Biology subjects

Miller, F. D.

Publications and source records attributed to Miller, F. D..

6 recordsLinked to original sources

bioRxiv2026

Activity-dependent myelination in prefrontal circuits signals the offset of infantile amnesia

Human and non-human infants can form memories for events, but these memories are not successfully consolidated into remote memory. While the neurobiological basis of this phenomenon-known as infantile amnesia-remains unclear, it is hypothesized that the neural circuits required for successful consolidation are insufficiently mature. Here we find that heightened activity in the prelimbic cortex of developing mice triggers a sequalae of maturational steps that culminates in adult-like memory persistence: Activity-dependent increases in brain-derived neurotrophic factor (BDNF) promote myelination of prelimbic circuits via activation of tyrosine kinase receptor B (TrkB) receptors on oligodendrocyte precursor cells (OPCs). Inhibiting any of these steps within a critical developmental window delays the offset of infantile amnesia, whereas promoting this sequalae results in the precocial emergence of memory persistence. Similar to critical periods in sensory cortices, our results indicate that developmental myelination is required for proper circuit maturation and emergence of adult-like memory function.

neuroscience↗

bioRxiv2026

The nail mesenchyme creates a regeneration-specific ligand environment that orchestrates mammalian regeneration versus fibrotic wound healing

The adult digit tip is one of a few privileged mammalian tissues that regenerate. Here, we asked why this is so. Using single cell spatial transcriptomics and genetic mouse models we show regeneration requires the nail organ and associated nail mesenchyme, and that in their absence fibrotic wound-healing occurs. We show the nail organ/mesenchyme orchestrates a highly-organized regenerative response that includes reprogramming of tissue-resident mesenchymal cells to a blastema state. It does this by creating a regeneration-specific ligand environment that includes multiple BMPs. Loss of the resultant downstream BMP signaling by genetic deletion of Smad4 in all mesenchymal cells or specifically in the nail mesenchyme inhibits multiple aspects of the regenerative response, including expression of regeneration-specific ligands. Thus, the nail mesenchyme creates a BMP-rich local ligand environment that reprograms mesenchymal cells and orchestrate tissues regeneration versus fibrotic wound-healing, findings with implications for tissue repair and anti-fibrosis strategies.

cell biology↗

bioRxiv2026

Single-cell multiomic approaches define a gradual, spatially-regulated epigenetic and transcriptional transition from embryonic to adult neural stem cells

Here, we ask how adult neural stem cells (NSCs) arise developmentally, focusing on murine cortical precursors that generate excitatory neurons embryonically and interneurons and glial cells postnatally. Using complementary single-cell spatial, transcriptomic, and epigenomic approaches, we show that postnatal NSC state acquisition involves a gradual transcriptional and epigenetic shift in the entire embryonic cortical precursor cell population and identify a distinct transition precursor state at E17/18 when both embryonic and the first postnatal progeny are being generated. Non-proliferative adult NSCs are also first seen at this transition timepoint, but they arise in a spatial domain distinct from that of the first postnatal progeny, indicating that NSC state acquisition is not a necessary prelude to the switch in cell genesis. These findings support a gradual epigenetically-continuous model for the transition from developing cortical precursors to NSCs and show that this is spatially separable from the transition to generating postnatal cell types.

developmental biology↗

bioRxiv2025

Single cell approaches define the murine leptomeninges:cortical brain interface as a distinct cellular neighborhood comprised of neural and nonneural cell types

The interface between the brain surface and the adjacent meninges is a selective barrier regulating fluid, protein and immune cell exchange between the CNS and periphery. However, the cell types that form this important interface are not yet fully defined. To address this limitation, we have used single cell RNA-sequencing (scRNA-seq) and single cell spatial transcriptomics together with morphological lineage tracing and immunostaining to analyze the adult murine cortex. We show that the cortical interface is comprised of three major cell types, leptomeningeal cells, border astrocytes and tissue-resident macrophages. On the peripheral side the interface is comprised of transcriptionally-distinct PDGFR-positive leptomeningeal mesenchymal cells that are intermingled with macrophages. This leptomeningeal pial layer is lined by a population of transcriptionally-distinct border astrocytes. The interface neighborhood is rich in growth factor mRNAs, including many leptomeningeal ligands predicted to act on both the border astrocytes and macrophages. On the CNS side of the interface is the relatively cell-sparse cortical layer one containing interneurons, microglia, parenchymal astrocytes, oligodendrocyte precursor cells and oligodendrocytes. Except for the border astrocytes, layer one cells are not closely-associated with the interface, suggesting that secreted ligands may be the major way the brain interface communicates with the underlying cortical parenchyma. Thus, our data provide a molecular/cellular resource describing the brain interface cell types and their interactions, thereby enabling future studies asking how this distinct cellular compartment regulates CNS:periphery interactions. Significance StatementRecent years have seen significant progress in identifying the diverse cell types within the meningeal space. However, the mechanisms by which these cells interact with glial and neuronal cells in layer one of the adult murine cortex remain poorly understood. During development, communication between radial precursors and meningeal layers is crucial for proper brain formation, but the role of this interaction in adulthood is still unclear. Additionally, how resident immune cells in the leptomeningeal space signal to layer one cortical cells or meningeal mesenchymal cells during homeostasis remains an open question. Understanding the identity, location, and interactions of these cells is essential for unraveling the complex dynamics at this critical brain interface.

neuroscience↗

bioRxiv2024

Single cell approaches define forebrain neural stem cell niches and identify microglial ligands that enhance precursor-mediated remyelination

Here we used single cell RNA-sequencing and single cell spatial transcriptomics to characterize the forebrain neural stem cell (NSC) niche under homeostatic and injury conditions. We define the dorsal and lateral ventricular-subventricular zones (V-SVZ) as two distinct neighborhoods, and show that following white matter injury, dorsal NSCs are locally activated to make oligodendrocytes for remyelination. This activation is coincident with a robust increase in transcriptionally-distinct microglia in the dorsal V-SVZ niche. We modeled ligand-receptor interactions within this changing niche and identified two remyelination-associated microglial ligands, IGF1 and OSM, that promote precursor proliferation and oligodendrogenesis in culture. Infusion of either ligand into the lateral ventricles also enhanced oligodendrogenesis, even in the lateral V-SVZ, where NSCs normally make neuroblasts. These data support a model where gliogenesis versus neurogenesis is determined by the local NSC neighborhood and where injury-induced niche alterations promote NSC activation, local oligodendrogenesis, and likely contribute to myelin repair.

neuroscience↗

bioRxiv2020

Inferring metabolic rewiring in embryonic neural development using single cell data

Metabolism is intricately linked with cell fate changes. Much of this understanding comes from detailed metabolomics studies averaged across a population of cells which may be composed of multiple cell types. Currently, there are no quantitative techniques sensitive enough to assess metabolomics broadly at the single cell level. Here we present scMetNet, a technique that interrogates metabolic rewiring at the single cell resolution and we apply it to murine embryonic development. Our method first confirms the key metabolic pathways, categorized into bioenergetic, epigenetic and biosynthetic, that change as embryonic neural stem cells differentiate and age. It then goes beyond to identify specific sub-networks, such as the cholesterol and mevalonate biosynthesis pathway, that drive the global metabolic changes during neural cortical development. Having such contextual information about metabolic rewiring provides putative mechanisms driving stem cell differentiation and identifies potential targets for regulating neural stem cell and neuronal biology.

systems biology↗