Combining in vitro and in silico approaches to model neural tube patterning and isthmic organizer formation.

During early embryonic development, the human neural tube is formed and patterned through spatial regionalization of cell identity, driven by gene regulatory responses to morphogen gradients. However, many of the underlying mechanisms remain unclear. Here, we integrate single-cell RNA sequencing data from in vitro emulation of neural tube patterning to develop computational models of rostral-caudal and dorsal-ventral patterning. By embedding these models in a 3D geometry, we reveal how transient morphogen signals induce irreversible patterns consistent with developmental biology and experimental data. Notably, our framework accurately captures the formation and maintenance of the isthmic organizer at the mid-hindbrain boundary, providing a realistic and mechanistic picture of neural tube patterning. This integrated approach bridges in vitro experimentation and computational modeling to uncover fundamental principles of neural development.