Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Microglia heterogeneity, modeling and cell-state annotation in development and neurodegeneration

Nature Neuroscience volume 28, pages 1381–1392 (2025)Cite this article

Subjects

Abstract

Within the CNS, microglia execute various functions associated with brain development, maintenance of homeostasis and elimination of pathogens and protein aggregates. This wide range of activities is closely associated with a plethora of cellular states, which may reciprocally influence or be influenced by their functional dynamics. Advancements in single-cell RNA sequencing have enabled a nuanced exploration of the intricate diversity of microglia, both in health and disease. Here, we review our current understanding of microglial transcriptional heterogeneity. We provide an overview of mouse and human microglial diversity encompassing aspects of development, neurodegeneration, sex and CNS regions. We offer an insight into state-of-the-art technologies and model systems that are poised to improve our understanding of microglial cell states and functions. We also provide suggestions and a tool to annotate microglial cell states on the basis of gene expression.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Guidelines for microglial cell-state annotation.
Fig. 2: Strategies to model microglia heterogeneity in vitro and in vivo.

Similar content being viewed by others

References

  1. Río-Hortega del, P. El ‘tercer elemento’ de los centros nerviosos. I. La microglia en estado normal. Bol. Soc. Esp. Biol. 8, 67–82 (1919).

    Google Scholar 

  2. Sierra, A. et al. The ‘Big-Bang’ for modern glial biology: translation and comments on Pío del Río-Hortega 1919 series of papers on microglia. Glia 64, 1801–1840 (2016).

    Google Scholar 

  3. Paolicelli, R. C. et al. Microglia states and nomenclature: a field at its crossroads. Neuron 110, 3458–3483 (2022).

    CAS  PubMed Central  Google Scholar 

  4. Matcovitch-Natan, O. et al. Microglia development follows a stepwise program to regulate brain homeostasis. Science 353, aad8670 (2016).

    Google Scholar 

  5. Hoeffel, G. & Ginhoux, F. Ontogeny of tissue-resident macrophages. Front. Immunol. 6, 486 (2015).

    PubMed Central  Google Scholar 

  6. Kierdorf, K. & Prinz, M. Factors regulating microglia activation. Front. Cell Neurosci. 7, 44 (2013).

    CAS  PubMed Central  Google Scholar 

  7. Cohen, M. et al. Chronic exposure to TGFβ1 regulates myeloid cell inflammatory response in an IRF7-dependent manner. EMBO J. 33, 2906–2921 (2014).

    PubMed Central  Google Scholar 

  8. Cronk, J. C. et al. Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia. J. Exp. Med. 215, 1627–1647 (2018).

    CAS  PubMed Central  Google Scholar 

  9. Elmore, M. R. P. et al. Colony-stimulating factor 1 receptor signaling is necessary for microglia viability, unmasking a microglia progenitor cell in the adult brain. Neuron 82, 380–397 (2014).

    CAS  PubMed Central  Google Scholar 

  10. Pridans, C. et al. Pleiotropic impacts of macrophage and microglial deficiency on development in rats with targeted mutation of the Csf1r locus. J. Immunol. 201, 2683–2699 (2018).

    CAS  PubMed Central  Google Scholar 

  11. Geirsdottir, L. et al. Cross-species single-cell analysis reveals divergence of the primate microglia program. Cell 179, 1609–1622 (2019).

    CAS  Google Scholar 

  12. Masuda, T. et al. Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution. Nature 566, 388–392 (2019).

    CAS  Google Scholar 

  13. Gosselin, D. et al. An environment-dependent transcriptional network specifies human microglia identity. Science 356, eaal3222 (2017).

    PubMed Central  Google Scholar 

  14. Hou, P. et al. The γ-secretase substrate proteome and its role in cell signaling regulation In brief. Mol. Cell 83, 4106–4122 (2023).

    CAS  Google Scholar 

  15. Wang, S. et al. TREM2 drives microglia response to amyloid-β via SYK-dependent and -independent pathways. Cell 185, 4153–4169 (2022).

    CAS  PubMed Central  Google Scholar 

  16. Ennerfelt, H. et al. SYK coordinates neuroprotective microglial responses in neurodegenerative disease. Cell 185, 4135–4152 (2022).

    CAS  PubMed Central  Google Scholar 

  17. Sun, N. et al. Human microglial state dynamics in Alzheimer’s disease progression. Cell 186, 4386–4403 (2023).

    CAS  PubMed Central  Google Scholar 

  18. Stogsdill, J. A. et al. Pyramidal neuron subtype diversity governs microglia states in the neocortex. Nature 608, 750–756 (2022).

    CAS  PubMed Central  Google Scholar 

  19. Lawrence, A. R. et al. Microglia maintain structural integrity during fetal brain morphogenesis. Cell 187, 962–980 (2024).

    CAS  PubMed Central  Google Scholar 

  20. Greenhalgh, A. D. & David, S. Differences in the phagocytic response of microglia and peripheral macrophages after spinal cord injury and its effects on cell death. J. Neurosci. 34, 6316–6322 (2014).

    CAS  PubMed Central  Google Scholar 

  21. Tay, T. L. et al. A new fate mapping system reveals context-dependent random or clonal expansion of microglia. Nat. Neurosci. 20, 793–803 (2017).

    CAS  Google Scholar 

  22. Lloyd, A. F. et al. Central nervous system regeneration is driven by microglia necroptosis and repopulation. Nat. Neurosci. 22, 1046–1052 (2019).

    CAS  PubMed Central  Google Scholar 

  23. McNamara, N. B. et al. Microglia regulate central nervous system myelin growth and integrity. Nature 613, 120–129 (2023).

    CAS  Google Scholar 

  24. Kent, S. A. & Miron, V. E. Microglia regulation of central nervous system myelin health and regeneration. Nat. Rev. Immunol. 24, 49–63 (2024).

    CAS  Google Scholar 

  25. Barclay, K. M. et al. An inducible genetic tool to track and manipulate specific microglial states reveals their plasticity and roles in remyelination. Immunity 57, 1394–1412 (2024).

    CAS  PubMed Central  Google Scholar 

  26. Lan, Y. et al. Fate mapping of Spp1 expression reveals age-dependent plasticity of disease-associated microglia-like cells after brain injury. Immunity 57, 349–363 (2024).

    CAS  Google Scholar 

  27. Mehl, L. C., Manjally, A. V., Bouadi, O., Gibson, E. M. & Tay, T. L. Microglia in brain development and regeneration. Development 149, dev200425 (2022).

    CAS  PubMed Central  Google Scholar 

  28. Reemst, K., Noctor, S. C., Lucassen, P. J. & Hol, E. M. The indispensable roles of microglia and astrocytes during brain development. Front. Hum. Neurosci. 10, 566 (2016).

    PubMed Central  Google Scholar 

  29. Pont-Lezica, L., Béchade, C., Belarif-Cantaut, Y., Pascual, O. & Bessis, A. Physiological roles of microglia during development. J. Neurochem. 119, 901–908 (2011).

    CAS  Google Scholar 

  30. Mendes, M. S. & Majewska, A. K. An overview of microglia ontogeny and maturation in the homeostatic and pathological brain. Eur. J. Neurosci. 53, 3525–3547 (2021).

    PubMed Central  Google Scholar 

  31. Thion, M. S. & Garel, S. Microglial ontogeny, diversity and neurodevelopmental functions. Curr. Opin. Genet. Dev. 65, 186–194 (2020).

    CAS  Google Scholar 

  32. Silvin, A., Qian, J. & Ginhoux, F. Brain macrophage development, diversity and dysregulation in health and disease. Cell. Mol. Immunol. 20, 1277–1289 (2023).

    CAS  PubMed Central  Google Scholar 

  33. Bian, Z. et al. Deciphering human macrophage development at single-cell resolution. Nature 582, 571–576 (2020).

    CAS  Google Scholar 

  34. Wang, Z. et al. An immune cell atlas reveals the dynamics of human macrophage specification during prenatal development. Cell 186, 4454–4471 (2023).

    CAS  Google Scholar 

  35. Han, C. Z. et al. Human microglia maturation is underpinned by specific gene regulatory networks. Immunity 56, 2152–2171 (2023).

    CAS  PubMed Central  Google Scholar 

  36. Kracht, L. et al. Human fetal microglia acquire homeostatic immune-sensing properties early in development. Science 369, 530–537 (2020).

    CAS  Google Scholar 

  37. Hammond, T. R. et al. Single-cell RNA sequencing of microglia throughout the mouse lifespan and in the injured brain reveals complex cell-state changes. Immunity 50, 253–271 (2019).

    CAS  Google Scholar 

  38. Arnò, B. et al. Neural progenitor cells orchestrate microglia migration and positioning into the developing cortex. Nat. Commun. 5, 5611 (2014).

    Google Scholar 

  39. Squarzoni, P. et al. Microglia modulate wiring of the embryonic forebrain. Cell Rep. 8, 1271–1279 (2014).

    CAS  Google Scholar 

  40. Hagemeyer, N. et al. Microglia contribute to normal myelinogenesis and to oligodendrocyte progenitor maintenance during adulthood. Acta Neuropathol. 134, 441–458 (2017).

    PubMed Central  Google Scholar 

  41. Li, Q. et al. Developmental heterogeneity of microglia and brain myeloid cells revealed by deep single-cell RNA sequencing. Neuron 101, 207–223 (2019).

    CAS  Google Scholar 

  42. Badimon, A. et al. Negative feedback control of neuronal activity by microglia. Nature 586, 417–423 (2020).

    CAS  PubMed Central  Google Scholar 

  43. Guillot-Sestier, M. V. et al. Microglial metabolism is a pivotal factor in sexual dimorphism in Alzheimer’s disease. Commun. Biol. 4, 711 (2021).

    PubMed Central  Google Scholar 

  44. Guneykaya, D. et al. Transcriptional and translational differences of microglia from male and female brains. Cell Rep. 24, 2773–2783 (2018).

    CAS  Google Scholar 

  45. Hanamsagar, R. et al. Generation of a microglial developmental index in mice and in humans reveals a sex difference in maturation and immune reactivity. Glia 65, 1504–1520 (2017).

  46. Rahimian, R., Cordeau, P. & Kriz, J. Brain response to injuries: when microglia go sexist. Neuroscience 405, 14–23 (2019).

    CAS  Google Scholar 

  47. Schwarz, J. M., Sholar, P. W. & Bilbo, S. D. Sex differences in microglial colonization of the developing rat brain. J. Neurochem. 120, 948–963 (2012).

    CAS  PubMed Central  Google Scholar 

  48. Li, X. et al. Transcriptional and epigenetic decoding of the microglial aging process. Nat. Aging 3, 1288–1311 (2023).

    PubMed Central  Google Scholar 

  49. Sala Frigerio, C. et al. The major risk factors for Alzheimer’s disease: age, sex, and genes modulate the microglia response to Aβ Plaques. Cell Rep. 27, 1293–1306 (2019).

    CAS  Google Scholar 

  50. Bordeleau, M., Carrier, M., Luheshi, G. N. & Tremblay, M. -È. Microglia along sex lines: from brain colonization, maturation and function, to implication in neurodevelopmental disorders. Semin. Cell Dev. Biol. 94, 152–163 (2019).

    Google Scholar 

  51. Yvanka de Soysa, T., Therrien, M., Walker, A. C. & Stevens, B. Redefining microglia states: lessons and limits of human and mouse models to study microglia states in neurodegenerative diseases. Semin. Immunol. 60, 101651 (2022).

    CAS  Google Scholar 

  52. Mancuso, R. et al. Stem-cell-derived human microglia transplanted in mouse brain to study human disease. Nat. Neurosci. 22, 2111–2116 (2019).

  53. Mancuso, R. et al. Xenografted human microglia display diverse transcriptomic states in response to Alzheimer’s disease-related amyloid-β pathology. Nat. Neurosci. 27, 886–900 (2024).

    CAS  PubMed Central  Google Scholar 

  54. Wang, Q. et al. Molecular profiling of human substantia nigra identifies diverse neuron types associated with vulnerability in Parkinson’s disease. Sci. Adv. 10, eadi8287 (2024).

    CAS  PubMed Central  Google Scholar 

  55. Smajic, S. et al. Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state. Brain 145, 964–978 (2022).

    Google Scholar 

  56. Lee, A. J. et al. Characterization of altered molecular mechanisms in Parkinson’s disease through cell type–resolved multiomics analyses. Sci. Adv. 9, eabo2467 (2023).

    CAS  PubMed Central  Google Scholar 

  57. Lall, D. & Baloh, R. H. Microglia and C9orf72 in neuroinflammation and ALS and frontotemporal dementia. J. Clin. Invest. 127, 3250–3258 (2017).

    PubMed Central  Google Scholar 

  58. Mathys, H. et al. Temporal tracking of microglia activation in neurodegeneration at single-cell resolution. Cell Rep. 21, 366–380 (2017).

    CAS  PubMed Central  Google Scholar 

  59. Keren-Shaul, H. et al. A unique microglia type associated with restricting development of Alzheimer’s disease. Cell 169, 1276–1290 (2017).

    CAS  Google Scholar 

  60. Krasemann, S. et al. The TREM2–APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity 47, 566–581 (2017).

    CAS  PubMed Central  Google Scholar 

  61. Sierksma, A. et al. Novel Alzheimer risk genes determine the microglia response to amyloid‐β but not to TAU pathology. EMBO Mol. Med. 12, e10606 (2020).

    CAS  PubMed Central  Google Scholar 

  62. Friedman, B. A. et al. Diverse brain myeloid expression profiles reveal distinct microglial activation states and aspects of Alzheimer’s disease not evident in mouse models. Cell Rep. 22, 832–847 (2018).

    CAS  Google Scholar 

  63. Kim, D. W. et al. Amyloid-beta and tau pathologies act synergistically to induce novel disease stage-specific microglia subtypes. Mol. Neurodegener. 17, 83 (2022).

    CAS  PubMed Central  Google Scholar 

  64. Lee, S. H. et al. Trem2 restrains the enhancement of tau accumulation and neurodegeneration by β-amyloid pathology. Neuron 109, 1283–1301 (2021).

    CAS  Google Scholar 

  65. Lee, S. H. et al. TREM2-independent oligodendrocyte, astrocyte, and T cell responses to tau and amyloid pathology in mouse models of Alzheimer disease. Cell Rep. 37, 110158 (2021).

    CAS  Google Scholar 

  66. Lodder, C. et al. CSF1R inhibition rescues tau pathology and neurodegeneration in an A/T/N model with combined AD pathologies, while preserving plaque associated microglia. Acta Neuropathol. Commun. 9, 108 (2021).

    CAS  PubMed Central  Google Scholar 

  67. Gratuze, M. et al. TREM2-independent microgliosis promotes tau-mediated neurodegeneration in the presence of ApoE4. Neuron 111, 202–219 (2023).

    CAS  Google Scholar 

  68. Schonhoff, A. M. et al. Border-associated macrophages mediate the neuroinflammatory response in an alpha-synuclein model of Parkinson disease. Nat. Commun. 14, 3754 (2023).

    CAS  PubMed Central  Google Scholar 

  69. Lui, H. et al. Progranulin deficiency promotes circuit-specific synaptic pruning by microglia via complement activation. Cell 165, 921–935 (2016).

  70. Götzl, J. K. et al. Opposite microglial activation stages upon loss of PGRN or TREM 2 result in reduced cerebral glucose metabolism. EMBO Mol. Med. 11, e9711 (2019).

    PubMed Central  Google Scholar 

  71. Zhang, J. et al. Neurotoxic microglia promote TDP-43 proteinopathy in progranulin deficiency. Nature 588, 459–465 (2020).

    CAS  PubMed Central  Google Scholar 

  72. Jordão, M. J. C. et al. Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation. Science 363, eaat7554 (2019).

    Google Scholar 

  73. Nugent, A. A. et al. TREM2 regulates microglial cholesterol metabolism upon chronic phagocytic challenge. Neuron 105, 837–854 (2020).

    CAS  Google Scholar 

  74. Fitz, N. F. et al. Trem2 deficiency differentially affects phenotype and transcriptome of human APOE3 and APOE4 mice. Mol. Neurodegener. 15, 41 (2020).

    CAS  PubMed Central  Google Scholar 

  75. van Lengerich, B. et al. A TREM2-activating antibody with a blood–brain barrier transport vehicle enhances microglial metabolism in Alzheimer’s disease models. Nat. Neurosci. 26, 416–429 (2023).

    PubMed Central  Google Scholar 

  76. Shi, Y. et al. ApoE4 markedly exacerbates tau-mediated neurodegeneration in a mouse model of tauopathy. Nature 549, 523–527 (2017).

    PubMed Central  Google Scholar 

  77. Gratuze, M. et al. Impact of TREM2 R47H variant on tau pathology-induced gliosis and neurodegeneration. J. Clin. Invest. 130, 4954–4968 (2020).

    CAS  PubMed Central  Google Scholar 

  78. Sayed, F. A. et al. AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation. Sci. Transl. Med. 13, eabe3947 (2021).

    CAS  PubMed Central  Google Scholar 

  79. Wang, S. et al. Anti-human TREM2 induces microglia proliferation and reduces pathology in an Alzheimer’s disease model. J. Exp. Med. 217, e20200785 (2020).

    PubMed Central  Google Scholar 

  80. Maniatis, S. et al. Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis. Science 364, 89–93 (2019).

    CAS  Google Scholar 

  81. Wang, H. -L. V. et al. Single nucleus multiome analysis of the prefrontal cortex from C9orf72 ALS/FTD patients illuminates pathways affected during disease progression. Preprint at bioRxiv https://doi.org/10.1101/2023.01.12.523820 (2023).

    Article  PubMed Central  Google Scholar 

  82. Zhao, N. et al. Elevating microglia TREM2 reduces amyloid seeding and suppresses disease-associated microglia. J. Exp. Med. 219, e20212479 (2022).

    CAS  PubMed Central  Google Scholar 

  83. Lall, D. et al. C9orf72 deficiency promotes microglial-mediated synaptic loss in aging and amyloid accumulation. Neuron 109, 2275–2291 (2021).

    CAS  PubMed Central  Google Scholar 

  84. Komine, O. et al. Genetic background variation impacts microglial heterogeneity and disease progression in amyotrophic lateral sclerosis model mice. iScience 27, 108872 (2024).

    CAS  PubMed Central  Google Scholar 

  85. Escoubas, C. C. et al. Type-I-interferon-responsive microglia shape cortical development and behavior. Cell 187, 1936–1954 (2024).

    CAS  PubMed Central  Google Scholar 

  86. Roy, E. R. et al. Concerted type I interferon signaling in microglia and neural cells promotes memory impairment associated with amyloid β plaques. Immunity 55, 879–894 (2022).

    Google Scholar 

  87. Roy, E. R. et al. Type I interferon response drives neuroinflammation and synapse loss in Alzheimer disease. J. Clin. Invest. 130, 1912–1930 (2020).

    PubMed Central  Google Scholar 

  88. Hinkle, J. T. et al. STING mediates neurodegeneration and neuroinflammation in nigrostriatal α-synucleinopathy. Proc. Natl Acad. Sci. USA 119, e2118819119 (2022).

    CAS  PubMed Central  Google Scholar 

  89. Hanisch, U. Microglia as a source and target of cytokines. Glia 40, 140–155 (2002).

    Google Scholar 

  90. Spangenberg, E. E. et al. Eliminating microglia in Alzheimer’s mice prevents neuronal loss without modulating amyloid-β pathology. Brain 139, 1265–1281 (2016).

    PubMed Central  Google Scholar 

  91. Olmos-Alonso, A. et al. Pharmacological targeting of CSF1R inhibits microglial proliferation and prevents the progression of Alzheimer’s-like pathology. Brain 139, 891–907 (2016).

    PubMed Central  Google Scholar 

  92. Mancuso, R. et al. CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice. Brain 142, 3243–3264 (2019).

    PubMed Central  Google Scholar 

  93. Chen, X. et al. Microglia-mediated T cell infiltration drives neurodegeneration in tauopathy. Nature 615, 668–677 (2023).

    CAS  PubMed Central  Google Scholar 

  94. De Schepper, S. et al. Perivascular cells induce microglial phagocytic states and synaptic engulfment via SPP1 in mouse models of Alzheimer’s disease. Nat. Neurosci. 26, 406–415 (2023).

    PubMed Central  Google Scholar 

  95. Grubman, A. et al. A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation. Nat. Neurosci. 22, 2087–2097 (2019).

    CAS  Google Scholar 

  96. Olah, M. et al. Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease. Nat. Commun. 11, 6129 (2020).

    CAS  PubMed Central  Google Scholar 

  97. Zhou, Y. et al. Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease. Nat. Med. 26, 131–142 (2020).

    CAS  PubMed Central  Google Scholar 

  98. Gerrits, E. et al. Distinct amyloid-β and tau-associated microglia profiles in Alzheimer’s disease. Acta Neuropathol. 141, 681–696 (2021).

    CAS  PubMed Central  Google Scholar 

  99. Gazestani, V. et al. Early Alzheimer’s disease pathology in human cortex involves transient cell states. Cell 186, 4438–4453 (2023).

    CAS  PubMed Central  Google Scholar 

  100. Alsema, A. M. et al. Profiling microglia from Alzheimer’s disease donors and non-demented elderly in acute human postmortem cortical tissue. Front. Mol. Neurosci. 13, 134 (2020).

    CAS  PubMed Central  Google Scholar 

  101. Green, G. S. et al. Cellular communities reveal trajectories of brain ageing and Alzheimer’s disease. Nature 633, 634–645 (2024).

    CAS  PubMed Central  Google Scholar 

  102. Cadiz, M. P. et al. Culture shock: microglial heterogeneity, activation, and disrupted single-cell microglial networks in vitro. Mol. Neurodegener. 17, 26 (2022).

    CAS  PubMed Central  Google Scholar 

  103. Popova, G. et al. Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids. Cell Stem Cell 28, 2153–2166 (2021).

    CAS  Google Scholar 

  104. Butovsky, O. & Weiner, H. L. Microglial signatures and their role in health and disease. Nat. Rev. Neurosci. 19, 622–635 (2018).

    CAS  PubMed Central  Google Scholar 

  105. Hasselmann, J. & Blurton-Jones, M. Human iPSC-derived microglia: a growing toolset to study the brain’s innate immune cells. Glia 68, 721–739 (2020).

    PubMed Central  Google Scholar 

  106. Svoboda, D. S. et al. Human iPSC-derived microglia assume a primary microglia-like state after transplantation into the neonatal mouse brain. Proc. Natl Acad. Sci. USA 116, 25293–25303 (2019).

    CAS  PubMed Central  Google Scholar 

  107. Hedegaard, A., Stodolak, S., James, W. S. & Cowley, S. A. Honing the double-edged sword: improving human iPSC-microglia models. Front. Immunol. 11, 614972 (2020).

    CAS  PubMed Central  Google Scholar 

  108. Guttikonda, S. R. et al. Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease. Nat. Neurosci. 24, 343–354 (2021).

    CAS  PubMed Central  Google Scholar 

  109. Fattorelli, N. et al. Stem-cell-derived human microglia transplanted into mouse brain to study human disease. Nat. Protoc. 16, 1013–1033 (2021).

    CAS  Google Scholar 

  110. Chen, S. W. et al. Efficient conversion of human induced pluripotent stem cells into microglia by defined transcription factors. Stem Cell Rep. 16, 1363–1380 (2021).

    CAS  Google Scholar 

  111. Hasselmann, J. et al. Development of a chimeric model to study and manipulate human microglia in vivo. Neuron 103, 1016–1033 (2019).

    CAS  PubMed Central  Google Scholar 

  112. Washer, S. J. et al. Single-cell transcriptomics defines an improved, validated monoculture protocol for differentiation of human iPSC to microglia. Sci. Rep. 12, 19454 (2022).

    CAS  PubMed Central  Google Scholar 

  113. Abud, E. M. et al. iPSC-derived human microglia-like cells to study neurological diseases. Neuron 94, 278–293 (2017).

    CAS  PubMed Central  Google Scholar 

  114. Dolan, M. J. et al. Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro. Nat. Immunol. 24, 1382–1390 (2023).

    CAS  PubMed Central  Google Scholar 

  115. Cakir, B. et al. Expression of the transcription factor PU.1 induces the generation of microglia-like cells in human cortical organoids. Nat. Commun. 13, 430 (2022).

  116. Speicher, A. M. et al. Deterministic programming of human pluripotent stem cells into microglia facilitates studying their role in health and disease. Proc. Natl Acad. Sci. USA 119, e2123476119 (2022).

    CAS  PubMed Central  Google Scholar 

  117. Sabate-Soler, S. et al. Microglia integration into human midbrain organoids leads to increased neuronal maturation and functionality. Glia 70, 1267–1288 (2022).

    CAS  PubMed Central  Google Scholar 

  118. Xu, R. et al. Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric mouse brain. Nat. Commun. 11, 1577 (2020).

    CAS  PubMed Central  Google Scholar 

  119. Kiani Shabestari, S. et al. Absence of microglia promotes diverse pathologies and early lethality in Alzheimer’s disease mice. Cell Rep. 39, 110961 (2022).

    CAS  Google Scholar 

  120. Balusu, S. et al. MEG3 activates necroptosis in human neuron xenografts modeling Alzheimer’s disease. Science 381, 1176–1182 (2023).

    CAS  PubMed Central  Google Scholar 

  121. Claes, C. et al. Plaque-associated human microglia accumulate lipid droplets in a chimeric model of Alzheimer’s disease. Mol. Neurodegener. 16, 50 (2021).

    CAS  PubMed Central  Google Scholar 

  122. McQuade, A. et al. Gene expression and functional deficits underlie TREM2-knockout microglia responses in human models of Alzheimer’s disease. Nat. Commun. 11, 5370 (2020).

    CAS  PubMed Central  Google Scholar 

  123. Schafer, S. T. et al. An in vivo neuroimmune organoid model to study human microglia phenotypes. Cell 186, 2111–2126 (2023).

    CAS  PubMed Central  Google Scholar 

  124. Jin, M. et al. Co-transplantation-based human-mouse chimeric brain models to study human glial-glial and glial-neuronal interactions. Preprint at bioRxiv https://doi.org/10.1101/2024.07.03.601990 (2024).

    Article  PubMed Central  Google Scholar 

  125. Warden, A. S. et al. Tools for studying human microglia: in vitro and in vivo strategies. Brain Behav. Immun. 107, 369–382 (2023).

    CAS  Google Scholar 

  126. Burgess, D. J. Spatial transcriptomics coming of age. Nat. Rev. Genet. 20, 317 (2019).

    CAS  Google Scholar 

  127. Chen, W. T. et al. Spatial transcriptomics and in situ sequencing to study Alzheimer’s disease. Cell 182, 976–991 (2020).

    CAS  Google Scholar 

  128. Zeng, H. et al. Integrative in situ mapping of single-cell transcriptional states and tissue histopathology in a mouse model of Alzheimer’s disease. Nat. Neurosci. 26, 430–446 (2023).

  129. Pham, D. et al. Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissues. Nat. Commun. 14, 7739 (2023).

    CAS  PubMed Central  Google Scholar 

  130. Ratz, M. et al. Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics. Nat. Neurosci. 25, 285–294 (2022).

    CAS  PubMed Central  Google Scholar 

  131. Liddelow, S. A. et al. Neurotoxic reactive astrocytes are induced by activated microglia. Nature 541, 481–487 (2017).

    CAS  PubMed Central  Google Scholar 

  132. Baxter, P. S. et al. Microglial identity and inflammatory responses are controlled by the combined effects of neurons and astrocytes. Cell Rep. 34, 108882 (2021).

  133. Jin, S. et al. Inference and analysis of cell-cell communication using CellChat. Nat. Commun. 12, 1088 (2021).

    CAS  PubMed Central  Google Scholar 

  134. Browaeys, R., Saelens, W. & Saeys, Y. NicheNet: modeling intercellular communication by linking ligands to target genes. Nat. Methods 17, 159–162 (2020).

    CAS  Google Scholar 

  135. Efremova, M., Vento-Tormo, M., Teichmann, S. A. & Vento-Tormo, R. CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes. Nat. Protoc. 15, 1484–1506 (2020).

    CAS  Google Scholar 

  136. Clark, I. C. et al. Barcoded viral tracing of single-cell interactions in central nervous system inflammation. Science 372, eabf1230 (2021).

    CAS  PubMed Central  Google Scholar 

Download references

Author information

Author notes

  1. These authors contributed equally: Laura Fumagalli, Alma Nazlie Mohebiany.

Authors and Affiliations

  1. Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium

    Laura Fumagalli, Alma Nazlie Mohebiany, Jessie Premereur, Paula Polanco Miquel, Baukje Bijnens, Nicola Fattorelli & Renzo Mancuso

  2. Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium

    Laura Fumagalli, Alma Nazlie Mohebiany, Jessie Premereur, Paula Polanco Miquel, Baukje Bijnens, Pieter Van de Walle, Nicola Fattorelli & Renzo Mancuso

Authors
  1. Laura Fumagalli
    View author publications

    Search author on:PubMed Google Scholar

  2. Alma Nazlie Mohebiany
    View author publications

    Search author on:PubMed Google Scholar

  3. Jessie Premereur
    View author publications

    Search author on:PubMed Google Scholar

  4. Paula Polanco Miquel
    View author publications

    Search author on:PubMed Google Scholar

  5. Baukje Bijnens
    View author publications

    Search author on:PubMed Google Scholar

  6. Pieter Van de Walle
    View author publications

    Search author on:PubMed Google Scholar

  7. Nicola Fattorelli
    View author publications

    Search author on:PubMed Google Scholar

  8. Renzo Mancuso
    View author publications

    Search author on:PubMed Google Scholar

Corresponding author

Correspondence to Renzo Mancuso.

Ethics declarations

Competing interests

R.M. has scientific collaborations with Alector, Nodthera and Alchemab and Roche, has been a consultant for Sanofi and is a consultant for Alector and Muna Therapeutics. The other authors declare no competing interests.

Peer review

Peer review information

Nature Neuroscience thanks Ido Amit, Marta Olah and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fumagalli, L., Nazlie Mohebiany, A., Premereur, J. et al. Microglia heterogeneity, modeling and cell-state annotation in development and neurodegeneration. Nat Neurosci 28, 1381–1392 (2025). https://doi.org/10.1038/s41593-025-01931-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41593-025-01931-4

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing