Agent-based modeling allows for the translation of biological mechanisms into programmable logic to observe in simulation environments. Using the BioDynaMo software platform — which helps scientists to create, run, and visualize multi-dimensional agent-based simulations — a team from the University of Surrey, UK, modeled virtual retinal “cells” that grow, divide, and make fate decisions based on internal gene-regulation logic, mimicking biological behavior.
The researchers tested different network designs for how genes might interact when cells decide what kind of neuron to become. Two designs –the Reentry and Multidirectional models – reproduced real biological data most accurately, suggesting that retinal cells may make their fate decisions through overlapping and flexible genetic pathways, rather than a fixed sequence.
This approach could help researchers better understand not only healthy eye development, but also what happens in retinal diseases, as well as impacting regenerative research exploring how stem cells might rebuild tissue.
The research team also simulated key stages of retinogenesis – the process by which identical progenitor cells diversify into the six types of neurons that make up the retina.
"We think that our research is a step forward in linking genetics, computation, and developmental biology to understand one of the body’s most complex neural structures," said Cayla Harris, lead researcher from the University of Surrey's Nature Inspired Computing and Engineering Group.
