Cell-extrinsic determinants of neocortical cell type identity and diversity

Neocortical cellular diversity emerges gradually through a prolonged maturation process shaped by the interplay between intrinsic genetic programs and extrinsic environmental cues. Cellular identity develops along a molecular hierarchy, in which broad class-defining characteristics appear first, followed by the emergence of subclass- and type-specific features. Although it is well established that extrinsic factors modulate the maturation of distinct cell types, a comprehensive assessment of how these influences shape the molecular maturation of cortical cells was lacking. This project investigates how neocortical identity and diversity develop under varying environmental and developmental conditions. Using the mouse (Mus musculus) as a reference, it examines how positional and circuit-level cues contribute to the acquisition and stabilization of molecular identity by altering developmental context in vivo, using transgenic models, and employing reductionist culture models in vitro. These approaches aim to clarify how local interactions and circuit integration influence molecular identity, and to determine which aspects of in vivo maturation are recapitulated at the type-specific level. Results show that the acquisition of cellular identity and diversity remains stable across in vivo transgenic models. In contrast, in vitro glutamatergic neurons display reduced expression of identity-defining genes, diminished diversity, and altered connectivity. Cellular identity and diversity most closely resemble in vivo conditions in organotypic cultures. These findings reveal population-specific responses to environmental context and underscore the role of extracellular factors in shaping cell diversity during cortical maturation. To further explore how prenatal and postnatal experiences affect these mechanisms, I examined the spiny mouse (Acomys dimidiatus), a precocial species closely related to Mus that completes much of its cortical maturation before birth. Comparing the timing and molecular trajectories of cortical development between Acomys and Mus allows assessment of how in utero versus ex utero environments influence the emergence of neuronal diversity and circuitry in the somatosensory barrel cortex. The analyses herein included, combining histology, electrophysiology, and single nucleus transcriptomics, show that Acomys neonates are born with a cortex exhibiting both structural organization and near-adult molecular maturity, equivalent to postnatal day 7–14 in Mus. Cortical layering, myelination, astrocyte colonization, and thalamocortical architecture are all established in utero in Acomys. However, a subset of intratelencephalically projecting neurons still requires postnatal experience to complete maturation. Comparative gene expression analyses indicate that these experience-dependent genes are involved in synaptic maturation and are expressed at later postnatal stage (P7–P14) in Mus. Overall, this project seeks to elucidate how intrinsic genetic programs interact with extrinsic cues to shape neocortical diversity. By integrating molecular, histological, and electrophysiological analyses across models of differential extrinsic modulation, it advances our understanding of the principles governing the emergence of cortical identity and diversity.