Cell differentiation processes as spatial networks: Identifying four-dimensional structure in embryogenesis

Abstract

One overarching principle of eukaroytic development is the generative spatial emergence and self-organization of cell populations. As cells divide and differentiate, they and their descendents form a spatiotemporal explicit and increasingly compartmentalized complex system. Yet despite this comparmentalization, there is selective functional overlap between these structural components. While contemporary tools such as lineage trees and molecular signaling networks prvide a window into this complexity, they do not characterize embryogenesis as a global process. Using a four-dimensional spatial representation, major features of the developmental process are revealed. To establish the role of developmental mechanisms that turn a spherical embryo into a highly asymmetrical adult phenotype, we can map the outcomes of the cell division process to a complex network model. This representational model provides information about the top-down mechanisms relevant to the differentiation process. In a complementary manner, looking for phenomena such as superdiffusive positioning and sublineage-based anatomical clustering incorporates dynamic information to our parallel view of embryogenesis. Characterizing the spatial organization and geometry of embryos in this way allows for novel indicators of developmental patterns both within and between organisms.

Keywords: Complex networks; Computational biology; Embryogenesis.