Biology subjects

Bocchi, R.

Publications and source records attributed to Bocchi, R..

7 recordsLinked to original sources

bioRxiv2026

Transplantation reveals birthdate-dependent post-mitotic competence in cortical neurons

Cortical glutamatergic neurons are generated through temporally ordered developmental programs that link neuronal birthdate to laminar position and identity. Yet, because differentiation continues after cell-cycle exit, it remains unclear how far post-mitotic identity can be reshaped by the environment and whether this residual competence varies across neuronal types. Here, we used transplantation to uncouple birthdate from final laminar position by placing newborn neurons in ectopic laminae in the postnatal mouse cortex. E13-born (i.e. deep layer-destined) and E15-born (i.e. superficial layer-destined) donor neurons displayed distinct birthdate-associated molecular programs before transplantation. After grafting into P0 hosts, both populations migrated and settled across cortical layers, enabling comparison across laminar environments. We simultaneously profiled transcriptomic, morphological and electrophysiological neuronal identities using Patch-seq. Transplanted neurons developed pyramidal morphologies and active membrane properties, but their final identity was not imposed by their laminar position. Thus, the postnatal cortex supports integration and maturation but does not impose canonical laminar identity. Critically, neuronal competence was asymmetric across birthdates. E15-born neurons remained committed toward a robust superficial layer neuron-like profile independently of cortical position, whereas E13-born neurons retained a broad, non-canonical differentiation rather than either converging on a deep- or superficial-layer reference state. This is consistent with the wider intrinsic repertoire of early-born neurons, which the postnatal environment does not resolve. Thus, post-mitotic identity is constrained by developmental history in a birthdate-dependent manner, with early- and late-born neurons retaining fundamentally different differentiation potentials after cell-cycle exit.

neuroscience↗

bioRxiv2026

Neocortical astrocyte diversity stems from distinct developmental origins

Key regulators of neural network activity in multiple advanced cognitive processes and essential components of the blood-brain barrier, astrocytes constitute a highly heterogeneous population at the morphological, molecular, and functional levels. However, how this diversity arises during mammalian brain development remains poorly investigated. Here, using a combination of multicolour genetic fate mapping, single-cell transcriptomic analyses, multichannel large-volume imaging and detailed 3D cell morphology reconstructions, we uncover a discrete subpopulation of neocortical astrocytes generated from an early restricted embryonic domain located outside of the dorsal pallium. Besides their separate lineage from pyramidal neurons, these astrocytes exhibit a developmental trajectory that differs from astrocytes produced by dorsal cortical progenitors, including different migratory pathways, spatial distributions and morphology. Overall, our results reveal the diversity of embryonic sources responsible for neocortical astrocyte genesis and provide key insights into the unsuspected complex developmental processes that underlie cortical astrocyte heterogeneity.

neuroscience↗

bioRxiv2026

Prenatal assembly of functional cortical circuits

The extent to which early brain maturation requires interactions with the outside world is a central question in neurobiology. Because much of cortical maturation occurs after birth in Mus, it has often been viewed as dependent on postnatal experience. However, studies addressing this issue have largely relied on postnatal sensory deprivation paradigms, which perturb normal development and cannot determine to what extent postnatal experience per se drives maturation. To address this question, here we compare two related rodents with markedly different gestation lengths: the precocial Acomys dimidiatus (39-day gestation) and the altricial Mus musculus (19-day gestation). By generating a novel Acomys reference genome and using histology, cellular birth dating, electrophysiology, single-nucleus transcriptomics, and quantitative behavior, we show that Acomys preserves the canonical sequence and timing of cortical development, while shifting major milestones of neuronal, circuit and behavioral maturation into prenatal life. At birth, Acomys cortex already shows advanced cytoarchitecture, neuronal physiology, thalamocortical barrels, transcriptional states, and sensorimotor behavior, with postnatal molecular programs in Mus unfolding prenatally in Acomys. Thus, birth is not a prerequisite for early cortical maturation. Instead, evolutionarily conserved developmental programs unfold across birth, with birth occurring at different stages of these programs, reflecting a species-specific balance between neonatal competence and prolonged postnatal plasticity.

neuroscience↗

bioRxiv2025

A single-cell transcriptomic atlas maps cerebellar astrocyte diversity and uncovers the transcriptional code underlying their maturation trajectories

Astrocytes are increasingly recognized as key regulators of neural circuit development and function, with mounting evidence revealing substantial heterogeneity within and across brain regions. Yet, the full extent of this diversity and its developmental mechanisms remain poorly understood. To address this, we leveraged the uniqueness of the mouse cerebellum, which hosts well-defined astrocyte types and established progenitor pools. Through complementary multi-modal omic approaches, including single-cell RNA sequencing, spatial transcriptomics, trajectory inference, clonal lineage reconstruction, and gene expression and regulatory network analyses, we systematically dissected the molecular diversity and ontogenesis of cerebellar astrocytes. We identified known types and uncovered new subtypes with functional specialization, inferring their developmental trajectories from multiple embryonic niches and postnatal progenitor sources with fate divergence, convergence, and restriction. We further predicted a hierarchical transcriptional regulator code governing this diversification, operating at multiple levels: distinct regulatory modules i) reflect embryonic regionalization and lineage; ii) determine broad astroglial identity; specify iii) Bergmann versus non-Bergmann fates; and guide iv) astrocyte type and v) subtype acquisition. Our findings map and temporally organize transcriptional programs that capture key determinants of astrocyte fate, integrating them along defined trajectories toward diverse astrocyte identities. This high-resolution framework for cerebellar glial diversification offers a model to be challenged across other brain regions.

neuroscience↗

bioRxiv2025

Transcription factor LHX2 suppresses astrocyte proliferation in the postnatal mammalian cerebral cortex

In the developing cerebral cortex astrocytes arise from progenitors in the ventricular and subventricular zones (V-SVZ), and also from local proliferation within the parenchyma. In the mouse neocortex, astrocytes that occupy upper versus deep layers (UL/DL) are known to be distinct populations in terms of molecular and morphological features. Transcription factor LHX2 is expressed both in V-SVZ gliogenic progenitors and in differentiated astrocytes throughout development and into adulthood. Here we show that loss of Lhx2 at birth results in an increased astrocyte proliferation in UL but not the DL of the cortex in the first postnatal week. Consistent with this, transcriptomic signatures of UL astrocytes increase. By 3 months, Lhx2 mutant astrocytes display upregulation of GFAP, and transcriptomic signatures associated with "reactive" astrocytes, in the absence of injury. These results demonstrate a novel role for Lhx2 in regulating proliferation and molecular features of cortical astrocytes. Summary StatementLoss of Lhx2 causes increased astrocyte proliferation in the upper but not deep layers of the mammalian cortex, and upregulation of reactive gliosis-like signatures in the absence of injury.

neuroscience↗

bioRxiv2023

Dual lineage origins of neocortical astrocytes

Astrocytes represent one of the most abundant cell types in the central nervous system, and play an essential role in nearly all aspects of brain functions1. Recent studies have challenged the notion that cortical astrocytes are a uniform population, and have highlighted their diverse characteristics at the morphological, molecular, and functional levels2-5. However, how this diversity originates and establishes during cortical development, remains largely unknown. Using single-cell RNA sequencing, we identified five distinct astrocyte subtypes displaying unique spatial patterns in the mouse neocortex, and discovered essential regulators for their formation. Furthermore, we used TrackerSeq6, a method that integrates heritable DNA barcodes into the genome of electroporated progenitors, to track clonally related astrocytes, and identified two distinct lineages that give rise to the five astrocyte subtypes. The first lineage derives from Emx1+ multipotent progenitors that first generate neurons and then switch to produce cortical astrocytes. The second lineage stems from a fate-restricted progenitor population that exclusively gives rise to a specific subset of cortical astrocytes, marked by Olig2. The knockout of this gene in cortical progenitors is sufficient to promote a fate switch between the two lineages. These findings offer novel insights into the cellular mechanisms underlying astrocyte diversity, highlighting the presence of multiple progenitor subtypes, responsible for generating distinct subtypes of astrocytes.

neuroscience↗

bioRxiv2023

Shared inflammatory glial cell signature after brain injury, revealed by spatial, temporal and cell-type-specific profiling of the murine cerebral cortex

Traumatic brain injury leads to a highly orchestrated immune- and glial cell response partially responsible for long-lasting disability and the development of secondary neurodegenerative diseases. A holistic understanding of the mechanisms controlling the responses of specific cell types and their crosstalk is required to develop an efficient strategy for better regeneration. Here, we combined spatial and single-cell transcriptomics to chart the transcriptomic signature of the injured murine cerebral cortex, and identified specific states of astrocytes, microglia, and oligodendrocyte precursor cells contributing to this signature. Interestingly, these cellular populations share a large fraction of injury-regulated genes, including inflammatory programs downstream of the innate immune-associated pathways Cxcr3 and Tlr1/2. Systemic manipulation of these pathways decreased the reactivity state of glial cells associated with poor regeneration. The functional relevance of the newly discovered shared signature of glial cells highlights the importance of our resource enabling comprehensive analysis of early events after brain injury.

neuroscience↗