Gorzek, R. | Search bioRxiv

bioRxiv2025

Comparative transcriptomics reveals shifts in cortical architecture at themetatherian/eutherian transition

The neocortex, a layered structure unique to mammals, supports higher-order functions including perception, learning, and decision-making. While its laminar architecture is broadly conserved, the cell type-specific organization of the cortical column has not been compared across species that diverged early in mammalian evolution. To address this, we used single-nucleus RNA sequencing and spatial transcriptomics to compare gene expression, cell types, and laminar architecture in the primary visual cortex (V1) of metatherian (Monodelphis domestica) and eutherian (Mus musculus) mammals. We show that spatio-transcriptomic distinctions between supragranular (layer 2/3) and infragranular (layer 5) intratelencephalic (IT) neurons are more pronounced in mice, consistent with lineage-specific specialization. Mouse cortex also exhibits a lower relative density of parvalbumin-positive (PV) GABAergic neurons and redistributed perineuronal nets, consistent with altered constraints on plasticity. Together, these findings demonstrate substantial variation in the cellular and spatial organization of the cortical column across deeply diverged mammals, challenging the view that local cortical architecture is uniformly conserved. Significance StatementThe neocortex supports perception and flexible behavior in mammals, yet how its cellular composition varies across early mammalian divergences has not been directly examined. By comparing transcriptomic cell types and their spatial organization in the primary visual cortex of a metatherian (opossum) and a eutherian (mouse), we show that major classes and laminar structure are broadly conserved, but intratelencephalic neurons differ substantially. These differences are accompanied by shifts in inhibitory circuitry and extracellular scaffolding, indicating divergent modes of cortical organization and plasticity across mammalian lineages. Our findings challenge the assumption that neocortical columns are uniformly conserved and identify specific cellular populations that vary across deeply diverged therian mammals.

neuroscience↗

bioRxiv2025

Establishing a continuum of cell types in the visual cortex

The mammalian cerebral cortex is composed of neurons whose properties vary in a continuous fashion rather than falling into discrete cell types. In the mouse visual cortex, excitatory neurons in layer 2 and 3 (L2/3) form such a continuum along cortical depth, patterned by the graded expression of hundreds of genes. Here we sought to understand how this continuum develops and contributes to cortical wiring. Using single-nucleus multiomics (RNA- and ATAC-Seq) and spatial transcriptomics, we show that the L2/3 continuum is established in two phases. During the first postnatal week, a genetically hardwired program establishes a primitive continuum of cell identities spanning the depth of L2/3. The second program, promoted by visual experience, is later superimposed upon the preexisting continuum. This second phase is driven by activity-regulated transcription factors that drive the L2/3 depth-dependent expression of genes linked to synaptic function and plasticity. We show that neurons at different positions along the L2/3 continuum project preferentially to distinct higher visual areas and that visual deprivation disrupts targeting to some higher visual areas while sparing others. Thus, cortical continua emerge through a stepwise process in which genetic programs and sensory experience specify neuronal identity and sculpt intracortical wiring specificity.

neuroscience↗