In the quest to decode the brain’s extraordinary complexity, the diversity of cortical cell types remains a fundamental puzzle. The cerebral cortex, central to cognition, sensory processing, and behavior, comprises an intricate mosaic of neurons. Recent advances in single-cell genomics have transformed our understanding of this cellular diversity, but significant questions remain. A groundbreaking study published in Nature Neuroscience in 2025 delves into the molecular underpinnings of cortical neurons, with a focus on contrasting the six-layered neocortex and the evolutionarily ancient three-layered piriform cortex, an integral part of the olfactory system.
This study leverages cutting-edge single-nucleus transcriptomics and chromatin accessibility profiling to intricately compare neuronal populations across different cortical regions in adult mice and extend these comparisons to other tetrapod species. By dissecting the gene expression patterns and epigenetic landscapes at a single-cell resolution, the researchers reveal a molecular portrait that challenges long-standing assumptions about cortical architecture and its evolutionary trajectory.
A striking conclusion emerges from their data: while the neocortex’s glutamatergic neurons—commonly associated with excitatory signaling—segregate into discrete types with distinct transcriptomic identities, the piriform cortex neurons display a continuous spectrum of gene expression. This discovery suggests that the piriform cortex, despite its simpler laminar organization, possesses a different organizational logic, more fluid yet equally complex, that underlies its functional capacity.
The implications of this continuous variation provoke a re-examination of how cortical areas are architecturally and functionally specialized. Unlike the neocortex, which boasts six well-defined layers with corresponding functional specializations, the piriform cortex’s three-layered structure appears to support a more integrated and less sharply divided neuronal identity landscape. This hints at fundamentally different modes of information processing and plasticity, likely related to the piriform cortex’s role in olfactory perception and associative learning.
Delving deeper into epigenetic regulation, the study identifies that distinct subsets of both piriform and neocortical glutamatergic neurons, despite sharing conserved transcriptomic profiles, exhibit area-specific chromatin accessibility patterns. This area-specific epigenetic modulation suggests that the same genetic programs are differentially tuned across cortical regions to meet unique functional demands. Such chromatin states could provide a versatile regulatory mechanism enabling diverse neuronal behaviors within conserved cell types.
One of the more unexpected findings of the study is the identification of a substantial population of immature neurons within the adult piriform cortex. These immature neurons resemble earlier developmental stages, suggesting ongoing neurogenesis or delayed maturation processes in this cortical region, which are notably absent or minimal in the neocortex at comparable stages. This raises intriguing questions about the potential for structural and functional plasticity in the adult olfactory cortex and its role in sensory adaptation or learning.
Moreover, the research highlights an intriguing divergence in piriform cortex neurons between laboratory mice and their wild-derived counterparts. While neocortical glutamatergic cells display remarkable transcriptomic consistency regardless of environmental or genetic variability, piriform neurons vary significantly, indicating a heightened sensitivity to environmental cues or evolutionary pressures. This plasticity in piriform cortex neurons underscores the adaptability of the olfactory system, potentially reflecting its evolutionary role in survival and environmental interaction.
Expanding the comparative scope, the team examined the transcriptomic profiles of piriform cortex neurons against homologous neurons in reptiles and amphibians, including turtles, lizards, and salamanders. Remarkably, they found a closer molecular resemblance of piriform neurons to these ancestral cortical neurons than to neocortical neurons, despite the hundreds of millions of years separating these lineages. This offers compelling molecular evidence supporting the theory that the olfactory cortex has conserved ancestral cortical features that predate the emergence of the more complex neocortex.
Such ancestral molecular signatures highlight the olfactory cortex as a living fossil within the brain, retaining primordial characteristics that have been largely lost or transformed in the neocortex. This evolutionary insight not only informs our understanding of cortical origins but also posits the olfactory cortex as a valuable model for exploring fundamental neuronal traits and their diversification over evolutionary timescales.
Throughout the study, the application of single-nucleus analyses enables an unprecedented resolution of neuronal identity, capturing nuances in gene expression and chromatin dynamics inaccessible by bulk tissue methods. This approach reveals the cellular heterogeneity underpinning cortical function and evolutionary history and sets the stage for future exploration of how molecular diversity translates into circuit properties and behavior.
The findings provoke broader considerations about how cortical complexity arises from underlying molecular mechanisms. The contrast between discrete neuronal types in the neocortex and continuous variation in the piriform cortex intimates different developmental programs and regulatory networks. Such diversity in organizational logic might reflect adaptation to distinct computational requirements—the high acuity and modular architecture of the neocortex versus the integrative and flexible processing necessary for olfactory function.
Furthermore, the observation of immature neurons persisting in the adult piriform cortex aligns with emerging concepts of adult neurogenesis and cellular plasticity in sensory areas. This plasticity could facilitate the dynamic remodeling of olfactory circuits in response to environmental stimuli, underpinning learning and memory associated with smell. Understanding the molecular cues governing this plasticity could open avenues for regenerative therapies and neurocognitive enhancement.
The epigenetic distinctions between områder-specific neurons emphasize the importance of chromatin remodeling in shaping neuronal identity beyond the genome. Such mechanisms might enable rapid adaptation to environmental changes or developmental signals, fine-tuning neuronal function in a context-dependent manner. Future studies exploring the causative role of these epigenetic landscapes will deepen our mechanistic understanding of cortical specialization.
Importantly, this research integrates cross-species comparisons that root cortical cell types within a broad evolutionary framework. By linking mammalian piriform cortex neurons to those of reptiles and amphibians, it underscores the continuity of certain neural traits and identifies conserved molecular programs that may be foundational to vertebrate brain organization. This evolutionary perspective enriches our grasp of how the brain’s complexity evolved in a stepwise fashion, with ancestral circuits co-opted and elaborated upon.
The study’s multidisciplinary approach—combining transcriptomics, epigenetics, developmental biology, and comparative genomics—exemplifies the power of integrative neuroscience. It illuminates not only the molecular diversity within a single species but also the evolutionary forces shaping cortical architecture. This comprehensive view is crucial for unraveling the origins of neural diversity and its implications for brain function, adaptation, and disease.
In sum, the investigation reveals that, despite millions of years of concurrent evolution with the neocortex, the olfactory cortex retains distinct molecular identities rooted in ancestral cortical structures. This discovery reframes our understanding of cortical evolution and underscores the olfactory cortex’s unique role as a window into the brain’s past and a guide for its future exploration. As neuroscience continues to bridge molecular and systems-level insights, studies like this will be pivotal in decoding the enigma of brain complexity and diversity.
Subject of Research: Single-cell genomics of cortical neurons comparing mouse piriform (olfactory) cortex and neocortex, with evolutionary analysis across tetrapods.
Article Title: Single-cell genomics of the mouse olfactory cortex reveals contrasts with neocortex and ancestral signatures of cell type evolution.
Article References:
Zeppilli, S., Gurrola, A.O., Demetci, P. et al. Single-cell genomics of the mouse olfactory cortex reveals contrasts with neocortex and ancestral signatures of cell type evolution. Nat Neurosci (2025). https://doi.org/10.1038/s41593-025-01924-3
Image Credits: AI Generated
Tags: chromatin accessibility profilingcomparative neuroscience in tetrapodscortical cell type diversityepigenetic landscapes in brainexcitatory signaling in cortical neuronsgene expression patterns in neuronsmolecular basis of cortical architecturemouse olfactory cortex evolutionneocortex vs piriform cortexolfactory system evolutionSingle-Cell Genomicssingle-nucleus transcriptomics
