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A dynamic and multimodal framework to define microglial states

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Abstract

The widespread use of single-cell RNA sequencing has generated numerous purportedly distinct and novel subsets of microglia. Here, we challenge this fragmented paradigm by proposing that microglia exist along a continuum rather than as discrete entities. We identify a methodological over-reliance on computational clustering algorithms as the fundamental issue, with arbitrary cluster numbers being interpreted as biological reality. Evidence suggests that the observed transcriptional diversity stems from a combination of microglial plasticity and technical noise, resulting in terminology describing largely overlapping cellular states. We introduce a continuous model of microglial states, where cell positioning along the continuum is determined by biological aging and cell-specific molecular contexts. The model accommodates the dynamic nature of microglia. We advocate for a parsimonious approach toward classification and terminology that acknowledges the continuous spectrum of microglial states, toward a robust framework for understanding these essential immune cells of the CNS.

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Fig. 1: Taxonomy of myeloid cell types in the CNS.
Fig. 2: Torus-like model of microglial activation.
Fig. 3: Multimodal approach to myeloid cell-state classification.

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Acknowledgements

R.S. is supported by the IMMediate Advanced Clinician Scientist-Program, Department of Medicine II, Medical Center, University of Freiburg and Faculty of Medicine, University of Freiburg, funded by the Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research), 01EO2103. Furthermore, R.S. is supported by the Fritz Thyssen Foundation. M.P. is supported by the DFG (CRC/TRR167 project ID 259373024 ‘NeuroMac’). M.P. is further supported by the Sobek Foundation, the Ernst-Jung Foundation, the Klaus Faber Foundation, the Novo Nordisk Prize, the German Research Foundation (SFB 992 project ID 192904750, SFB 1160, SFB-1479 project ID 441891347, TRR 359 project ID 491676693 and Gottfried Wilhelm Leibniz Prize) and by the DFG under Germany’s Excellence Strategy (CIBSS EXC-2189 project ID 390939984). The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript.

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Sankowski, R., Prinz, M. A dynamic and multimodal framework to define microglial states. Nat Neurosci 28, 1372–1380 (2025). https://doi.org/10.1038/s41593-025-01978-3

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