Differential equation modeling of cell population dynamics in skeletal muscle regeneration from single-cell transcriptomic data

Skeletal muscle regeneration is a complex process orchestrated by diverse cell populations within a dynamic niche. In response to muscle damage and intercellular signaling, these cells undergo cell fate and migration decisions including quiescence, activation, proliferation, differentiation, infiltration, apoptosis, and exfiltration. The emergence of single-cell RNA sequencing (scRNA-seq) studies of muscle regeneration offers a significant opportunity to refine models of regeneration and enhance our understanding of cellular interactions. To better understand how crosstalk between cell types governs cell fate decisions and cell population dynamics, we developed a novel non-linear ordinary differential equation model guided by scRNA-seq data. Our model consists of 9 variables and 17 parameters, capturing the dynamics of key myogenic lineage and immune cell types. We calibrated time-series scRNA-seq data to units of cells per cubic millimeter of tissue and fit our model’s parameters to capture the observed dynamics, validating on an independent time series. The model successfully captures key features of regeneration dynamics, particularly after incorporating a novel regulatory interaction between M2 macrophages and satellite cells that has been hypothesized in the literature. Our model lays a foundation for future computational explorations of muscle regeneration, modeling of disease conditions, and in silico testing of therapeutic strategies.