In a groundbreaking study published in Nature, researchers have unveiled the intricate and continuous diversification of GABAergic neurons in the developing mouse visual cortex. Utilizing cutting-edge single-cell transcriptomics and trajectory inference techniques, this work meticulously maps how inhibitory interneurons arise, differentiate, and diversify with an unprecedented resolution throughout embryonic and postnatal development. The findings not only deepen our fundamental understanding of cortical interneuron specification but also illuminate the molecular pathways guiding diverse neuronal identities that are essential for visual processing and cortical circuit formation.
The earliest GABAergic progenitor populations are detected as early as embryonic day 11.5 (E11.5), characterized by the expression of key transcription factors such as Dlx1, Dlx2, Ascl1, and Gsx2. These gene programs orchestrate the fate specification of all inhibitory neurons emerging from the subpallium. Notably, these progenitors undertake long-range tangential migrations from their origin in the ganglionic eminence toward the developing cortex—a journey that begins their pre-specification before cortical integration. Although the initial stages of these migratory paths occur outside the cortical field and were not fully captured in this postnatal-focused dataset, the research team successfully inferred multiple distinct developmental trajectories within cortical regions.
By embryonic day 14.5, a subset of medial ganglionic eminence (MGE) progenitors called MGE GABA radial glia (RG) give rise to intermediate neuronal precursors (IMNs). Previous hypotheses suggested that the somatostatin-positive (Sst) and parvalbumin-positive (Pvalb) interneurons originate from spatially segregated MGE domains; however, surprisingly, this study did not detect clear spatial segregation at the progenitor level. Instead, the divergence into Sst and Pvalb subclasses—marked by unique gene signatures such as Shisa6 and Pou3f3 in Sst neurons versus Adamts17 and Shisa9 in Pvalb neurons—becomes evident only later in development. Additional rare and highly specialized MGE subclasses, including Sst chandelier cells and Lamp5 Lhx6 interneurons, are detected around postnatal days 1 and 5, indicating early lineage bifurcation that may occur before cortical entry.
The maturation of Pvalb and Sst subclasses unfolds through distinct developmental trajectories, mapping closely to previously characterized morphoelectric transcriptomic (MET) types. Within the Pvalb subclass, five main trajectories representing various fast-spiking basket cell types distributed across cortical layers were identified, along with a specialized chandelier cell population. Each trajectory revealed unique marker genes—for example, Gpr149 and Reln define early groups corresponding to specific MET clusters in layer 5, while Sema3e marks a separate group in layer 6. Among these, a parvalbumin-positive cluster expressing Th displayed ambiguous developmental origins, consistent with transitional properties bridging Pvalb and Sst lineages. This nuanced insight refines the classical understanding of interneuron differentiation by revealing transitional states and lineage convergence.
Similarly, the Sst subclass demonstrates extensive transcriptomic heterogeneity, with thirteen distinct Sst MET-types emerging predominantly in layer-specific patterns postnatally. These clusters form five developmental groups distinguished by gene sets including Crh, Calb2, and Hpse, highlighting unique functional identities such as Martinotti and non-Martinotti cell varieties. The diversification of Sst cells suggests a complex developmental program underpinning the formation of diverse local inhibitory circuits. Intriguingly, some Sst clusters appear as transitional forms overlapping with Pvalb-like signatures, indicating plasticity between major inhibitory neuron classes during cortical circuit assembly.
Cortical interneurons of caudal ganglionic eminence (CGE) origin emerge slightly later, around E15.5, and segregate during later embryonic to early postnatal stages into distinct subclasses marked by Vip, Sncg, and Lamp5 expression profiles. The Vip subclass, known for its bipolar or bitufted morphologies, reveals five developmental trajectories, with differential layer localization predominantly in superficial cortical laminae. Notably, one Vip developmental group includes cells with negligible Vip expression, raising the possibility of under-sampled or as-yet-unclassified interneuron types. Meanwhile, Sncg interneurons, primarily comprising cholecystokinin-positive (CCK+) basket cells, follow a single major developmental trajectory, whereas the Lamp5 subclass divides into multiple trajectories including the well-characterized neurogliaform neurons largely situated in layer 1.
Importantly, the study underscores the strong correlation between transcriptomic developmental trajectories and morphoelectrical neuronal phenotypes. Each major inhibitory subtype—Sst, Pvalb, Vip, Sncg, and Lamp5—exhibits transcriptomic signatures that align with mature morphoelectric cell types. This convergence supports the model that early molecular specification imprints on the functional properties and layer-specific targeting of interneurons. However, for certain subtypes such as the diverse Sst Martinotti and non-Martinotti cells, multiple transcriptomically distinct clusters correspond to trajectory groups, reflecting their elaborate role in shaping refined local circuit motifs.
This work advances neuroscientific paradigms by charting how developmental programs underpinning genetically specified interneuron classes scaffold the formation of functionally relevant cortical inhibitory networks. It highlights that inhibitory neuron diversity emerges not as a sudden bifurcation but via continuous diversification processes, with late postnatal refinements—coinciding with critical periods of sensory input such as eye opening—driving further specialization. These findings have profound implications for understanding normal cortical function and may offer crucial insights into neurodevelopmental disorders implicating interneuron dysfunction.
The comprehensive mapping of trajectory clusters advances prior approaches by integrating genetic markers, spatial localization, and developmental timing, significantly enhancing the granularity of neuronal classification. These insights also challenge simplified binary models of interneuron fate and encourage the study of interneuron plasticity, lineage interconversion, and transitional states as fundamental components of cortical development. The elucidation of early progenitor gene programs and subsequent trajectory evolutions offers promising avenues for targeted manipulation of specific interneuron types in models of neurological disease.
Moreover, this study serves as an invaluable resource for the neuroscience community, providing a detailed developmental atlas of cortical interneurons with potential applications in brain organoid modeling, regenerative therapies, and bioengineering of neural circuits. By elucidating the molecular logic that governs interneuron lineage commitment, diversification, and maturation, it paves the way for interventions aimed at restoring inhibitory circuit balance in conditions like epilepsy, schizophrenia, and autism spectrum disorders.
In conclusion, the continuous and highly orchestrated diversification of GABAergic neurons during mouse visual cortex development underscores how complex cortical inhibitory networks are molecularly programmed from early embryogenesis through postnatal maturation. This research exemplifies the power of modern single-cell technologies and integrative developmental biology to unravel the enigmatic processes of brain circuit assembly and functional specialization. As the neuroscience field moves forward, such high-resolution developmental mappings will be crucial for decoding the cellular logic of brain function and dysfunction.
Subject of Research: Developmental diversification and specification of GABAergic inhibitory neurons in the mouse visual cortex.
Article Title: Continuous cell-type diversification in mouse visual cortex development.
Article References:
Gao, Y., van Velthoven, C.T.J., Lee, C. et al. Continuous cell-type diversification in mouse visual cortex development. Nature 647, 127–142 (2025). https://doi.org/10.1038/s41586-025-09644-1
DOI: 06 November 2025
