Biology subjects

Kirby, E. D.

Publications and source records attributed to Kirby, E. D..

11 recordsLinked to original sources

bioRxiv2026

Classic and novel features of the dentate gyrus vascular niche quantified through 3D vessel reconstruction

Adult neurogenesis, the continued generation of new neurons throughout life, supports a variety of emotional and cognitive functions in mammals. Lifelong neurogenesis occurs in the dentate gyrus (DG) of the hippocampus, where a neurogenic niche supports the survival and growth of neural stem cells (NSCs), which divide to generate new neurons. A key component of this niche is the surrounding vasculature, thought to give NSCs access to circulating support molecules, oxygen, and nutrient metabolites. The DG vasculature is strikingly variable across layers. Vascular density and linearity, for example, have been noted to differ substantially in the different cell layers that make up the DG. Most of these prior descriptions of the DG vasculature have been qualitative, and other important aspects of vessel morphology, like vessel diameter, have not been previously reported to our knowledge. To provide a more complete and quantitative description of the adult DG vasculature, we used a 3D imaging technique to fully characterize the vasculature of each DG cellular layer. Our 3D reconstructions of DG blood vessels provide a quantitative method for measuring several known, qualitative features of the neurogenic niche, such as blood vessel density and tortuosity. In some cases, we reproduce qualitative observations, such as affirming that vessel density is high in the subgranular zone (SGZ) where NSCs reside and low in the granule cell layer. In other cases, our findings go counter to what qualitative observations suggest. For example, the SGZ is often described as having uniquely linear blood vessels, but we found that linearity was similar between the SGZ and hilus layer. We also report new measures of features of DG layer vascular architecture: vessel diameter and branching. Together, these findings offer a global, quantitative characterization of the DG vascular niche in adult mice. Beyond providing more detailed characterization of DG vasculature, we also anticipate our methods and estimates of variance in mice will be useful for investigators wishing to plan their own quantitative studies of changes in the vascular structure of the DG.

neuroscience↗

bioRxiv2025

Postnatal development of the dentate gyrus vascular niche

Lifelong neurogenesis in the dentate gyrus (DG) of the hippocampus supports cognitive and emotional functions in most adult mammals. The subgranular zone (SGZ) of the DG contains dense vasculature where neural stem and progenitor cells (NSPCs) reside in close proximity to local capillaries. This arrangement likely supports NSPCs by providing access to oxygen, circulating molecules, and endothelial-derived factors. While SGZ vessel density and NSPC association with vessels are well established in adulthood, when these niche attributes emerge in development remains unclear. Here, we show that while blood vessel density in the SGZ remained stable from initial layer formation (2 weeks of age) into young adulthood (9 weeks of age) in male and female mice, the average distance from NSPC somas to the nearest blood vessel decreased progressively over postnatal development. This finding was accompanied by a symmetrical compression of proliferating cells within the SGZ, and a gradual shift of quiescent neural stem cell somas towards the granule cell layer of the DG. Our findings imply that the DG neurogenic vascular niche continues to refine postnatally, suggesting that the NSPC vascular niche has a unique functional role in supporting mature adult neurogenesis.

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bioRxiv2023

Females exhibit smaller and less variable patterns of brain activation across a range of motor tasks

Past work has shown that brain structure and function differ between females and males. Males have larger cortical and sub-cortical volume and surface area (both total and subregional), while females have greater cortical thickness in most brain regions. Functional differences are also reported in the literature, yet to date little work has systematically considered whether patterns of brain activity indexed with functional magnetic resonance imaging (fMRI) differ between females and males. Recently, an attempt to modernize and improve our understanding of the homunculus, a somatotopic representation of the human body within the brain, was made. Still, in the decades since it was introduced, no research has considered sex differences in the somatotopic representation. The current study sought to remediate this issue by employing brain somatotopic motor mapping from a previously published and openly available dataset. We tested differences in patterns of functional brain activity associated with 12 voluntary movement patterns in females versus males. Results suggest that females exhibited smaller volumes of brain activation across all 12 movement tasks, and lower patterns of variability in 10 of the 12 movements. We also observed that females had greater cortical thickness, which is in alignment with previous analyses of structural differences. Overall, these findings provide a basis for considering biological sex in future fMRI research and provide a foundation of understanding differences in how neurological pathologies present in females vs males.

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bioRxiv2023

Neural stem and progenitor cells support and protect adult hippocampal function via vascular endothelial growth factor secretion.

Adult neural stem and progenitor cells (NSPCs) reside in the dentate gyrus (DG) of the hippocampus throughout the lifespan of most mammalian species. In addition to generating new neurons, NSPCs may alter their niche via secretion of growth factors and cytokines. We recently showed that adult DG NSPCs secrete vascular endothelial growth factor (VEGF), which is critical for maintaining adult neurogenesis. Here, we asked whether NSPC-derived VEGF alters hippocampal function independent of adult neurogenesis. We found that loss of NSPC-derived VEGF acutely impaired hippocampal memory, caused neuronal hyperexcitability and exacerbated excitotoxic injury. We also found that NSPCs generate substantial proportions of total DG VEGF and VEGF disperses broadly throughout the DG, both of which help explain how this anatomically-restricted cell population could modulate function broadly. These findings suggest that NSPCs actively support and protect DG function via secreted VEGF, thereby providing a non-neurogenic functional dimension to endogenous NSPCs.

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bioRxiv2022

Excitatory amino acid transporter 1 supports adult hippocampal neural stem cell self-renewal.

Within the adult mammalian dentate gyrus (DG) of the hippocampus, glutamate stimulates neural stem cell (NSC) self-renewing proliferation, providing a link between adult neurogenesis and local circuit activity. Here, we show that glutamate-induced self-renewal of adult DG NSCs requires glutamate transport via excitatory amino acid transporter 1 (EAAT1) to stimulate lipogenesis. Loss of EAAT1 prevented glutamate-induced self-renewing proliferation of NSCs in vitro and in vivo, with little role evident for canonical glutamate receptors. Transcriptomics and further pathway manipulation revealed that glutamate simulation of NSCs relied on EAAT1 transport-stimulated lipogenesis. Our findings demonstrate a critical, direct role for EAAT1 in stimulating NSCs to support neurogenesis in adulthood, thereby providing insights into a non-canonical mechanism by which NSCs sense and respond their niche.

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bioRxiv2021

Robust transcriptional profiling and identification of differentially expressed genes with low input RNA sequencing of adult hippocampal neural stem and progenitor populations

Multipotent neural stem cells (NSCs) are found in several isolated niches of the adult mammalian brain where they have unique potential to assist in tissue repair. Modern transcriptomics offer high-throughput methods for identifying disease or injury associated gene expression signatures in endogenous adult NSCs, but they require adaptation to accommodate the rarity of NSCs. Bulk RNA sequencing (RNAseq) of NSCs requires pooling several mice, which impedes application to labor-intensive injury models. Alternatively, single cell RNAseq can profile hundreds to thousands of cells from a single mouse and is increasingly used to study NSCs. The consequences of the low RNA input from a single NSC on downstream identification of differentially expressed genes (DEGs) remains largely unexplored. Here, to clarify the role that low RNA input plays in NSC DEG identification, we directly compared DEGs in an oxidative stress model of cultured NSCs by bulk and single cell sequencing. While both methods yielded DEGs that were replicable, single cell sequencing DEGs derived from genes with higher relative transcript counts compared to all detected genes and exhibited smaller fold changes than DEGs identified by bulk RNAseq. The loss of high fold-change DEGs in the single cell platform presents an important limitation for identifying disease-relevant genes. To facilitate identification of such genes, we determined an RNA-input threshold that enables transcriptional profiling of NSCs comparable to standard bulk sequencing and used it to establish a workflow for in vivo profiling of endogenous NSCs. We then applied this workflow to identify DEGs after lateral fluid percussion injury, a labor-intensive animal model of traumatic brain injury. Our work suggests that single cell RNA sequencing may underestimate the diversity of pathologic DEGs but population level transcriptomic analysis can be adapted to capture more of these DEGs with similar efficacy and diversity as standard bulk sequencing. Together, our data and workflow will be useful for investigators interested in understanding and manipulating adult hippocampal NSC responses to various stimuli.

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bioRxiv2021

Oral and injected tamoxifen alter adult hippocampal neurogenesis in female and male mice

Inducible Cre recombinase facilitates temporal control of genetic recombination in numerous transgenic model systems, a feature which has made it a popular tool for studies of adult neurogenesis. One of the most common forms of inducible Cre, CreERT2, requires activation by the synthetic estrogen tamoxifen (TAM) to initiate recombination of LoxP-flanked sequences. To date, most studies deliver TAM via intraperitoneal injection. But the introduction of TAM-infused commercial chows has recently expanded the possible modes of TAM delivery. Despite the widespread use of TAM-inducible genetic models in adult neurogenesis research, the comparative efficiency and off-target effects of TAM administration protocols is surprisingly infrequently studied. Here we compare a standard, 5 day TAM injection regimen with voluntary consumption of TAM-infused chow. First, we used adult NestinCreERT2;Rosa-LoxP-STOP-LoxP-EYFP reporter mice to show that 2 weeks of TAM chow and 5 days of injections led to LoxP recombination in a similar phenotypic population of neural stem and progenitor cells in the adult dentate gyrus. However, TAM chow resulted in substantially less overall recombination than injections. TAM administration also altered adult neurogenesis, but in different ways depending on administration route: TAM injection disrupted neural progenitor cell proliferation 3 weeks after TAM, whereas TAM chow increased neuronal differentiation of cells generated during the diet period. These findings provide guidance for selection of TAM administration route and appropriate controls in adult neurogenesis studies using TAM-inducible Cre mice. They also highlight the need for better understanding of off-target effects of TAM in other neurological processes and organ systems.

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bioRxiv2021

Intracrine Vascular Endothelial Growth Factor Maintains Hippocampal Neural Stem Cell Quiescence

The vasculature is a key component of adult brain neural stem cell (NSC) niches. In the adult mammalian hippocampus, NSCs reside in close contact with a dense capillary network. How this niche is maintained is unclear. We recently found that adult hippocampal NSCs express vascular endothelial growth factor (VEGF), a soluble factor with chemoattractive properties for vascular endothelia. Here, we show that NSC-specific VEGF loss led to dissociation of NSCs from local vasculature but surprisingly found no changes in vascular density. Instead, we found that NSC-derived VEGF supports the motility of NSCs themselves via a cell internal signaling loop. We further found that this internal autocrine loop also independently maintained NSC quiescence cell autonomously. Combined, our findings suggest that NSCs maintain their populations via 2 mechanisms that are dependent on cell internal VEGF signaling: self-stimulated motility towards vasculature and cell autonomous maintenance of quiescence programs.

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bioRxiv2019

Stereological characterization of the major cell lineages in the mouse dorsal dentate gyrus

Adult neurogenesis in the dorsal dentate gyrus (DG) subregion of the mammalian hippocampus supports critical cognitive processes related to memory. Local DG cell populations form a neurogenic niche specialized to regulate adult neurogenesis. Recently, DG astrocytes, microglia, endothelia, and neural stem cells have been identified as sources of neurogenesismodulating secreted factors. Accurately estimating the size of these cell populations is useful for elucidating their relative contributions to niche physiology. Previous studies have characterized these cell types individually, but to our knowledge no comprehensive study of all these cell types exists. This is problematic because considerable variability in reported population size complicates comparisons across studies. Here, we apply consistent stereological methods within a single study to estimate cell density for neurogenesis-modulating secretory cell types in the dorsal DG of adult mice. We used immunohistochemical phenotypic markers to quantify cell density and found that stellate astrocytes were the most numerous followed by endothelia, intermediate progenitors, microglia, and neural stem cells. We did not observe any significant sex differences in cell density. We expect our data will facilitate efforts to elucidate the role of DG secretory cell populations in regulating adult neurogenesis.

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bioRxiv2019

Poor concordance of floxed sequence recombination in single neural stem cells: Implications for cell autonomous studies

To manipulate target gene function in specific adult cell populations, tamoxifen-dependent CreERT2 is widely used to drive inducible, site-specific recombination of LoxP flanked sequences. In studies of cell autonomous target gene function, it is common practice to combine these CreERT2-lox systems with a ubiquitously-expressed stop-floxed fluorescent reporter gene to identify single cells supposedly undergoing target gene recombination. Here, we studied the reliability of using Cre-induced recombination of one gene to predict recombination in another gene at the single cell level in adult hippocampal neural stem and progenitor cells. Using two separate stop-floxed reporters plus a Nestin promoter-driven CreERT2, we found that, in individual cells, expression of one reporter was a poor predictor of expression of the other. These findings imply that use of stop-floxed reporters to investigate cell autonomous gene function is likely to lead to false conclusions because recombination in separate genes shows poor concordance in individual cells.

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bioRxiv2019

Defining the adult hippocampal neural stem cell secretome: in vivo versus in vitro transcriptomic differences and their correlation to secreted protein levels

Recent evidence shows that adult hippocampal neural stem and progenitor cells (NSPCs) secrete a variety of proteins that affect tissue function. Though several individual NSPC-derived proteins have been shown to impact cellular processes like neuronal maturation and stem cell maintenance, a broad characterization of NSPC-secreted factors is lacking. Secretome profiling of low abundance stem cell populations is typically achieved via proteomic characterization of in vitro, isolated cells. Here, we analyzed the in vitro NSPC secretome using conditioned media from cultured adult mouse hippocampal NSPCs and detected over 200 different bioactive proteins with an antibody array. We next assessed the NSPC secretome on a transcriptional level with RNA sequencing (RNAseq) of cultured NSPCs. This comparison revealed that quantification of gene expression did not accurately predict relative protein abundance for several factors. Furthermore, comparing our transcriptional data with previously published single cell RNA sequencing datasets of freshly isolated hippocampal NSPCs, we found key differences in gene expression of secreted proteins between cultured and acutely isolated NSPCs. Understanding the components and functions of the NSPC secretome is essential to understanding how these cells may modulate the hippocampal neurogenic niche, as well as how they can be applied therapeutically. Cumulatively, our data emphasize the importance of using proteomic analysis in conjunction with transcriptomic studies and highlights the need for better methods of global unbiased secretome profiling.

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