ArticleNature immunology2026
A transcriptomic microglia taxonomy across mouse and human pathologies.
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Article in Nature immunology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13citing papers in PubMed
–field-weighted citation impact
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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Who cites it
13 citing papers in PubMed.
- Microglial states revisited: from homeostasis to disease.Nature reviews. Neuroscience · 2026Review
- Tissue-Resident Macrophages: Linking Physiology and Inflammation in Infection.Clinical reviews in allergy & immunology · 2026Review
- Hypothalamic neurovascular and extracellular matrix remodeling: Cellular niche orchestration of immune-metabolic adaptation to nutritional stress.Reviews in endocrine & metabolic disorders · 2026Review
- Activated microglial phenotypes in the hippocampal CA2 subfield are implicated in Lewy body disease progression.Acta neuropathologica · 2026Article
- Microglia-Mediated Vascular Network Remodeling After Ischemic Stroke: An Immunovascular Repair Framework.Cells · 2026Review
- From Xenobiotic Exposure to Neuroinflammation: Mechanisms Linking Lipopolysaccharide Signaling to Depressive-like Behavior.Journal of xenobiotics · 2026Review
- Recent advances in Alzheimer's disease: From molecular mechanisms to therapeutic strategies.Cell · 2026Review
- 1 Hz Low-Frequency Repetitive Transcranial Magnetic Stimulation Ameliorates Epilepsy by Suppressing Interferon-γ Signaling-Dependent Microglial Synaptic Phagocytosis in Mice.CNS neuroscience & therapeutics · 2026Article
- A transcriptomic microglia taxonomy across mouse and human pathologies.Nature immunology · 2026Article
- EBV Triggers a Distinct Antiviral Response in HMC3 Cells.bioRxiv : the preprint server for biology · 2026Article
- Representation Methods of Transcriptomics with Applications in Neuroimmune Biology.bioRxiv : the preprint server for biology · 2026Article
- Assessing microglial phagocytosis of apoptotic neuronsFrontiers in neuroscience · 2026Article
- Perioperative neurocognitive disorders as a neuroimmune landscape disorder: microglial priming, state heterogeneity, and time-dependent neuroinflammation.Frontiers in immunology · 2026Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
55 authors.
Chintan ChhatbarInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0002-5824-5209
Roman SankowskiInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0001-9215-8021
Michael SchulzInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.
Takashi ShimizuInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.
Marius SchwabenlandInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.
Ori StaszewskiInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0002-0579-6701
Christian ScheiweClinic for Neurosurgery, Faculty of Medicine, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0003-1695-8689
Stefan NesslerDepartment of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.
Katharina BorstInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.
Anaelle Aurelie DumasInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.
Ella TrostInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.
Daniel BerchtoldDepartment of Neurology with Experimental Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany.ORCID http://orcid.org/0000-0002-7865-4157
Wesley BrandãoAnn Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Omar MossadInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.
Adrià Dalmau GasullInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0002-8410-8048
Maximilian FroschInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0002-5418-0962
Daniel ErnyInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0001-6000-8838
Martin DieboldInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0001-9636-6936
Elena GuffartInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.
Katharina TernkaDepartment of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany.ORCID http://orcid.org/0000-0003-3773-4625
Mihaela GurandaDepartment of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.ORCID http://orcid.org/0009-0005-9296-7095
Janaki Manoja VinnakotaFaculty of Biology, University of Freiburg, Freiburg, Germany.
Marina FriesenFaculty of Biology, University of Freiburg, Freiburg, Germany.
Koliane OukNeuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin Berlin and DZNE, Berlin, Germany.
Inken WaltlInstitute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.
Michael LaMorteSanofi Neurology Research, Cambridge, MA, USA.
Timothy R HammondSanofi Neurology Research, Cambridge, MA, USA.
Giovanni Di LibertoDepartment of Pathology and Immunology, University of Geneva, Geneva, Switzerland.
Ilena VincentiDepartment of Pathology and Immunology, University of Geneva, Geneva, Switzerland.
Mario KreutzfeldtDepartment of Pathology and Immunology, University of Geneva, Geneva, Switzerland.ORCID http://orcid.org/0000-0003-0335-2733
Ibrahim T MughrabiInstitute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA.
Yousef Al-AbedInstitute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA.ORCID http://orcid.org/0000-0001-5478-0506
Thomas BlankInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0002-3969-405X
Melanie Meyer-LuehmannDepartment of Neurology and Clinical Neuroscience, Medical Center - University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0003-3661-2220
Yanick J CrowMRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0001-7211-7564
Nellwyn HagenSanofi Neurology Research, Cambridge, MA, USA.
Dimitry OfengeimSanofi Neurology Research, Cambridge, MA, USA.
Robert ZeiserDepartment of Medicine I - Medical centre - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0001-6565-3393
Matthias KettwigDepartment of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany.ORCID http://orcid.org/0000-0003-4804-7716
Jutta GärtnerDepartment of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany.
Andreas MeiselDepartment of Neurology with Experimental Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany.ORCID http://orcid.org/0000-0001-7233-5342
Martin SchwemmleInstitute of Virology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0002-2972-6855
Ulrich KalinkeInstitute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.ORCID http://orcid.org/0000-0003-0503-9564
Jürgen BeckClinic for Neurosurgery, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
Bertram BengschGerman Cancer Consortium (DKTK), partner site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany.ORCID http://orcid.org/0000-0003-2552-740X
Robert ThimmeFaculty of Medicine, Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0003-1417-4135
Oleg ButovskyAnn Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-0186-8867
Tamara SeredeninaAC Immune, Lausanne, Switzerland.
Richard M RansohoffThird Rock Ventures, Boston, MA, USA.ORCID http://orcid.org/0000-0003-0175-6910
Francisco J QuintanaAnn Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-8156-0736
Katrin KierdorfInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0002-9272-4780
Doron MerklerDepartment of Pathology and Immunology, University of Geneva, Geneva, Switzerland.ORCID http://orcid.org/0000-0002-0247-2007
Christine StadelmannDepartment of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.
Josef PrillerNeuropsychiatry and Laboratory of Molecular Psychiatry, Charité - Universitätsmedizin Berlin and DZNE, Berlin, Germany.ORCID http://orcid.org/0000-0001-7596-0979
Marco PrinzInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany. marco.prinz@uniklinik-freiburg.de.ORCID http://orcid.org/0000-0002-0349-1955
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell studies have revealed substantial microglial diversity in development, homeostasis and disease. However, a framework enabling comparison and stratification of microglial states across contexts is needed. Here we generated an atlas of myeloid cell states by single-cell RNA sequencing more than one million central nervous system cells from more than 30 physiological and pathological conditions. This atlas enables us to establish a comprehensive taxonomy of myeloid cell states across brain disorders and related mouse models, comprising 27 superclusters and 192 clusters that are prevalent across diseases and largely conserved. We augment this taxonomic framework with spatial transcriptomics to map how immune cell states are organized within tissue and interact with their local cellular environment. Using in vivo perturbations, we also show that activation-associated microglial states are dependent on interferon and colony-stimulating factor 1 receptor signaling. Together, these findings provide a spatially aware taxonomic framework for central nervous system immune cells in health and disease.
Indexed as
Brain DiseasesMicrogliaTranscriptomeAnimalsBrainDisease Models, AnimalHumansMiceSignal TransductionSingle-Cell AnalysisSingle-Cell Gene Expression AnalysisSpatial Transcriptomics
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