Cell-extrinsic controls over neocortical neuron fate and diversity [snRNAseq]

Neocortical cellular diversity emerges gradually during development. Cell-extrinsic interactions shape this extended maturation, yet cell-type-specific dependence on such cues has not been systematically examined. To address this, we compared how cell identity and diversity unfolds in different conditions during neocortical development. Conditions were modified in vivo using genetically modified mice models in which position or innervation are altered and in vitro using two-dimensional cultures. This approach revealed a molecular hierarchy in which cell class-distinguishing features emerge first, followed by subclass- and type-related characteristics. Acquisition of cellular identity and diversity remained stable across in vivo models. In contrast, in vitro glutamatergic neurons showed decreased expression of identity-defining genes, reduced diversity and alterations in connectivity. Cellular identity and diversity were closest to in vivo values in organotypic cultures. These findings reveal population-specific responses to environmental conditions and highlight the role of extracellular context in shaping cell diversity in the maturing neocortex. Single nucleus transcriptomics of in vivo and invitro models of extrinsic factors of mouse neuronal maturation