A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development

Author summary Starting as fertilized eggs, mammal embryos develop into fetuses with complex functions through robust spatiotemporal trajectotries. Correct timing of various regulatory mechanisms is an essential prerequisite that keeps developing biological systems on the right track. At the earliest stages of embryo development, cells make robust fate decisions to form inner cell mass which later develops into two cell types forming a particular spatial pattern. Through the lens of a multiscale three-dimensional model with the resolution of single cells in a realistic geometry, we study how timing of regulatory mechanisms ensures the robust developmental process in a tight time window. Assisted by single-cell transcriptomics data, the model revealed how the timing of a gene regulatory mechanism and a spatial mechanistic mechanism impact the pattern formation in early embryo development. We showed that both individual timings of these two mechanisms and the time overlap between them are essential to ensure correct pattern formation. We further validated our findings using distinct subsets of single-cell gene expression data and spatial imaging data. This data-informed multiscale modeling framework has a potential in studying other biological systems and developmental processes utilizing the emerging high-throughput and high-resolution data resources. During early mammalian embryo development, a small number of cells make robust fate decisions at particular spatial locations in a tight time window to form inner cell mass (ICM), and later epiblast (Epi) and primitive endoderm (PE). While recent single-cell transcriptomics data allows scrutinization of heterogeneity of individual cells, consistent spatial and temporal mechanisms the early embryo utilize to robustly form the Epi/PE layers from ICM remain elusive. Here we build a multiscale three-dimensional model for mammalian embryo to recapitulate the observed patterning process from zygote to late blastocyst. By integrating the spatiotemporal information reconstructed from multiple single-cell transcriptomic datasets, the data-informed modeling analysis suggests two major processes critical to the formation of Epi/PE layers: a selective cell-cell adhesion mechanism (via EphA4/EphrinB2) for fate-location coordination and a temporal attenuation mechanism of cell signaling (via Fgf). Spatial imaging data and distinct subsets of single-cell gene expression data are then used to validate the predictions. Together, our study provides a multiscale framework that incorporates single-cell gene expression datasets to analyze gene regulations, cell-cell communications, and physical interactions among cells in complex geometries at single-cell resolution, with direct application to late-stage development of embryogenesis.