A Single-Cell RNA Sequencing Study Reveals Cellular and Molecular Dynamics of the Hippocampal Neurogenic Niche
Open accessAbstract
Adult neurogenesis in the murine dentate gyrus occurs in a specialized microenvironment that sustains the generation of neurons during life. To fully understand adult neurogenesis, it is essential to determine the neural stem cell (NSC) and progenitor developmental stages, their molecular determinants, and the niche cellular and molecular composition. We report on a single-cell RNA sequencing study of the hippocampal niche, performed by isolating all the non-neuronal cell populations. Our analysis provides a comprehensive description of the dentate gyrus cells, and it allows the identification of exclusive cell-type-specific markers. We define the developmental stages and transcriptional dynamics of NSCs and progenitors, and we find that, while NSCs represent a heterogeneous cellular continuum, progenitors can be grouped into distinct subtypes. We determine the oligodendrocyte lineage and transcriptional dynamics, and we describe the microglia transcriptional profile and activation state. The combined data constitute a valuable resource to understand regulatory mechanisms of adult neurogenesis.
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In the mouse brain, single-cell RNA-seq analyses indicate that the number of activated neural stem cells (NSCs) and neuroblasts decreases with ageing in both the subventricular zone (SVZ) NSC niche and the hippocampal NSC niche.
“For example, in the mouse brain, single-cell RNA-seq analyses indicate that the number of activated neural stem cells (NSCs) and neuroblasts (progeny) decreases with ageing in both the subventricular zone (SVZ) NSC niche and the hippocampal NSC niche6–9 — the main locations of NSCs.”
From Ageing and rejuvenation of tissue stem cells and their niches (2023) · cites this paper as [6]
In the brain, old age is accompanied by an increase in the number of quiescent NSCs and a decrease in their ability to activate.
“In the brain, old age is accompanied by an increase in the number of quiescent NSCs and a decrease in their ability to activate6–8.”
From Ageing and rejuvenation of tissue stem cells and their niches (2023) · cites this paper as [6]
Owing to the infiltration of immune cells, the activation of macrophages and microglia, and the presence of senescent cells, the NSC niche milieu likely becomes extremely inflammatory during ageing.
“For example, owing to the infiltration of immune cells, the activation of macrophages and microglia, and the presence of senescent cells, the NSC niche milieu likely becomes extremely inflammatory during ageing6–8.”
From Ageing and rejuvenation of tissue stem cells and their niches (2023) · cites this paper as [6]
Activated NSCs exhibit fewer overall transcriptomic changes with ageing than quiescent NSCs.
“Interestingly, activated NSCs exhibit fewer overall transcriptomic changes with ageing than quiescent NSCs6–9,63,64, perhaps because activated NSCs are recently generated and do not have the time to accumulate damage, or because they ‘dilute’ the damage as they proliferate.”
From Ageing and rejuvenation of tissue stem cells and their niches (2023) · cites this paper as [6]
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- Authors
- Artegiani, B., Lyubimova, A., Muraro, M., van Es, J. H., van Oudenaarden, A., & Clevers, H.
- Affiliations
- Royal Netherlands Academy of Arts and Sciences (NL)
- Corresponding author
- Clevers, Hans
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2017-12
- Volume
- 21
- Issue
- 11
- Pages
- 3271-3284
- ISSN
- 2211-1247 (ISSN-L)
- OpenAlex
- W2773573309
- Cited by
- 259
- References
- 57
- Citations by year
- 2026: 15 · 2025: 34 · 2024: 28 · 2023: 35 · 2022: 38 · 2021: 28 · 2020: 34 · 2019: 27 · 2018: 20
- FWCI
- 9.38
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- KNAW research portal (Royal Academy of Art and Sciences (KNAW)) (publishedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- FEBS
- Veni (NWO/VENI 863.15.015)
- Topics
- Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
- Keywords
- adult neurogenesis, dentate gyrus, neural stem cells, neural progenitor cells, progenitor heterogeneity, cell type-specific markers, transcriptional dynamics, oligodendrocyte lineage, microglial activation, non-neuronal cells, single-cell transcriptomics
- MeSH terms
- Animals, Cell Differentiation, Female, Hippocampus, Male, Mice, Inbred C57BL, Nerve Tissue Proteins, Neurons, Oligodendroglia, RNA, Messenger, Transcription, Genetic, Biomarkers, Sequence Analysis, RNA, Microglia, Dentate Gyrus, Cell Lineage, Mice, Neurogenesis, Molecular Dynamics Simulation, Neural Stem Cells, Single-Cell Analysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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