Analyzing microglial phenotypes across neuropathologies: a practical guide

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Microglia Biology: One Century of Evolving Concepts

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Microglia emerge from erythromyeloid precursors via Pu.1- and Irf8-dependent pathways

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An environment-dependent transcriptional network specifies human microglia identity

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Block of A1 astrocyte conversion by microglia is neuroprotective in models of Parkinson’s disease

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High-Dimensional Single-Cell Mapping of Central Nervous System Immune Cells Reveals Distinct Myeloid Subsets in Health, Aging, and Disease

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Innate immune memory in the brain shapes neurological disease hallmarks

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Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease

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The single-cell pathology landscape of breast cancer

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Cell type- and brain region-resolved mouse brain proteome

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Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation

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TREM2 regulates microglial cholesterol metabolism upon chronic phagocytic challenge

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Coupled Proliferation and Apoptosis Maintain the Rapid Turnover of Microglia in the Adult Brain

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Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease

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Histone Deacetylases 1 and 2 Regulate Microglia Function during Development, Homeostasis, and Neurodegeneration in a Context-Dependent Manner

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PET imaging of microglia by targeting macrophage colony-stimulating factor 1 receptor (CSF1R)

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Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation

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A Binary Cre Transgenic Approach Dissects Microglia and CNS Border-Associated Macrophages

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Imaging Microglial Activation with TSPO PET: Lighting Up Neurologic Diseases?

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The physiology of foamy phagocytes in multiple sclerosis

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Activated microglia do not increase 18 kDa translocator protein ( TSPO ) expression in the multiple sclerosis brain

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Characteristic microglial features in patients with hereditary diffuse leukoencephalopathy with spheroids

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Loss of USP18 in microglia induces white matter pathology

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cGAS–STING drives ageing-related inflammation and neurodegeneration

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The Impact of Systemic Inflammation on Alzheimer’s Disease Pathology

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Microglia in multiple sclerosis: protectors turn destroyers

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Detection of SARS-CoV-2 viral proteins and genomic sequences in human brainstem nuclei

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CNS border-associated macrophages in the homeostatic and ischaemic brain

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Revisiting the intersection of microglial activation and neuroinflammation in Alzheimer's disease from the perspective of ferroptosis

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The niche matters: Origin, function and fate of CNS-associated macrophages during health and disease

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Regulatory T cells promote functional recovery after spinal cord injury by alleviating microglia inflammation via STAT3 inhibition

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Dynamic Brain Lipid Profiles Modulate Microglial Lipid Droplet Accumulation and Inflammation Under Ischemic Conditions in Mice

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The contribution of neuropathology to multiple sclerosis research

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Engineered Extracellular Vesicle-Based Nanoformulations That Coordinate Neuroinflammation and Immune Homeostasis, Enhancing Parkinson’s Disease Therapy

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The heterogeneity of microglial activation and its epigenetic and non-coding RNA regulations in the immunopathogenesis of neurodegenerative diseases

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Lycium Barbarum Polysaccharide‐Derived Nanoparticles Protect Visual Function by Inhibiting RGC Ferroptosis and Microglial Activation in Retinal Ischemia‒Reperfusion Mice

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Cholesterol 25-hydroxylase mediates neuroinflammation and neurodegeneration in a mouse model of tauopathy

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Microglia–neuron crosstalk through Hex–GM2–MGL2 maintains brain homeostasis

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Endocannabinoid signaling in microglia

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A mouse model of hepatic encephalopathy: bile duct ligation induces brain ammonia overload, glial cell activation and neuroinflammation

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Early microglial response, myelin deterioration and lethality in mice deficient for very long chain ceramide synthesis in oligodendrocytes

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Astrocytic Neuroimmunological Roles Interacting with Microglial Cells in Neurodegenerative Diseases

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Tools for studying human microglia: In vitro and in vivo strategies

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USP25 Inhibits Neuroinflammatory Responses After Cerebral Ischemic Stroke by Deubiquitinating TAB2

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Anti–PD-1 cancer immunotherapy induces central nervous system immune-related adverse events by microglia activation

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Histone H3 lysine 18 lactylation attenuates neuroinflammation and neurological damage by regulating microglial plxnb2 after ischemic stroke.

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New Insights into Microglial Mechanisms of Memory Impairment in Alzheimer’s Disease

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TREM2 affects DAM-like cell transformation in the acute phase of TBI in mice by regulating microglial glycolysis

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Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment

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Differential perivascular microglial activation in the deep white matter in vascular dementia developed post‐stroke

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Exploring the Disease-Associated Microglia State in Amyotrophic Lateral Sclerosis

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Activation of the microglial P2X7R/NLRP3 inflammasome mediates central sensitization in a mouse model of medication overuse headache

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A transcriptomic microglia taxonomy across mouse and human pathologies

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Microglia in brain aging: An overview of recent basic science and clinical research developments

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A Novel Hypoxia-inducible Factor 1α Inhibitor KC7F2 Attenuates Oxygen-induced Retinal Neovascularization

Tang, X., Cui, K., Lü, X., Wu, P., Yu, S., Yang, B., Xu, Y., & Liang, X. (2022) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.63.6.13 · Cited by 19 · see citing works

Young COVID-19 Patients Show a Higher Degree of Microglial Activation When Compared to Controls

Matschke, J., Lahann, H., Krasemann, S., Altmeppen, H. C., Pfefferle, S., Galliciotti, G., Fitzek, A., Sperhake, J., Ondruschka, B., Busch, M., et al. (2022) · Frontiers in Neurology · doi:10.3389/fneur.2022.908081 · Cited by 19 · see citing works

Dendrimer-enabled targeted delivery attenuates glutamate excitotoxicity and improves motor function in a rabbit model of cerebral palsy

Zhang, F., Zhang, Z., Alt, J., Kambhampati, S. P., Sharma, A., Singh, S., Nance, E. A., Thomas, A. G., Rojas, C. J., Rais, R., et al. (2023) · Journal of Controlled Release · doi:10.1016/j.jconrel.2023.04.017 · Cited by 19 · see citing works

Mass‐Guided Single‐Cell MALDI Imaging of Low‐Mass Metabolites Reveals Cellular Activation Markers

Cairns, J. L., Huber, J., Lewen, A., Jung, J., Maurer, S. J., Bausbacher, T., Schmidt, S., Levkin, P. A., Sévin, D. C., Göpfrich, K., et al. (2024) · Advanced Science · doi:10.1002/advs.202410506 · Cited by 20 · see citing works

A novel automated morphological analysis of Iba1+ microglia using a deep learning assisted model

Stetzik, L. A., Mercado, G., Smith, L., Sonia, G., Emmanuel, Q., Luda, K. M., Emily, S., Meyerdirk, L. K., Lindquist, A., Bergsma, A. L., et al. (2022) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2022.944875 · Cited by 19 · see citing works

Microglia subtypes in acute, subacute, and chronic multiple sclerosis

Prineas, J. W., & Lee, S. (2023) · Journal of Neuropathology &amp; Experimental Neurology · doi:10.1093/jnen/nlad046 · Cited by 16 · see citing works

Mutated Toll-like receptor 9 increases Alzheimer’s disease risk by compromising innate immunity protection

Cacace, R., Zhou, L., de Craen, E. H. V., Buist, A., Hoogmartens, J., Sieben, A., Cras, P. P., Vandenberghe, R. R., Deyn, P. P. D., Oehlrich, D., et al. (2023) · Molecular Psychiatry · doi:10.1038/s41380-023-02166-0 · Cited by 15 · see citing works

Microglia activation in periplaque white matter in multiple sclerosis depends on age and lesion type, but does not correlate with oligodendroglial loss

Kessler, W., Thomas, C., & Kuhlmann, T. (2023) · Acta Neuropathologica · doi:10.1007/s00401-023-02645-2 · Cited by 16 · see citing works

Neuroimmune mechanisms in autism etiology - untangling a complex problem using human cellular models

Vacharasin, J. M., Ward, J. A., McCord, M. M., Cox, K., Imitola, J., & Lizarraga, S. B. (2024) · Oxford Open Neuroscience · doi:10.1093/oons/kvae003 · Cited by 16 · see citing works

Regulation of disease-associated microglia in the optic nerve by lipoxin B4 and ocular hypertension

Maurya, S., Lin, M., Karnam, S., Singh, T., Kumar, M., Ward, E., Sivak, J. M., Flanagan, J. G., & Gronert, K. (2024) · Molecular Neurodegeneration · doi:10.1186/s13024-024-00775-z · Cited by 15 · see citing works

Role of astrocytes and microglia in hepatic encephalopathy associated with advanced chronic liver disease: lessons from animal studies

Claeys, W., Geerts, A. M., Hoecke, L. V., Steenkiste, C. V., & Vandenbroucke, R. E. (2024) · Neural Regeneration Research · doi:10.4103/nrr.nrr-d-24-00600 · Cited by 16 · see citing works

Positron Emission Tomography of Neuroimmune Responses in Humans: Insights and Intricacies

Raval, N. R., Wetherill, R. R., Wiers, C. E., Dubroff, J. G., & Hillmer, A. T. (2022) · Seminars in Nuclear Medicine · doi:10.1053/j.semnuclmed.2022.08.008 · Cited by 15 · see citing works

Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis

Westfall, J. J., Schwind, W. N., Sran, S., Navarro, J. B., Leonard, J. R., Pindrik, J., Pierson, C. R., Boué, D. R., Koboldt, D. C., Ostendorf, A. P., et al. (2022) · Acta Neuropathologica Communications · doi:10.1186/s40478-022-01472-y · Cited by 16 · see citing works

Microglia in Microbiota-Gut-Brain Axis: A Hub in Epilepsy

Liu, Y., Jia, N., Tang, C., Long, H., & Wang, J. (2024) · Molecular Neurobiology · doi:10.1007/s12035-024-04022-w · Cited by 15 · see citing works

The cGAS-STING axis: a comprehensive review from immune defense to disease pathogenesis

Sood, A. (2025) · Immunologic Research · doi:10.1007/s12026-025-09648-z · Cited by 14 · see citing works

Possible Implications of Obesity-Primed Microglia that Could Contribute to Stroke-Associated Damage

Carreto, R. J. R., Rodríguez-Cortés, Y. M., Guerrero, H. T., & Chavarría, A. (2023) · Cellular and Molecular Neurobiology · doi:10.1007/s10571-023-01329-5 · Cited by 15 · see citing works

Glial receptor PLXNB2 regulates schizophrenia-related stress perception via the amygdala

Xuan, F., Yan, L., Li, Y.-L., Fan, F., Deng, H.-H., Gou, M.-Z., Chithanathan, K., Heinla, I., Yuan, L., Seppa, K., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1005067 · Cited by 12 · see citing works

Long-acting acid-sensitive ketal-linked dexamethasone microcrystals for treating experimental autoimmune uveitis

Cai, M., Xu, Z., Zhou, X., Li, L., Hua, X., Guo, S., & Yuan, X. (2022) · APL Bioengineering · doi:10.1063/5.0118311 · Cited by 14 · see citing works

Curcumin-dependent phenotypic transformation of microglia mediates resistance to pseudorabies-induced encephalitis

Feng, L., Luo, G., Li, Y., Zhang, C., Liu, Y., Liu, Y., Chen, H., He, D., Zhu, Y., & Gan, L. (2023) · Veterinary Research · doi:10.1186/s13567-023-01149-x · Cited by 14 · see citing works

Intermittent hypoxia exacerbated depressive and anxiety-like behaviors in the bleomycin-induced pulmonary fibrosis mice

Xiong, M., Wu, Z., Zhao, Y., Zhao, D. B., Pan, Z., Wu, X., Liu, W. Q., & Hu, K. (2023) · Brain Research Bulletin · doi:10.1016/j.brainresbull.2023.04.008 · Cited by 13 · see citing works

Endothelial progenitor cell transplantation attenuates synaptic loss associated with enhancing complement receptor 3-dependent microglial/macrophage phagocytosis in ischemic mice

Ma, Y., Liu, Z., Jiang, L., Wang, L., Li, Y., Liu, Y., Wang, Y., Yang, G., Ding, J., & Zhang, Z. (2022) · Journal of Cerebral Blood Flow & Metabolism · doi:10.1177/0271678x221135841 · Cited by 12 · see citing works

Design, synthesis, and biological evaluation of a series of new anthraquinone derivatives as anti-ZIKV agents

Zhu, Y., Yu, J., Chen, T., Liu, W., Huang, Y., Li, J., Zhang, B., Zhu, G., He, Z., Long, Y., et al. (2023) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2023.115620 · Cited by 12 · see citing works

Emerging roles of microglia and neuroinflammation in Huntington's disease: From pathophysiology to clinical trials

Abedrabbo, M., Kazemian, P., Connolly, C., & Leavitt, B. R. (2025) · Journal of Huntington s Disease · doi:10.1177/18796397251330144 · Cited by 11 · see citing works

CSF1R-Mediated Myeloid Cell Depletion Prolongs Lifespan But Aggravates Distinct Motor Symptoms in a Model of Multiple System Atrophy

Battis, K., Florio, J. B., Mante, M., Lana, A. J., Naumann, I., Gauer, C., Lambrecht, V., Müller, S. J., Cobo, I., Fixsen, B. R., et al. (2022) · Journal of Neuroscience · doi:10.1523/jneurosci.0417-22.2022 · Cited by 11 · see citing works

Midkine attenuates amyloid-β fibril assembly and plaque formation

Zaman, M., Yang, S., Huang, Y., Yarbro, J. M., Hao, Y., Wang, Z., Liu, D., Harper, K. E., Soliman, H., Hemphill, A., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01657-8 · Cited by 15 · see citing works

The kynurenic acid analog SZR104 induces cytomorphological changes associated with the anti-inflammatory phenotype in cultured microglia

Szabó, M., Lajkó, N., Dulka, K., Barczánfalvi, G., Lőrinczi, B., Szatmári, I., Mihály, A., Vécsei, L., & Gulya, K. (2023) · Scientific Reports · doi:10.1038/s41598-023-38107-8 · Cited by 10 · see citing works

Increased Parenchymal Macrophages are associated with decreased Tyrosine Hydroxylase mRNA levels in the Substantia Nigra of people with Schizophrenia and Bipolar Disorder

Victoriano, G. M., Zhu, Y., Middleton, F. A., Massa, P. T., Ajulu, K., Webster, M. J., & Weickert, C. S. (2024) · Psychiatry Research · doi:10.1016/j.psychres.2024.116141 · Cited by 10 · see citing works

Prolonged exposure of neonatal mice to sevoflurane leads to hyper-ramification in microglia, reduced contacts between microglia and synapses, and defects in adult behavior

Li, H., Zhou, B., Liao, P. S., Liao, D., Yang, L., Wang, J., Liu, J., Jiang, R., & Chen, L. (2023) · Frontiers in Neurology · doi:10.3389/fneur.2023.1142739 · Cited by 10 · see citing works

Effects of NADPH Oxidase Isoform-2 (NOX2) Inhibition on Behavioral Responses and Neuroinflammation in a Mouse Model of Neuropathic Pain

Teixeira-Santos, L., Veríssimo, E., Martins, S., Sousa, T., Albino‐Teixeira, A., & Pinho, D. (2023) · Biomedicines · doi:10.3390/biomedicines11020416 · Cited by 9 · see citing works

A potential mechanism clue to the periodic storm from microglia activation and progressive neuron damage induced by paraquat exposure

Shi, G., Zhang, C., Bai, X., Sun, J. P., Wang, K., Meng, Q., Li, Y., Hu, G., Hu, R., Cai, Q., et al. (2024) · Environmental Toxicology · doi:10.1002/tox.24053 · Cited by 9 · see citing works

From glial cells to pain pathways: ICAM-1 as a central player in neuroinflammation and neuropathy

Chaudhari, A., Padmar, J., Awathale, S. N., Goyal, S. N., Nakhate, K. T., & Sherikar, A. K. (2025) · Discover Neuroscience · doi:10.1186/s13064-025-00201-0 · Cited by 9 · see citing works

Distinct origins and niches determine the cellular responsiveness of CNS macrophages after repopulation

Fliegauf, M., Levard, D., Cardamone, F., Frosch, M., Kuhn, S., Sankowski, R., Provinciali, M., Dumas, A. A., Gasull, A. D., Aktories, P., et al. (2026) · Nature Immunology · doi:10.1038/s41590-026-02457-y · Cited by 11 · see citing works

High throughput spatial immune mapping reveals an innate immune scar in post-COVID-19 brains

Schwabenland, M., Hasavci, D., Frase, S., Wolf, K., Deigendesch, N., Buescher, J. M., Mertz, K. D., Ondruschka, B., Altmeppen, H. C., Matschke, J., et al. (2024) · Acta Neuropathologica · doi:10.1007/s00401-024-02770-6 · Cited by 9 · see citing works

Increased Acetylcholine Levels and Other Brain Effects in 5XFAD Mice after Treatment with 8,14-Dihydroxy Metabolite of Efavirenz

Mast, N., Li, Y., & Pikuleva, I. A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23147669 · Cited by 9 · see citing works

Microglia and Microbiome-Gut-Brain Axis

Filho, A. M. C., Gomes, N. S., Lós, D. B., Leite, I. B., Tremblay, M., & Macêdo, D. S. (2024) · Advances in neurobiology · doi:10.1007/978-3-031-55529-9_17 · Cited by 8 · see citing works

A Comprehensive Review of the Pathophysiology of Neonatal Stroke and a Critique of Current and Future Therapeutic Strategies

Mondal, V., Ross-Munro, E., Balasuriya, G. K., Kumari, R., Hossen, M. M., Ageeli, M., Firipis, K., Nisbet, D. R., King, G. F., Williams, R. J., et al. (2025) · Cells · doi:10.3390/cells14120910 · Cited by 10 · see citing works

Repopulation of microglia and its implications for CNS disorders: Insights from the single-cell era

Chen, C., Qiao, G., Tang, D., Xu, F., Dong, J., Zhang, J., & Jin, B. (2025) · Neurobiology of Disease · doi:10.1016/j.nbd.2025.107066 · Cited by 8 · see citing works

Characterization of microglia/macrophage phenotypes in the spinal cord following intervertebral disc herniation

Kühl, B., Beyerbach, M., Baumgärtner, W., & Gerhauser, I. (2022) · Frontiers in Veterinary Science · doi:10.3389/fvets.2022.942967 · Cited by 8 · see citing works

DEXMEDETOMIDINE AMELIORATES ACUTE BRAIN INJURY INDUCED BY MYOCARDIAL ISCHEMIA-REPERFUSION VIA UPREGULATING THE HIF-1 PATHWAY

Yang, X., Wu, J., Cheng, H., Chen, S., & Wang, J. (2023) · Shock · doi:10.1097/shk.0000000000002217 · Cited by 8 · see citing works

In Vivo Visualization of Macrophage-Like Cells in Patients with Uveitis by Use of En Face Swept Source Optical Coherence Tomography

Pichi, F., Neri, P., Aljeneibi, S., Hay, S., Chaudhry, H., Saturno, M. C., & Carreño, E. (2023) · Ocular Immunology and Inflammation · doi:10.1080/09273948.2023.2254369 · Cited by 8 · see citing works

Targeting Cholesterol Homeostasis Improves Recovery in Experimental Optic Neuritis

Godwin, C. R., Anders, J. J., Cheng, L. Z., Elwood, B. W., Kardon, R. H., & Gramlich, O. W. (2022) · Biomolecules · doi:10.3390/biom12101437 · Cited by 8 · see citing works

Harnessing IGF-1 and IL-2 as biomarkers for calcineurin activity to tailor optimal FK506 dosage in α-synucleinopathies

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Potential Anti-Toxoplasmosis Efficiency of Phoenix dactylifera Extracts Loaded on Selenium Nanoparticles

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The Impact of Dipyridamole on Disease-Associated Microglia Phenotypic Transformation in White Matter Lesions Induced by Chronic Cerebral Hypoperfusion

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Improved gene regulatory network inference from single cell data with dropout augmentation

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A deep learning framework for classifying microglia activation state using morphology and intrinsic fluorescence lifetime data

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Human induced pluripotent stem cell–derived therapies for regeneration after central nervous system injury

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A novel deep learning-based method for automatic stereology of microglia cells from low magnification images

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Metabolic control of microglia

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Protein kinase R induced by type I interferons is a main regulator of reactive microglia in Zika virus infection

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Increased levels of GFAP and purinergic P2X7 receptor in Alzheimer’s disease brain are associated with Aβ, tau pathologies and synaptic loss

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Apolipoprotein E drives microglia activation in the development of autoimmune uveitis through up-regulation of peptidyl prolyl isomerase F

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Dipeptidyl peptidase 4 deficiency improves survival after focal cerebral ischemia in mice and ameliorates microglia activation and specific inflammatory markers

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Anatomy, histology and ultrastructure of the adult human olfactory peduncle: Blood vessel and corpora amylacea assessment

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Novel insights into pathomechanisms of retinal neuronal degeneration and reactive gliosis in a murine model of GM1-gangliosidosis

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Shenling Kaixin granules attenuate depression via multi-target mechanisms: evidence from CSDS model and cellular studies

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Nexus of virus and brain: recent advances in flavivirus and enterovirus neuro-infection

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Hypoxia or tobacco-smoke exposure induce region-specific microvascular remodeling in the brain

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The Spectrum of Microglia: Decoding Heterogeneity and Plasticity for Therapeutic Gain in Neurological Disorders

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Mapping microglia states in the human brain through the integration of high-dimensional techniques

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Mapping microglia states in teh human brain through the integration of high-dimensional techniques

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Microglia Diversity in Healthy and Diseased Brain: Insights from Single-Cell Omics

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Current tools to interrogate microglial biology

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