ArticleCell stem cell2021
Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids.
Open access · greenAbstract read
In one paragraph
Article in Cell stem cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 130 papers, 2 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
130citing papers in PubMed, 2 pooled it
13.9field-weighted citation impact, top 1% of its field
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
130 citing papers in PubMed, 2 syntheses or guidelines pooled it, 216 citations in OpenAlex.
- Mapping the Cerebral Organoid Landscape: A Systematic Review of Preclinical 3D Models in Neuroscience.Advanced healthcare materials · 2026Pooled it
- Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue.PLoS biology · 2024Pooled it
- PBRM1 Deficiency in Microglia Leads to Excessive Neurogenesis and Autism-Like Behaviors via the CCL5-CCR1/5-β-catenin Signaling Axis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Translational modelling of human microglia from cultures to chimeras.Experimental & molecular medicine · 2026Review
- Article
- Expanding Genetic Code to Generate Human Brain Organoids with Both Vasculature and Microglia-Like Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Human iPSC models revealResearch square · 2026Article
- Brain organoids in Alzheimer disease and related tauopathies: Challenges and opportunities for translational readiness.Stem cell reports · 2026Review
- A reproducible three-dimensional model of human brain tissue to investigate physiological and disease-associated microglia phenotypes.Nature neuroscience · 2026Article
- Induced pluripotent stem cells from discovery to translation.Nature medicine · 2026Review
- Revisiting oligodendrocytes in amyotrophic lateral sclerosis using human multicellular stem cell models.Trends in cell biology · 2026Review
- Sexual Dimorphism in the Microglial Inflammatory Response After Traumatic Brain Injury.Shock (Augusta, Ga.) · 2026Article
- Construction Strategies, Microenvironmental Modelling and Precision-Therapy Applications of Glioma Organoid Models.Cancers · 2026Review
- Emerging Regenerative Medicine for Spinal Cord Injury: Spinal Cord Organoids-on-a-Chip.International journal of molecular sciences · 2026Review
- Glucocorticoid Signaling in PSC-Derived Neural Systems to Elucidate Mechanisms of Stress-Induced Psychiatric Vulnerability.Molecular neurobiology · 2026Review
- Advances and applications of brain organoids in central nervous system disorders: Bridging the gap from laboratory to clinic.Neural regeneration research · 2026Article
- Human induced pluripotent stem cell-derived inner ear organoids reveal hair cell damage and plasticity after cisplatin and gentamicin exposure.Disease models & mechanisms · 2026Article
- 3D cortical microtissue with innate microglia for studying real-time cell behavior across maturation and inflammatory response.bioRxiv : the preprint server for biology · 2026Article
- Review
- A scalable human-zebrafish xenotransplantation model reveals gastrosome-mediated processing of dying neurons by human microglia.Communications biology · 2026Article
70 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
19 authors at 5 institutions in 1 country.
Galina PopovaDepartment of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
Sarah S SolimanDepartment of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
Chang N KimDepartment of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
Matthew G KeefeDepartment of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
Kelsey M HennickDepartment of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
Samhita JainDivision of Neonatology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
Tao LiEli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
Dario TejeraEli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
David ShinDepartment of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
Bryant B ChhunChan Zuckerberg Biohub, San Francisco, CA, USA.
Christopher S McGinnisDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA USA.
Matthew SpeirGenomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Zev J GartnerChan Zuckerberg Biohub, San Francisco, CA, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA USA; Center for Cellular Construction, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
Shalin B MehtaChan Zuckerberg Biohub, San Francisco, CA, USA.
Maximilian HaeusslerGenomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Keith B HengenDepartment of Biology, Washington University in St. Louis, St. Louis, MO, USA.
Richard R RansohoffDepartment of Cell Biology, Harvard Medical School, Boston, MA, USA.
Xianhua PiaoEli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Division of Neonatology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Newborn Brain Research Institute, University of California, San Francisco, San Francisco, CA, USA.
Tomasz J NowakowskiDepartment of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA. Electronic address: tomasz.nowakowski@ucsf.edu.
University of California, San Francisco · USChan Zuckerberg Initiative (United States) · USUniversity of California, Santa Cruz · USHarvard University · USWashington University in St. Louis · US
Funding
The UCSC Genome BrowserU41HG002371 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI KENT, WILLIAM JAMES · 2012 to 2021
$36.6MThe UCSC Genome BrowserU24HG002371 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Maximilian Haeussler · 2022 to 2026
$17.6MGENETICS OF EUCARYOTIC AND PROCARYOTIC ORGANISMST32GM007810 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ASHRAFI, KAVEH, NARLIKAR, GEETA J · 1985 to 2020
$15.1MPREDOCTORAL TRAINING IN DEVELOPMENTAL BIOLOGYT32HD007470 · NICHD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Todd Nystul · 1994 to 2026
$7.7MGlial Mechanisms Of Developmental Synapse RefinementR01NS108446 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI PIAO, XIANHUA · 2018 to 2022
$2.9MMassively parallel characterization of psychiatric disease associated regulatory elements in defined cell typesU01MH116438 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, POLLARD, KATHERINE S. · 2018 to 2021
$2.7MMapping Developmental Lineage Relationships in the Cerebral CortexRF1MH121268 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI NOWAKOWSKI, TOMASZ · 2019 to 2019
$2.1MRobust circuit computation in freely behaving animals.RF1NS118442 · NINDS · WASHINGTON UNIVERSITY · PI HENGEN, KEITH B. · 2020 to 2020
$1.8MRobust circuit computation in freely behaving animals.R01NS118442 · NINDS · WASHINGTON UNIVERSITY · PI HENGEN, KEITH B. · 2023 to 2024
$1.0MA visualization interface for BRAIN single cell data, integrating transcriptomics, epigenomics and spatial assaysRF1MH132662 · NIMH · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI HAEUSSLER, MAXIMILIAN · 2023 to 2023
$866kElucidating molecular mechanisms regulatingspatiotemporal heterogeneity of microglia in the developing human brainF32MH118785 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI POPOVA, GALINA · 2018 to 2022
$211kNHGRI NIH HHS U24 HG002371NHGRI NIH HHS U41 HG002371NICHD NIH HHS T32 HD007470NIGMS NIH HHS T32 GM007810NIMH NIH HHS F32 MH118785NIMH NIH HHS RF1 MH121268NIMH NIH HHS RF1 MH132662NIMH NIH HHS U01 MH116438NINDS NIH HHS R01 NS108446NINDS NIH HHS R01 NS118442NINDS NIH HHS RF1 NS118442
Abstract
Microglia are resident macrophages in the brain that emerge in early development and respond to the local environment by altering their molecular and phenotypic states. Fundamental questions about microglia diversity and function during development remain unanswered because we lack experimental strategies to interrogate their interactions with other cell types and responses to perturbations ex vivo. We compared human microglia states across culture models, including cultured primary and pluripotent stem cell-derived microglia. We developed a "report card" of gene expression signatures across these distinct models to facilitate characterization of their responses across experimental models, perturbations, and disease conditions. Xenotransplantation of human microglia into cerebral organoids allowed us to characterize key transcriptional programs of developing microglia in vitro and reveal that microglia induce transcriptional changes in neural stem cells and decrease interferon signaling response genes. Microglia additionally accelerate the emergence of synchronized oscillatory network activity in brain organoids by modulating synaptic density.
Indexed as
Induced Pluripotent Stem CellsNeural Stem CellsBrainCell DifferentiationHumansMicrogliaModels, TheoreticalOrganoidsdouble-stranded DNA breakshuman microgliainduced microgliainterferon responseiPSCmicrogliamicroglia cultureneuro-immuneorganoid activityorganoids
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.