BCNNM: A Framework for in silico Neural Tissue Development Modeling

Dmitrii V. Bozhko, Georgii K. Galumov*, Aleksandr I. Polovian, Sofiia M. Kolchanova, Vladislav O. Myrov, Viktoriia A. Stelmakh, Helgi B. Schiöth

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

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Abstract

Cerebral (“brain”) organoids are high-fidelity in vitro cellular models of the developing brain, which makes them one of the go-to methods to study isolated processes of tissue organization and its electrophysiological properties, allowing to collect invaluable data for in silico modeling neurodevelopmental processes. Complex computer models of biological systems supplement in vivo and in vitro experimentation and allow researchers to look at things that no laboratory study has access to, due to either technological or ethical limitations. In this paper, we present the Biological Cellular Neural Network Modeling (BCNNM) framework designed for building dynamic spatial models of neural tissue organization and basic stimulus dynamics. The BCNNM uses a convenient predicate description of sequences of biochemical reactions and can be used to run complex models of multi-layer neural network formation from a single initial stem cell. It involves processes such as proliferation of precursor cells and their differentiation into mature cell types, cell migration, axon and dendritic tree formation, axon pathfinding and synaptogenesis. The experiment described in this article demonstrates a creation of an in silico cerebral organoid-like structure, constituted of up to 1 million cells, which differentiate and self-organize into an interconnected system with four layers, where the spatial arrangement of layers and cells are consistent with the values of analogous parameters obtained from research on living tissues. Our in silico organoid contains axons and millions of synapses within and between the layers, and it comprises neurons with high density of connections (more than 10). In sum, the BCNNM is an easy-to-use and powerful framework for simulations of neural tissue development that provides a convenient way to design a variety of tractable in silico experiments.

Original languageEnglish
Article number588224
Number of pages21
JournalFRONTIERS IN COMPUTATIONAL NEUROSCIENCE
Volume14
DOIs
Publication statusPublished - 20 Jan 2021
MoE publication typeA1 Journal article-refereed

Keywords

  • axon guidance
  • brain organoid
  • neurogenesis
  • neuronal connectivity
  • simulation
  • tissue development

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