PhysiMeSS - A New PhysiCell Addon for Extracellular Matrix Modelling

Abstract

The extracellular matrix is a complex assembly of macro-molecules, such as collagen fibres, which provides structural support for surrounding cells. In the context of cancer metastasis, it represents a barrier for the cells, that the migrating cells needs to degrade in order to leave the primary tumor and invade further tissues. Agent-based frameworks, such as PhysiCell, are often use to represent the spatial dynamics of tumor evolution. However, typically they only implement cells as agents, which are represented by either a circle (2D) or a sphere (3D). In order to accurately represent the extracellular matrix as a network of fibres, we require a new type of agent represented by a segment (2D) or a cylinder (3D). In this article, we present PhysiMeSS, an addon of PhysiCell, which introduces a new type of agent to describe fibres, and their physical interactions with cells and other fibres. PhysiMeSS implementation is publicly available at https://github.com/PhysiMeSS/PhysiMeSS, as well as in the official PhysiCell repository. We also provide simple examples to describe the extended possibilities of this new framework. We hope that this tool will serve to tackle important biological questions such as diseases linked to dis-regulation of the extracellular matrix, or the processes leading to cancer metastasis.

A simple framework for agent-based modeling with extracellular matrix

“…Examples of the discrete force-based frameworks include Schülter et al and Nöel et al where migrating cells and individual matrix fibers are embodied as agents with direct forces dictating motility and realignment respectively [21, 22]. Macnamara et al also adopt this paradigm and couple it with a model of blood vessel-cell interactions [23].…”