MiSTR_atlas

Our knowledge of the factors underlying accurate regionalization of the developing brain is extracted mainly from model organisms. We have previously introduced the Microfluidic Stem Cell Regionalisation (MiSTR) model, which recapitulates the rostro-caudal patterning of the developing human neural tube. In this study, we applied the MiSTR rostro-caudal model as well as an additional dorso-ventral model of the forebrain to perform temporal single-cell RNA sequencing (scRNAseq), capturing the development of the dorsal and ventral neural tube across 9 different timepoints. This comprehensive dataset allowed us to create a temporal map of early neural tube patterning, revealing that rostral and caudal subtypes are specified already at 24 hours after initiation of the WNTa gradient and that neuralisation occurs only several days later. Moreover, we show that the pioneering neuralisation factors are divergent in the rostral (PAX6+) versus caudal (SOX1+) domains. In contrast, ventralisation in the telencephalon was found to be a much more delayed process which was stalled in part by the suppression of the SHH receptor PTCH1 in WNTi-exposed tissued up until day 9. In addition, our model uncovers the temporal events involved in human MHB formation and provide novel insights into the role of FOXA2 and IRX1 in diencephalic development, contributing to our knowledge on how cells in the blastocyst develop into region-specific neural fates and secondary signalling centers along the neural axis.