns.

Date of Award	3 Nov 2025
Original language	English
Awarding Institution	Universitat Autònoma de Barcelona (UAB)
Supervisor	Isaac Salazar Ciudad (Director)